gebhart/patrepeval huggingface dataset:
The influence of intramolecular chain dynamics on the diffusion of small penetrants in semicrystalline aromatic polymers (1999)

A recently developed molecular model for diffusion in dense aromatic polymers, which attempts to explain penetrant jump frequencies in terms of phenyl ring partial flips, is investigated via molecular simulation. The model polymer system under consideration in this paper corresponds to the interfacial domains generated by the lateral chain invariant (LCI) grain boundaries between crystallites of a stiff chain polyamide, poly(p-phenylene terephthalamide) (PPTA), and the low molecular weight penetrant selected for study is water. Fully atomistic constraint molecular dynamics simulations are conducted with interatomic and intramolecular interactions described by the DREIDING potential [S. L. Mayo, B. D. Olafson, and W. A. Goddard III, J. Phys. Chem. 94, 8897 (1990).] The coupling of the diffusive motion of water with the local polymer chain dynamics is examined at two temperatures and over a range of grain boundary densities.
The Capacity of Finite-State Markov Channels With Feedback (2005)

We consider a class of finite-state Markov channels with feedback. We first introduce a simplified equivalent channel model, and then construct the optimal stationary and nonstationary input processes that maximize the long-term directed mutual information. Furthermore, we give a sufficient condition under which the channel's Shannon capacity can be achieved by a stationary input process. The corresponding converse coding theorem and direct coding theorem are proved.
Intranasal vaccination against angiotensin II type 1 receptor and pneumococcal surface protein A attenuates hypertension and pneumococcal infection in rodents (2017)

Intranasal immunization with AT1R-PspA vaccine has the potential to simultaneously attenuate the development of hypertension and protect from lethal pneumococcal infection.
Functionalized nanospheres for targeted delivery of paclitaxel (2013)

Targeted delivery of anti-cancer agents to cancer cells is a mature line of investigation that has yet to realize its full potential. In this study we report on the development of a delivery platform with the future goal of merging two thus far parallel methods for selective elimination of cancer cells: targeted nanospheres and pretargeted radioimmunotherapy. Several clinical trials have shown the promise of pretargeted radioimmunotherapy, which leverages the specificity of antibodies for targeted cell populations and delivers a localized dose of a biotinylated radionuclide that is most often administered following binding of a biotinylated antibody and streptavidin (StA) to the target cells. The work presented here describes the development of biotinylated nanospheres based on an ABA-type copolymer comprised of a tyrosine-derived oligomer as the B-block and poly(ethylene glycol) (PEG) A-blocks. The biotinylated nanospheres encapsulate paclitaxel (PTX) to the same extent as unbiotinylated nanospheres. Efficacy of targeting was shown on CD44 positive cells in the SUM159 breast cancer cell line by incubating the cells sequentially with a biotinylated anti-CD44 antibody, StA and the biotinylated nanospheres encapsulating PTX. Targeted nanospheres achieved the half maximal inhibitory concentration of PTX on SUM159 cells at a 5-10 fold lower concentration than that of PTX applied in either non-targeted nanospheres or free drug approaches. Moreover, targeted nanospheres selectively eliminated CD44 positive SUM159 cells compared to free PTX and untargeted nanospheres. This new generation of nano-sized carrier offers a versatile platform that can be adopted for a wide variety of drug and target specific applications and has the potential to be combined with the clinically emerging method of pretargeted radioimmunotherapy.
Electrogastrography: Basic knowledge, recording, processing and its clinical applications (2005)

The slow wave (SW) of the gastrointestinal (GI) tract mainly functions to trigger the onset of spike to elicit smooth muscle contraction, which provides the essential power of motility. Smooth muscle myogenic control activity or SW is believed to originate in the interstitial cells of Cajal (ICC). The electrical coupling promotes interaction between muscle cells, and ICC additionally contribute to SW rhythmicity. Stomach SW originates in the proximal body showing the continuous rhythmic change in the membrane potential and propagates normally to the distal antrum with a regular rhythm of approximately 3 c.p.m. A technique using electrodes positioned on the abdominal skin to pick up stomach rhythmic SW refers to electrogastrography (EGG). The stomach SW amplitude is very weak, while many visceral organs also produce rhythmic electricities, for example heartbeat, respiration, other organs of the GI tract and even body movements. Thus noise other than SW should be filtered out during the recording, while motion artifacts are visually examined and deleted. Finally, the best signal among all recordings is selected to compute EGG parameters based on spectral analysis. The latter is done not only to tranform frequency domain to time domain but also to provide information of time variability in frequency. Obtained EGG parameters include dominant frequency/power, % normal rhythm, % bradygastria, % tachygastria, instability coefficient and power ratio. Clinical experience in EGG has been markedly accumulated since its rapid evolution. In contrast, lack of standardized methodology in terms of electrode positions, recording periods, test meals, analytic software and normal reference values makes the significance of EGG recording controversial. Unlike imaging or manometrical studies, stomach motility disorders are not diagnosed based only on abnormal EGG parameters. Limitations of EGG recording, processing, computation, acceptable normal parameters, technique and reading should be known to conduct subjective assessments when EGG is used to resolve stomach dysfunction. Understanding basic SW physiology, recording methodology and indications may open EGG as a new domain to approach the stomach motor dysfunction.
Coselection of features and instances for unsupervised rare category analysis (2010)

Abstract Rare category analysis is of key importance both in theory and in practice. Previous research work focuses on supervised rare category analysis, such as rare category detection and rare category classification. In this paper, for the first time, we address the challenge of unsupervised rare category analysis, including feature selection and rare category selection. We propose to jointly deal with the two correlated tasks, so that they can benefit from each other. To this end, we design an optimization framework which is able to coselect the relevant features and the examples from the rare category (a.k.a. the minority class). It is well justified theoretically. Furthermore, we develop the Partial Augmented Lagrangian Method (PALM) to solve the optimization problem. Experimental results on both synthetic and real data sets show the effectiveness of the proposed method. Copyright © 2010 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 3: 417‐430, 2010
Molecular Physiology, Biochemistry, and Pharmacology of Alzheimer's Amyloid Precursor Protein (APP)a (1996)

The function of APP is not yet known in detail but growing evidence exists that APP may mediate cell interactions with the cell surface or soluble glycoproteins and defense mechanisms in the CNS involving the immune system. We describe here the finding that almost all CD4+ lymphocytes and the majority of CD8+ lymphocytes were positive for A beta and the antibodies against A beta or APP did not inhibit the [3H]-thymidine uptake of mitogen-treated lymphocytes significantly. There were no differences in the A beta immunoreactivity on the cell surface of lymphocytes between Alzheimer's disease (AD) and control samples. Excessive amyloidogenic pathway of APP processing may be the final common pathway involved in the pathogenesis of AD. Thus, the identification of proteases or factors leading to aberrant proteolysis which process APP to yield a variety of potentially amyloidogenic fragments would promise pharmacological targets to develop anti-AD drugs. In attempts to define the proteases or factors which alter the balance between nonamyloidogenic and amyloidogenic processing pathways, our study indicates that thrombin or acetylcholinesterase(AChE)-associated protease may be involved in the amyloidogenic processing pathway of APP in vivo to generate amyloidogenic intermediates linked to amyloid deposition. Highly specific and dose-dependent direct modulation of APP processing by biologically available metal ions including Ca2+, Zn2+, Fe2+/Fe3+ and Al3+ suggest the disrupted metal homeostasis as factors leading to overaccumulation of APP and subsequent aberrant proteolysis utilizing excessive amyloidogenic processing pathway. There is mounting evidence that at least some of the neurotoxicity associated with AD is due to fragments from APP. Most research has focused on the toxic effect and the ion channel activity of A beta in causation of the disease. The possible role of other cleaved products of APP is less clear. We investigated the channel-forming ability of various products of APP when applied to Xenopus oocytes and their neurotoxicity in vitro. CT105 peptide was found to be exceedingly potent at 500 nM concentration in forming nonselective ion channels during application from either outside or inside the oocyte and more toxic than either of the A beta fragments, A beta 25-35, or A beta 1-40. Taken together, these results suggest the possible involvement of CT peptide in inducing the neurotoxicity characteristic of AD through the direct damage on the cell membrane. Therefore, we hypothesize that amyloidogenic CT may make nonselective ion channels or pores in the membrane and may cause neuronal death in the early stage of AD and then further metabolized to more stable and less toxic A beta which may be finally deposited in the brain where it could inflict further toxicity to neurons. Here we report successful inhibition of APP gene expression by antisense oligodeoxynucleotides at the mRNA or the protein level in in vitro and cell culture systems.
[Environmental stimuli-sensitive biodegradable drug delivery systems]. (2005)

Environmental stimuli-sensitive biodegradable drug delivery systems are drawing more and more attentions because of their advantages such as smart properties, high efficiency and easy-to-handle properties. On the basis of a large quantity of references on this topic, a review has been made on the developments of the thermosensitive and pH-sensitive intelligent polymeric systems for drug delivery.
Drug choices in autoimmune hepatitis: Part A – steroids (2012)

Prednisone and prednisolone are the mainstays of treatment for autoimmune hepatitis. Prednisone is converted in the liver to the active metabolite, prednisolone. The principal therapeutic action of prednisolone is to suppress cytokine gene expression and to inhibit the differentiation and proliferation of activated lymphocytes. It also has anti-inflammatory effects that include decreased production of adhesion molecules, increased apoptosis of lymphocytes and decreased hepatic collagen deposition. Advanced liver disease does not sufficiently suppress hepatic conversion of prednisone to warrant the preferential use of prednisolone. Budesonide combined with azathioprine has been more effective and safer than the conventional prednisone-based regimen when given for 6 months to treatment-naive patients. It is emerging as a frontline treatment, especially for noncirrhotic patients with uncomplicated disease.
Mesoporous TiO<sub>2</sub> films: New catalytic electrode fabricating amperometric biosensors based on oxidases (1997)

Abstract A novel catalytic material (mesoporous TiO 2 films) for the cathodic detection of hydrogen peroxide in air‐saturated aqueous solution is described. The immobilization of glucose oxidase (GOD) as enzyme model onto the TiO 2 electrode provides an efficient biosensor for the amperometric detection of glucose at −0.15 V (vs. SCE). GOD molecules were immobilized in an inorganic laponite gel and cross‐linked by glutaraldehyde. The highest sensitivity and detection limit were 3.33 mAM −1 cm −2 and 15 μM, respectively. In addition different procedures of enzyme immobilization including cross‐linking with glutaraldehyde and physical entrapment in a functionalized polypyrrole film have been compared.
Modeling of Antigenomic Therapy of Mitochondrial Diseases by Mitochondrially Addressed RNA Targeting a Pathogenic Point Mutation in Mitochondrial DNA (2014)

Defects in mitochondrial genome can cause a wide range of clinical disorders, mainly neuromuscular diseases. Presently, no efficient therapeutic treatment has been developed against this class of pathologies. Because most of deleterious mitochondrial mutations are heteroplasmic, meaning that wild type and mutated forms of mitochondrial DNA (mtDNA) coexist in the same cell, the shift in proportion between mutant and wild type molecules could restore mitochondrial functions. Recently, we developed mitochondrial RNA vectors that can be used to address anti-replicative oligoribonucleotides into human mitochondria and thus impact heteroplasmy level in cells bearing a large deletion in mtDNA. Here, we show that this strategy can be also applied to point mutations in mtDNA. We demonstrate that specifically designed RNA molecules containing structural determinants for mitochondrial import and 20-nucleotide sequence corresponding to the mutated region of mtDNA, are able to anneal selectively to the mutated mitochondrial genomes. After being imported into mitochondria of living human cells in culture, these RNA induced a decrease of the proportion of mtDNA molecules bearing a pathogenic point mutation in the mtDNA ND5 gene.
Synthesis and Magnetic Properties of a Superparamagnetic Nanocomposite “Pectin‐Magnetite Nanocomposite” (2013)

Magnetic nanocomposites composed of superparamagnetic magnetite nanoparticles in a pectin matrix were synthesized by an in situ coprecipitation method. The pectin matrix acted as a stabilizer and size control host for the magnetite nanoparticles (MNPs) ensuring particle size homogeneity. The effects of the different reactant ratios and nanocomposite drying conditions on the magnetic properties were investigated. The nanocomposites were characterized by X‐ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X‐ray spectroscopy (EDX), Fourier‐transform infrared (FT‐IR) spectroscopy, and superconducting quantum interference device magnetometer (SQUID). Superparamagnetic magnetite nanoparticles with mean diameters of 9 and 13 nm were obtained, and the freeze‐dried nanocomposites had a saturation magnetization of 54 and 53 emu/g, respectively.
Detailed Mechanistic and Optimization of the Photochemical Production Method of Superoxide (2007)

The highly reactive nature of superoxide anion presents an analytical challenge to prepare stable standards for instrument calibration. McDowell et al. (1983) developed a convenient method of superoxide production based on continuous photolysis of benzophenone and acetone in oxygen saturated, alkaline, 2-propanol solution. In the McDowell reaction, ketones are photolyzed to their triplet state, and then reacted with alcohol to produce ketyl radicals that react with oxygen to produce superoxide. This study investigated the mechanism and rate of these reactions by Laser Flash Photolysis (LFP). Reaction rate constants for the reaction between the benzophenone triplet and ethanol was 5.5 x 105 M-1s-1, and between the benzophenone ketyl radical and oxygen was 1.8 x 109 M-1s-1, consistent with published literature values. The reaction rates and mechanism were incorporated into a STELLA-based kinetic model to predict superoxide production and decay on a time scale of minutes. The model provided optimal conditions for superoxide production in terms of pH and alcohol concentration. The model predictions of superoxide production agree with experimental photolysis results. The model shows that the optimal condition of superoxide production is at 12 M alcohol concentration (ethanol) at pH 13. The actual photolysis results show that the optimal alcohol concentration is 6-9 M at pH 13.
A phase I trial of solubilized DR2:MBP <sup>84-102</sup> (AG284) in multiple sclerosis (2000)

AG284 as administered during this study was safe and well tolerated. Further studies are warranted to determine the biologic activity and clinical efficacy of this potential treatment for MS.
The Identification of an Adenovirus Receptor by Using Affinity Capture and Mass Spectrometry (2004)

A tandem mass spectrometry--based approach is demonstrated for detecting a receptor for Ad37, one of the causative agents for epidemic keratoconjunctivitis. Partial purification of membrane glycoproteins was performed by using lectin-affinity chromatography and SDS-PAGE. Gel bands that were shown to bind Ad37 by using Viral Overlay Protein Blot Assay (VOPBA) were excised, proteolyzed and analyzed by using nanoLC-MS/MS to identify putative receptors contained in a mixture of proteins. Four candidate receptors were identified among approximately 50 proteins based on a search against a protein database. Inhibition of gene delivery mediated by an Ad37 vector, with antibodies against the glycoproteins identified by tandem mass spectrometry, strongly indicated that Membrane Cofactor Protein (MCP), a member of the complement regulatory family of proteins, is the receptor. This rapid and sensitive MS/MS-based strategy is perceived to have wide potential applications for the detection of viral receptors.
Glaucoma Surgery and Aqueous Outflow (2002)

BLEBS. SHALLOW CHAMBERS. Bleb leaks. Flat chambers. Dellen. Blebitis. No bleb. Late failure. Hypotony. Choroidal effusions. Maculopathy. Is there a better way? If the problem is in the meshwork, why do we cut a hole in the eye?
PET of EGFR Antibody Distribution in Head and Neck Squamous Cell Carcinoma Models (2009)

The results from this study provide a possible explanation for the lack of an observed correlation between therapeutic efficacy of cetuximab and panitumumab and EGFR expression level as determined by immunohistochemistry or fluorescent in situ hybridization and may shed new light on the complications of anti-EGFR mAb therapy for HNSCC and other malignancies.
Seeing the World Behind the Image: Spatial Layout for 3D Scene Understanding (2007)

When humans look at an image, they see not just a pattern of color and texture, but the world behind the image. In the same way, computer vision algorithms must go beyond the pixels and reason about the underlying scene. In this dissertation, we propose methods to recover the basic spatial layout from a single image and begin to investigate its use as a foundation for scene understanding. Our spatial layout is a description of the 3D scene in terms of surfaces, occlusions, camera viewpoint, and objects. We propose a geometric class representation, a coarse categoriza-tion of surfaces according to their 3D orientations, and learn appearance-based models of geometry to identify surfaces in an image. These surface estimates serve as a basis for re-covering the boundaries and occlusion relationships of prominent objects. We further show that simple reasoning about camera viewpoint and object size in the image allows accurate inference of the viewpoint and greatly improves object detection. Finally, we demonstrate the potential usefulness of our methods in applications to 3D reconstruction, scene synthe-sis, and robot navigation. Scene understanding from a single image requires strong assumptions about the world. We show that the necessary assumptions can be modeled statistically and learned from training data. Our work demonstrates the importance of robustness through a wide variety of image cues, multiple segmentations, and a general strategy of soft decisions and gradual inference of image structure. Above all, our work manifests the tremendous amount of 3D information that can be gleaned from a single image. Our hope is that this dissertation will inspire others to further explore how computer vision can go beyond pattern recognition and produce an understanding of the environment.
X-chromosome inactivation and human genetic disease (2002)

The inactivation of one X-chromosome in females in early development is the process by which the effective dosage of X-linked genes is equalized between XX females and XY males. The mechanism that brings this about is the subject of intense research. The X-linked gene Xist is a key player, which is necessary but not sufficient for the initiation of X-inactivation. It codes for an untranslated RNA that coats the inactive X-chromosome, which takes on properties characteristic of heterochromatin, but how this change in chromatin is brought about remains unknown. Because of X-inactivation, females heterozygous for X-linked genes are mixtures of two types of cells and show a variable phenotype. The proportion s of the two types of cells can depart from equality due to cell selection either at the tissue or whole organism level. In rare cases, changes in the Xist gene can cause skewing of X-inactivation. A few genes escape from X-inactivation either wholly or partially. Conclusion: X-chromosome inactivation is a physiological mechanism that equalizes gene-dosage effects on the sex chromosomes. The occurrence of this normal process affects the phenotype seen in females carrying X-linked mutant genes or chromosome anomalies.
A cell line (SCaBER) derived from squamous cell carcinoma of the human urinary bladder (1976)

An established cell line derived from a documented squamous cell carcinoma of human urinary bladder is described. The cultured cells retained the characteristic morphology of the tumor of origin for 40 in vitro passages. Numerous desmosomes were found between cultured cells. Chromosome analysis showed hypotetraploidy with no obvious modal number, while distinctive marker chromosomes and a male karyotype were present.
Adenovirus-mediated transfer of a gene encoding cholesterol 7 alpha-hydroxylase into hamsters increases hepatic enzyme activity and reduces plasma total and low density lipoprotein cholesterol. (1995)

Clinical interventions that accelerate conversion of cholesterol to bile acids reduce circulating low density lipoprotein (LDL) cholesterol concentrations. The initial and rate-limiting step in the bile acid biosynthetic pathway is catalyzed by hepatic cholesterol 7 alpha-hydroxylase. To examine the effects of transient primary overexpression of this enzyme on sterol metabolism and lipoprotein transport, we constructed a recombinant adenovirus in which a cDNA encoding rat 7 alpha-hydroxylase is expressed from the human cytomegalovirus immediate-early promoter (AdCMV7 alpha). Syrian hamsters administered AdCMV7 alpha intravenously accumulated transgene-specific mRNA in the liver and demonstrated a dose-dependent increase in hepatic microsomal 7 alpha-hydroxylase activity. The increased conversion of cholesterol to bile acids resulted in a compensatory increase in hepatic cholesterol synthesis. In addition, overexpression of 7 alpha-hydroxylase reduced the rate of LDL cholesterol entry into the plasma space and, in animals maintained on a Western-type diet, restored hepatic LDL receptor expression. As a consequence, plasma LDL concentrations fell by approximately 60% in animals maintained on control diet and by approximately 75% in animals consuming a Western-type diet. Plasma high density lipoprotein cholesterol levels were reduced to a lesser degree. These results demonstrate that transient upregulation of bile acid synthesis by direct transfer of a 7 alpha-hydroxylase gene favorably alters circulating lipoprotein profiles and suggest one potential molecular target for genetic strategies aimed at reducing cardiovascular risk.