gebhart/patrepeval huggingface dataset:
Production of methanol from methane by methanotrophic bacteria (2004)

AbstractMethanotrophs can oxidize methane to carbon dioxide through sequential reactions catalyzed by a series of enzymes including methane monooxygenase, methanol dehydrogenase, formaldehyde dehydrogenase, and formate dehydrogenase. When suspensions of methanotrophic bacteria of Methylosinus trichosporium IMV 3011 were incubated at 32°C with methane and oxygen, there was an extracellular accumulation of methanol from methane oxidation in response to carbon dioxide addition. Maximal accumulation of methanol was achieved with 40% carbon dioxide in the mixed reaction gases. A continuous experiment was performed in a continuous ultrafiltration reactor. The optimum gas mixture containing 20% (v v−1) methane, 20% oxygen, 20% nitrogen and 40% carbon dioxide was used to provide substrates and to maintain the transmembrane pressure. The product (methanol) was removed in the eluate buffer. The initial methanol concentration in the eluate buffer was 8.22 μmol L−1. The bioreactor was operated continuously for 198 h without obvious loss of productivity.KeywordsCarbon dioxidemethane oxidationmethanol biosynthesisMethanotrophMethylosinus trichosporium IMV 3011continuous reaction
Anxiety, depression, sexual dysfunction and quality of life in prostate cancer based on stage of the disease (2013)

Background: Prostate cancer is common in men and in many studies quality of life, mental health problems and sexual dysfunction were examined in this population. However, there are relatively few studies examining the impact of the disease according to the stages. In this study we aimed to compare the levels of anxiety, depression, quality of life and sexual dysfunction of the prostate cancer patients according to their stages. Method: 80 patients with prostate cancer who applied to urology outpatient clinic were enrolled to the study. Patients were divided into three groups according to their stages; localized/organ-confined, local spread and metastatic spread. Short Form 36 (SF-36), Hospital Anxiety and Depression Scale (HAD) and the Arizona Sexual Experience Scale (ASEX) were performed. Results: According to the stage of prostate cancer, physical functioning subscale of quality of life was significantly lower in patients with metastatic prostate cancer than in patients with organ-confined prostate cancer (F= 4.53, p= 0.014). There were no associations between anxiety and depression scores and the stage of prostate cancer. Sexual desire was better in organ-confined prostate cancer patients compared to metastatic prostate cancer patients (F= 5.32, p= 0.007). Conclusion: The patients with prostate cancer might have different levels of physical functioning and sexual aversion problems at different stages of the disease. The clinicians should consider these two issues during follow-up of these patients.
Neutral beam based on positive ions with direct energy conversion (1977)

Positive ions can make efficient neutral beams when direct energy conversion is incorporated at energies up to 150 keV for D/sup 0/, 225 keV for T/sup 0/ and 300 keV for /sup 3/He/sup 0/. Above these energies the efficiency is low (<50%) and falling rapidly, requiring other means for making neutral beams such as negative ions. The virtues of /sup 3/He/sup 0/ beams as a heater are discussed. The role of direct conversion is discussed and the various conversion concepts and the experimental data base are reviewed. The development problems facing direct conversion are: space charge handling, secondary and primary electron suppression, and the fractional energy ions. The next step in the development of efficient neutral beams based on positive ions is argued to be a developmental beam which integrates an advanced ion source with a neutralizer, cryopump, direct converter, heat removal system, and power conditioning system.
Real-time prediction of respiratory motion based on local regression methods (2007)

Recent developments in modulation techniques enable conformal delivery of radiation doses to small, localized target volumes. One of the challenges in using these techniques is real-time tracking and predicting target motion, which is necessary to accommodate system latencies. For image-guided-radiotherapy systems, it is also desirable to minimize sampling rates to reduce imaging dose. This study focuses on predicting respiratory motion, which can significantly affect lung tumours. Predicting respiratory motion in real-time is challenging, due to the complexity of breathing patterns and the many sources of variability. We propose a prediction method based on local regression. There are three major ingredients of this approach: (1) forming an augmented state space to capture system dynamics, (2) local regression in the augmented space to train the predictor from previous observation data using semi-periodicity of respiratory motion, (3) local weighting adjustment to incorporate fading temporal correlations. To evaluate prediction accuracy, we computed the root mean square error between predicted tumor motion and its observed location for ten patients. For comparison, we also investigated commonly used predictive methods, namely linear prediction, neural networks and Kalman filtering to the same data. The proposed method reduced the prediction error for all imaging rates and latency lengths, particularly for long prediction lengths.
Lower extremity functional neuromuscular stimulation in cases of spinal cord injury (1984)

Current concepts of brain perfusion focus on the importance of rheological factors in the determination of cerebral blood flow. Blood viscosity, a primary determinant of blood flow, increases as the shear rate (velocity gradient) decreases, thereby impeding cerebral perfusion. Hematocrit, erythrocyte aggregation, erythrocyte flexibility, platelet aggregation, and plasma viscosity differentially influence blood flow through the conductance vessels and microcirculation of the brain. In addition, the microcirculation is also affected by the Fahraeus effect, the inversion phenomenon, and the screening effect. Knowledge of these factors affecting blood flow provides a rationale for experimental and clinical rheological therapies in the treatment or prevention of acute focal cerebral ischemia. (Neurosurgery 15:125-131, 1984)
Anti-HER2 CD4+ T-helper type 1 response is a novel immune correlate to pathologic response following neoadjuvant therapy in HER2-positive breast cancer (2015)

Anti-HER2 CD4(+) Th1 response is a novel immune correlate to pathologic response following neoadjuvant T + C. In non-pCR patients, depressed Th1 responses are not immunologically "fixed" and can be restored with HER2-directed Th1 immune interventions. In such high-risk patients, combining HER2-targeted therapies with strategies to boost anti-HER2 Th1 immunity may improve outcomes and mitigate recurrence.
<scp>LCAO–MO</scp> similarity measures and taxonomy (1987)

Abstract Similarity measures between pairs of molecular wave functions are described. They are based on the geometrical structure of the LCAO–MO framework and upon multivariate analysis ideas. The theoretical framework is presented, and formulae for some integrals needed are given. Two main measures, distance and correlation coefficients, are used. Distance and correlation matrices induce relationships in the whole MO set, which can be depicted through minimal spanning tree techniques. Furthermore, principal component analysis allows a two‐dimensional visualization of the Mo manifold geometrical relationships. Various examples are given in order to obtain information on how basis set, environment, excitation, bending, stretching, and electronegativity affect the induced order. For this purpose “ab initio” SCF–LCAO–MO calculations with double‐ and single‐zeta quality basis sets have been used for various simple molecular structures: H 2 O, NH 3 , CH 4 , N 2 , O 2 , C 2 , NO, CN, and CO. The results obtained can open the way to LCAO–MO taxonomy. Using this information, other areas of interest are connected with similarity measures ( SCF and CI , localization procedures, etc.), proving in this manner their potential utility.
Atomic Force Microscopy to Study Mechanics of Living Mitotic Mammalian Cells (2011)

While biochemical pathways within mitotic cells have been intensively studied, the mechanics of dividing cells is only poorly understood. In our recent report, an experimental system combining fluorescence and atomic force microscopy was set up to study dynamics of mitotic rounding of mammalian cells. We show that cells have a rounding pressure that increases upon mitotic entry. Using specific inhibitors or perturbations, we revealed biological processes required for force generation that underpin the cell rounding shape change during mitosis. The significance of the finding and an outlook are discussed.
DNA electrophoresis in microfluidic post arrays under moderate electric fields (2006)

The dynamics of long DNA moving through microfluidic arrays of micron-sized posts under a moderate electric field are modeled by a Scher-Lax continuous-time random walk. The microscale model consists of a repetitive sequence of three steps: (i) collision with the post and extension into two arms, (ii) electric-field-driven unhooking from the post, and (iii) uniform translation until the next collision. The model features two random variables: the initial offset between the two arms of the polymer during a given collision and the distance traveled between collisions. For experimentally realistic values of the electric field strength and DNA molecular weight, scaling laws indicate that the chain will generally be in a stem-flower conformation when unhooking from the post. Compared to a taut-chain model at the same field strength, the stem-flower conformation reduces the time engaged with the post and increases the collision frequency. Analytical expressions for the mean velocity and dispersivity are derived as a function of the post density, post spacing, free-solution mobility, Kuhn length, and sequence length. The incomplete extension of the chain does not strongly affect the mean velocity, but tends to increase the dispersivity relative to a taut chain. As a result, the separation resolution decreases as the field decreases for a moderate field, in agreement with experiments. The quantitative agreement between the model and experimental data is satisfactory, especially considering that the model contains no adjustable parameters.
The complexation of halide ions by a calix[6]pyrrole (2000)

The X-ray crystal structures of the 1∶1 complexes formed by calix[6]pyrrole 1b with Bun4NCl and Bun4NBr show the macrocycle to adopt D3d symmetry and to encapsulate the halide ions within the macroring cavity via six N–H···X– hydrogen bonds; the macrocycle subtly adjusts its conformation to accommodate the differently sized anions; preliminary extraction experiments indicate that 1b is a dramatically stronger chloride ion complexing agent than its smaller analogue calix[4]pyrrole 1a.
The Tight Junction Protein ZO-1 Establishes a Link between the Transmembrane Protein Occludin and the Actin Cytoskeleton (1998)

The tight junction protein ZO-1 belongs to a family of multidomain proteins known as the membrane-associated guanylate kinase homologs (MAGUKs). ZO-1 has been demonstrated to interact with the transmembrane protein occludin, a second tight junction-specific MAGUK, ZO-2, and F-actin, although the nature and functional significance of these interactions is poorly understood. To further elucidate the role of ZO-1 within the epithelial tight junction, we have introduced epitope-tagged fragments of ZO-1 into cultured MDCK cells and identified domains critical for the interaction with ZO-2, occludin, and F-actin. A combination of in vitro and in vivo binding assays indicate that both ZO-2 and occludin interact with specific domains within the N-terminal (MAGUK-like) half of ZO-1, whereas the unique proline-rich C-terminal half of ZO-1 cosediments with F-actin. Consistent with these observations, we found that a construct encoding the N-terminal half of ZO-1 is specifically associated with tight junctions, whereas the unique C-terminal half of ZO-1 is distributed over the entire lateral surface of the plasma membrane and other actin-rich structures. In addition, we have identified a 244-amino acid domain within the N-terminal half of ZO-1, which is required for the stable incorporation of ZO-1 into the junctional complex of polarized MDCK cells. These observations suggest that one functional role of ZO-1 is to organize components of the tight junction and link them to the cortical actin cytoskeleton.
Release of granulocyte-macrophage colony-stimulating factor by alveolar macrophages in the lung of HIV-1-infected patients. A mechanism accounting for macrophage and neutrophil accumulation (1992)

In this paper, the release of granulocyte-macrophage colony-stimulating factor (GM-CSF) in the lung of patients with HIV-1 infection was evaluated. This cytokine has well recognized effects on granulocyte and macrophage growth and differentiation and plays some role in the mechanisms leading to the accumulation of alveolar macrophages (AM) in patients with interstitial lung disease. Detectable levels of GM-CSF (up to 10 pg/ml) were demonstrated in unconcentrated bronchoalveolar lavage fluid retrieved from HIV-1-seropositive patients, thus suggesting that the GM-CSF is released in vivo in the lung during HIV-1 infection. A statistically significant correlation was demonstrated between the bronchoalveolar lavage concentrations of GM-CSF and the absolute numbers of AM and lung neutrophils. Cell-free supernatants obtained from unstimulated 24-h cultured AM isolated from HIV-1-infected patients contained discrete amounts of GM-CSF, as demonstrated by an immunoenzymatic assay. AM lost the capability of releasing GM-CSF after 72 h of culture, thus suggesting that the production of GM-CSF is not constitutive in AM. After exposition of AM with LPS, the release of GM-CSF and the expression of its mRNA significantly increased with respect to the baseline values; interestingly, the amount of GM-CSF released by LPS-stimulated AM was more than 10-fold higher in HIV-1-infected patients than in healthy subjects. As demonstrated by flow cytometry analysis, more than 70% of freshly isolated AM efficiently bound phycoerythrin-GM-CSF, thus indicating that they express the receptor for GM-CSF. Determination of AM in G1, S, and G2+M by flow cytometry showed that, after 48 h of culture with GM-CSF, 5.5 to 7% of AM entered the proliferative phase of the cell cycle. Taken together, these findings suggest that AM might represent an important source of GM-CSF production in HIV-1 infection. In particular, the hypothesis is formulated that pulmonary opportunists might trigger AM to synthesize GM-CSF in situ. The local overproduction of this cytokine is likely to play a role in the pathogenic events leading to the local proliferation of AM and recruitment of neutrophils in AIDS-associated interstitial lung disease.
DESIGN AND DEVELOPMENT OF AN ENVIRONMENTAL CELL FOR DYNAMIC IN SITU OBSERVATION OF GAS-SOLID REACTIONS AT ELEVATED TEMPERATURES (2008)

In situ monitoring of events in transmission electron microscopy provides information on how materials behave in their true state while varying environmental conditions (i.e. temperature and pressure) and exposure to reactant gas mixtures. In-situ results are usually different from static, post-reaction observations because they provide valuable real time - rather than post mortem - information. To facilitate applications that demand in situ observations, a transmission electron microscope specimen holder assembly has been developed in this dissertation. This assembly incorporates a gas flow and heating mechanism along with a novel window-type environmental cell. A controlled mixture of up to four different gases can be circulated through the cell during an experiment. In addition, the specimen can be heated up to a temperature of 1500 °C using a specially designed carbon dioxide laser mechanism. This heating technique provides major advantages over conventional methods in terms of product life, specimen heating time and design size. The cell design incorporates a gas reaction chamber less than 1 mm in height, enclosed between a pair of 20 nm thick silicon nitride windows. The chamber can accommodate a specimen or a grid having a diameter of 3 mm and thicknesses in the range of 50 to 100 microns. The volume for the gas environment within the chamber is approximately 3 mmc and the gas path length is less than 1 mm. This holder has been designed by incorporating cutting edge heating and MEMS technology to achieve excellent resolution along with a low thermal drift. Successful application of the holder has been shown to provide scientists with an economical alternative to dedicated transmission electron microscopes for a vast array of in situ applications. These applications include understanding the basic material properties, catalysis reactions, semiconductor device development, and nano structure fabrication.
A Comparison of Catalysts to Promote Imidazolide Couplings Including the Identification of 2-Hydroxy-5-nitropyridine as a New, Safe, and Effective Catalyst (2005)

Five catalysts were compared with respect to their safety and catalytic effectiveness for promoting imidazolide couplings. Reaction rate enhancement, shock sensitivity, and differential scanning calorimetry (DSC) data were considered in this analysis. 6-Chloro-1-hydroxybenzotriazole, which has been described in the literature as a safe catalyst, was found to be shock sensitive. 2-Hydroxy-5-nitropyridine is a new catalyst for this type of reaction and was found to be safe, effective, readily available, and similar in price to that of the 1-hydroxybenzotriazole, a common catalyst for promoting acylation reactions.
Temporal evolution in caveolin 1 methylation levels during human esophageal carcinogenesis (2014)

CAV1 promoter hypermethylation is a frequent event in human esophageal carcinomas and is associated with early neoplastic progression in Barrett's esophagus.
Hybrid Metal/Organo Relay Catalysis Enables Enynes To Be Latent Dienes for Asymmetric Diels–Alder Reaction (2012)

The hybrid Au(I)/Brønsted acid binary catalyst system enables enynes to serve as latent 1,3-silyloxydienes capable of participating in the first cascade hydrosiloxylation of an enynyl silanol/asymmetric Diels-Alder reaction. A variety of polycyclic compounds bearing multistereogenic centers were obtained in high yields and excellent enantioselectivities from the relay catalytic cascade reaction between (2-(but-3-en-1-ynyl)phenyl) silanols and quinones catalyzed by the combined achiral gold complex and chiral N-triflyl phosphoramide.
In Plants, 3-<i>O</i>-Methylglucose Is Phosphorylated by Hexokinase But Not Perceived as a Sugar (2003)

Abstract In plants, sugars are the main respiratory substrates and important signaling molecules in the regulation of carbon metabolism. Sugar signaling studies suggested that sugar sensing involves several key components, among them hexokinase (HXK). Although the sensing mechanism of HXK is unknown, several experiments support the hypothesis that hexose phosphorylation is a determining factor. Glucose (Glc) analogs transported into cells but not phosphorylated are frequently used to test this hypothesis, among them 3-O-methyl-Glc (3-OMG). The aim of the present work was to investigate the effects and fate of 3-OMG in heterotrophic plant cells. Measurements of respiration rates, protein and metabolite contents, and protease activities and amounts showed that 3-OMG is not a respiratory substrate and does not contribute to biosynthesis. Proteolysis and lipolysis are induced in 3-OMG-fed maize (Zea mays L. cv DEA) roots in the same way as in sugar-starved organs. However, contrary to the generally accepted idea, phosphorous and carbon nuclear magnetic resonance experiments and enzymatic assays prove that 3-OMG is phosphorylated to 3-OMG-6-phosphate, which accumulates in the cells. Insofar as plant HXK is involved in sugar sensing, these findings are discussed on the basis of the kinetic properties because the catalytic efficiency of HXK isolated from maize root tips is five orders of magnitude lower for 3-OMG than for Glc and Man.
Chromic Acid Oxidation of Organoboranes. A Convenient Route to 6-Keto Steroids (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChromic Acid Oxidation of Organoboranes. A Convenient Route to 6-Keto SteroidsJehan F. Bagli, Peter F. Morand, and R. GaudryCite this: J. Org. Chem. 1962, 27, 8, 2938–2940Publication Date (Print):August 1, 1962Publication History Published online1 May 2002Published inissue 1 August 1962https://pubs.acs.org/doi/10.1021/jo01055a519https://doi.org/10.1021/jo01055a519research-articleACS PublicationsRequest reuse permissionsArticle Views61Altmetric-Citations8LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Peptide Hydrogel as an Intraocular Drug Delivery System for Inhibition of Postoperative Scarring Formation (2010)

A biocompatible hydrogel self-assembled from a peptide comprised of a peptide backbone containing Arg-Gly-Asp (RGD) sequence and a hydrophobic N-fluorenyl-9-methoxycarbonyl (FMOC) tail was designed and prepared to load antiproliferative model drug (5-fluorouracil, 5-Fu). After administering this 5-Fu-loaded peptide hydrogel in the filtering surgery of rabbit eyes, because of the sustained release of 5-Fu from the hydrogel to inhibit the scleral flap fibrosis efficiently, the pathology and immunohistochemistry demonstrate that the filtration fistula is patent without postoperative scarring formation, resulting in the significantly low intraocular pressure (IOP) of the rabbit eyes within postoperative 28 days. In a comparison with the conventional 5-Fu exposure, the strategy demonstrated here presents several advantages including providing convenience and preventing the toxicity of 5-Fu to the surrounding ocular tissues efficiently, suggesting a feasibility of this peptide hydrogel as a potential implanted drug delivery system for the inhibition of postoperative scarring formation.
Community Collaborative Filtering for E-Learning (2008)

Recommender systems for e-learning need to consider the specific demands and requirements and to improve the 'educational aspects' for the learners. In this paper, we present a novel hybrid recommender system from a perspective of considering learner community structures to collaborative filtering. In our approach, multiple types of information are explored and exploited, including learners and learning items and learner social information. Leveraging the types of information, we apply multiple techniques from data mining, including multi-relational data mining and graph data mining, to explicitly discovery learner community structures, which in turn are used in collaborative filtering. Our experiments suggest that our approach provides improved accurate recommendations than other approaches.