gebhart/patrepeval huggingface dataset:
Analysis of DNA in Phosphate Buffered Saline Using Kinetic Capillary Electrophoresis (2016)

Kinetic capillary electrophoresis (KCE) methods are useful in the study of kinetics and equilibrium properties of interactions between DNA and its binding partners (ligands). KCE experiments are typically performed in a narrow set of "conventional" low-conductivity run buffers while DNA-ligand interactions in biological systems occur in physiological fluids, characterized by high ionic strengths. The nature and ionic strength of the buffer, in which DNA-ligand interaction occurs, can significantly influence the binding. Therefore, KCE experiments meant to study such interactions would greatly benefit if they could be performed in physiological buffers, such as phosphate buffered saline (PBS). No previous KCE studies of DNA used PBS as the run buffer. Here, we test the feasibility of using PBS as a KCE run buffer for analysis of DNA and show that its usage under standard KCE conditions renders DNA undetectable. We uncover the causes of this previously unreported detrimental effect and come up with a modification of KCE which allows one to overcome it. We apply the modified KCE method to an experimental model of a platelet-derived growth factor (PDGF) protein and its DNA aptamer, which was selected in PBS, and show that the results obtained in PBS run buffer are much closer to previously reported values than those which were obtained with a conventional low-conductivity capillary electrophoresis (CE) buffer.
H/sub 2/ iterative model refinement and control robustness enhancement (2002)

Many practical applications of control system design based on input-output measurements permit the repeated application of a system identification procedure operating on closed-loop data together with successive refinement of the designed controller. A paradigm is developed for such an iterative design. The key to the procedure is to account for evaluated modeling error in the control design and, equally, to allow for the requirements of the closed-loop controller in performing the identification. With an H/sub 2/ control problem, this is achieved by frequency weighting the linear quadratic control criterion and by filtering the identifier signals in a logical fashion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
MRSA Case Studies (2007)

Staphylococcus aureus is a versatile pathogen associated with diverse clinical presentations. Only recently have the genetic factors underlying the virulence of this bacterial species become understood in a significant way. Methicillin-resistant S. aureus (MRSA) strains have been extremely important as nosocomial pathogens in health care facilities for more than three decades. Additionally, infections resulting from community-associated MRSA strains have emerged in the last decade and become a public health problem of global proportions. This changing epidemiology has spurred renewed interest in translating knowledge of the molecular determinants of virulence into rational prevention and control strategies. Four case histories are provided (three involving MRSA and one involving a methicillin-sensitive strain of S. aureus) that highlight the diversity of clinical presentations and relative virulence of S. aureus infections in humans. The molecular characterization of clonality and virulence gene profile is compared among the four cases. Significant genetic diversity exists among MRSA and sensitive strains of S. aureus. It is obvious that various combinations of virulence factors contribute to disease manifestations of infected patients.
Enhanced growth of tumors in SPARC null mice is associated with changes in the ECM (2003)

SPARC, a 32-kDa glycoprotein, participates in the regulation of morphogenesis and cellular differentiation through its modulation of cell-matrix interactions. Major functions defined for SPARC in vitro are de-adhesion and antiproliferation. In vivo, SPARC is restricted in its expression to remodeling tissues, including pathologies such as cancer. However, the function of endogenous SPARC in tumor growth and progression is not known. Here, we report that implanted tumors grew more rapidly in mice lacking SPARC. We observed that tumors grown in SPARC null mice showed alterations in the production and organization of ECM components and a decrease in the infiltration of macrophages. However, there was no change in the levels of angiogenic growth factors in comparison to tumors grown in wild-type mice, although there was a statistically significant difference in total vascular area. Whereas SPARC did inhibit the growth of tumor cells in vitro, it did not have a demonstrable effect on the proliferation or apoptosis of tumor cells in vivo. These data indicate that host-derived SPARC is important for the appropriate organization of the ECM in response to implanted tumors and highlight the importance of the ECM in regulating tumor growth.
Image Restoration Using Functional and Anatomical Information Fusion with Application to SPECT‐MRI Images (2009)

Image restoration is usually viewed as an ill-posed problem in image processing, since there is no unique solution associated with it. The quality of restored image closely depends on the constraints imposed of the characteristics of the solution. In this paper, we propose an original extension of the NAS-RIF restoration technique by using information fusion as prior information with application in SPECT medical imaging. That extension allows the restoration process to be constrained by efficiently incorporating, within the NAS-RIF method, a regularization term which stabilizes the inverse solution. Our restoration method is constrained by anatomical information extracted from a high resolution anatomical procedure such as magnetic resonance imaging (MRI). This structural anatomy-based regularization term uses the result of an unsupervised Markovian segmentation obtained after a preliminary registration step between the MRI and SPECT data volumes from each patient. This method was successfully tested on 30 pairs of brain MRI and SPECT acquisitions from different subjects and on Hoffman and Jaszczak SPECT phantoms. The experiments demonstrated that the method performs better, in terms of signal-to-noise ratio, than a classical supervised restoration approach using a Metz filter.
Fluorescent in situ hybridization of the telomere repeat sequence in hamster sperm nuclear structures (1993)

Abstract The flat, hooked‐shaped architecture of the hamster sperm nucleus makes this an excellent model for in situ hybridization studies of the three dimensional structure of the genome. We have examined the structure of the telomere repeat sequence (TTAGGG) n with respect to the various nuclear structures present in hamster spermatozoa, using fluorescent in situ hybridization. In fully condensed, mature sperm nuclei, the telomere sequences appeared as discrete spots of various sizes interspersed throughout the volume of the nuclei. While the pattern of these signals was non‐random, it varied significantly in different nuclei. These discrete telomere foci were seen to gradually lengthen into linear, beaded signals as sperm nuclei were decondensed, in vitro, and were not associated with the nuclear annulus. We also examined the relationship of telomeres to the sperm nuclear matrix, a residual nuclear structure that retains the original size and shape of the nucleus. In these structures the DNA extends beyond the perimeter of the nucleus to form a halo around it, representing the arrangement of the chromosomal DNA into loop domains attached at their bases to the nuclear matrix. Telomere signals in these structures were also linear and equal in length to those of the decondensed nuclei, and each signal represented part of a single DNA loop domain. The telomeres were attached at one end to the nuclear matrix and extended into the halo. Sperm nuclear matrices treated with Eco RI retained the telomere signals. These data support sperm DNA packaging models in which DNA is coiled into discrete foci, rather than spread out linearly along the length of the sperm nucleus.
Microfabrication and Laser Diagnosis of Pressure-Swirl Atomizers (2004)

In this work, we used deep-molding manufacture of three kinds to fabricate micro pressure-swirl atomizers to promote their performance, and a phase doppler particle analyzer (PDPA) to measure the characteristic distributions of the spray flow field of these atomizers. The deep-molding techniques were X-ray LIGA process, ICP-LIGA process (inductive coupling plasma etching), and injection molding LIGA process. Parameters of atomizers examined here include configuration of flow channel, diameter of exit orifice, the ratio of diameters of swirl chamber and discharge orifice, and the thickness of atomizer. Experimental results showed that the manufacturing process combining injection molding with electroplating had large yields and that the technique is highly reliable; enable manufacture of an atomizer at small cost and great quality. Moreover, these microatomizers are assembled well with other components and can be readily applied. The results of PDPA diagnosis further revealed that the spray features are related to the design parameters of atomizer dimensions.
Simulation of carbon-13 nuclear magnetic resonance spectra of methyl-substituted norbornan-2-ols (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSimulation of carbon-13 nuclear magnetic resonance spectra of methyl-substituted norbornan-2-olsDebra S. Egolf, Elizabeth B. Brockett, and Peter C. JursCite this: Anal. Chem. 1988, 60, 24, 2700–2706Publication Date (Print):December 15, 1988Publication History Published online1 May 2002Published inissue 15 December 1988https://pubs.acs.org/doi/10.1021/ac00175a012https://doi.org/10.1021/ac00175a012research-articleACS PublicationsRequest reuse permissionsArticle Views47Altmetric-Citations5LEARN 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
Survival outcomes of early autologous stem cell transplant (ASCT) followed by lenalidomide, bortezomib, and dexamethasone (RVD) maintenance in patients with high-risk multiple myeloma (MM). (2012)

8100 Background: Despite markedly improved survival rates for MM pts in the last decade, 15-20% of pts with high risk genetics continue to have dismal outcomes with a median PFS of 18.5 months (Kapoor P et al). In this subset of pts, efforts are needed to improve response rates and prolong the response duration, but doing so without genotoxic therapy as this has been shown not to improve outcomes (Barlogie et al). Methods: We evaluated 37 pts with high risk features [del17p (n=16), t(4;14) (n=1), t(14;16) (n=4) by FISH/CTG; hypodiploidy (n=9), del 13 (n=16); complex karyotype (n=14) by CTG; PCL (n=7) and atypical presentation (n=4)]. After completing induction therapy, all pts underwent ASCT followed by RVD maintenance. 60 days after ASCT following hematological recovery, pts began maintenance [lenalidomide 10 mg/day (days1–21), bortezomib 1.3 mg/m2 and dexamethasone 40 mg once a week (days 1, 8, 15) every 28 days]. Results: The response rates are summarized in the table. 7/36 pts progressed while on RVD maintenance. The median PFS and OS for pts on RVD maintenance has not been reached. Pts with <VGPR pre-ASCT and with <VGPR on RVD maintenance have median PFS of 28 months and 11 months, respectively. 4 pts with prior h/o DVT received anticoagulation, while all others received ASA for DVT prophylaxis. No thrombotic events were seen. There were no grade 3/4 toxicities or treatment-related mortality. The most common toxicities during maintenance schedule were: PN-40% (G1: 26%; G2:14%); G1 rash-10% and G1 fatigue in 78% pts. Cytopenias were seen in 25% pts and dose reductions were made in 50% pts. There is no report of secondary malignancies. Conclusions: Early ASCT followed by RVD maintenance delivers superior response rates in this high risk segment achieving sCR in 47% and ≥VGPR in 73% pts and prevents early relapses. The median PFS and OS have not been reached. RVD maintenance regimen is well tolerated and promising. [Table: see text]
Hydrophobic and moisture-stable metal–organic frameworks (2015)

Metal-organic frameworks (MOFs) have proved to be very attractive for applications including gas storage, separation, sensing and catalysis. In particular, CO(2) separation from flue gas in post-combustion processes is one of the main focuses of research among the scientific community. One of the major issues that are preventing the successful commercialization of these novel materials is their high affinity towards water that not only compromises gas sorption capacity but also the chemical stability. In this paper, we demonstrate a novel post-synthesis modification approach to modify MOFs towards increasing hydrophobic behaviour and chemical stability against moisture without compromising CO(2) sorption capacity. Our approach consists of incorporating hydrophobic moieties on the external surface of the MOFs via physical adsorption. The rationale behind this concept is to increase the surface hydrophobicity in the porous materials without the need of introducing bulky functionalities inside the pore which compromises the sorption capacity toward other gases. We herein report preliminary results on routinely studied MOF materials [MIL-101(Cr) and NiDOBDC] demonstrating that the polymer-modified MOFs retain CO(2) sorption capacity while reducing the water adsorption up to three times, with respect to the un-modified materials, via an equilibrium effect. Furthermore, the water stability of the polymer-functionalized MOFs is significantly higher than the water stability of the bare material. Molecular dynamic simulations demonstrated that this equilibrium effect implies a fundamental and permanent change in the water sorption capacity of MOFs. This approach can also be employed to render moisture stability and selectivity to MOFs that find applications in gas separations, catalysis and sensing where water plays a critical role in compromising MOF performance and recyclability.
Plant Anticancer Agents X. Isolation of Camptothecin and 9-Methoxycamptothecin From Ervatamia heyneaya (1979)

The anticancer activity of the roots of Ervatamia heyneana (Apocynaceae) was found to be due principally to the known alkaloid, camptothecin (1). The closely related, but less active, 9-methoxycamptothecin (2) was also obtained. This is the first reported isolation of these biogenetically interesting alkaloids from the indole alkaloid rich Apocynaceae.
Ring‐Opening Metathesis Polymerization Based Pore‐Size‐Selective Functionalization of Glycidyl Methacrylate Based Monolithic Media: Access to Size‐Stable Nanoparticles for Ligand‐Free Metal Catalysis (2010)

Monolithic polymeric supports have been prepared by electron-beam-triggered free-radical polymerization using a mixture of glycidyl methacrylate and trimethylolpropane triacrylate in 2-propanol, 1-dodecanol, and toluene. Under appropriate conditions, phase separation occurred, which resulted in the formation of a porous monolithic matrix that was characterized by large (convective) pores in the 30 μm range as well as pores of <600 nm. The epoxy groups in pores of >7 nm were hydrolyzed by using poly(styrenesulfonic acid) (Mw = 69,400 g mol(-1), PDI=2.4). The remaining epoxy groups inside pores of <7 nm were subjected to aminolysis with norborn-5-en-2-ylmethylamine (2) and provided covalently bound norborn-2-ene (NBE) groups inside these pores. These NBE groups were then treated with the first-generation Grubbs initiator [RuCl2 (PCy3 )2 (CHPh)]. These immobilized Ru-alkylidenes were further used for the surface modification of the small pores by a grafting approach. A series of monomers, that is, 7-oxanorborn-5-ene-2,3-dicarboxylic anhydride (3), norborn-5-ene-2,3-dicarboxylic anhydride (4), N,N-di-2-pyridyl-7-oxanorborn-5-ene-2-carboxylic amide (5), N,N-di-2-pyridylnorborn-5-ene-2-carboxamide (6), N-[2-(dimethylamino)ethyl]bicyclo[2.2.1]hept-5-ene-2-carboxamide (7), and dimethyl bicyclo[2.2.1]hept-5-en-2-ylphosphonate (8), were used for this purpose. Finally, monoliths functionalized with poly-5 graft polymers were used to permanently immobilize Pd(2+) and Pt(4+), respectively, inside the pores. After reduction, metal nanoparticles 2 nm in diameter were formed. The palladium-nanoparticle-loaded monoliths were used in both Heck- and Suzuki-type coupling reactions achieving turnover numbers of up to 167,000 and 63,000, respectively.
Research and implementation of ARINC653 configuration tool based on AADL (2011)

Applications must be integrated into a system configuration which satisfies all the requirements of applications in the ARINC653 system. The goal of this paper is to assist system integrator to generate correct configuration tables. Architecture Analysis and Design Language (AADL) is widely used in avionics systems modeling and analysis. In order to model and analyze avionics systems that meet the ARINC653 standard, we need to extend AADL existing standard to satisfy the requirements of ARINC653. This paper presents an approach to augment the modeling ability of AADL to describe ARINC653 configuration instance, details a modeling approach exploiting the new property sets of AADL for the design of ARINC653 architectures, and implement an automatic ARINC653 configuration tool based on AADL which generates the static configuration files that meet the qualification of ARINC653 schema for the instance model. The correct configurations generated by this tool verify the validity and feasibility of this method.
Multi-mode control method based on fuzzy selector in the four wheel steering control system (2010)

To solve the problem that an alone control method can't suit to every running condition of the four-wheel-steering (4WS) vehicle, a multi-mode control strategy was suggested based on fuzzy selector that can get perfect control effect for the four-wheel-steering vehicle. The strategy could be used to achieve the optimal yawing angular velocity, centroid edge angle and bodywork heeling angle by controlling the steering angles of the front and rear wheels. The analysis of the steering behaviors under the different working condition was carried out by fuzzy selector to choose the appropriate control mode and determine the corresponding control arithmetic to improve the vehicle's steering characteristics under various working conditions. The numerical simulation was carried out with the selector which combined the proportional control and the self-adaptation control as an example. The results indicate that the multi-mode control strategy can meet the requirements of the four wheel steering under the different working conditions and has better control efficiency than a single mode control strategy.
Long‐Term continuous culture of hepatocytes in a packed‐bed reactor utilizing porous resin (1994)

As part of our attempt to develop a hybrid artificial liver support system using cultured hepatocytes, we investigated the long-term metabolic function of hepatocytes incubated in a packed-bed type reactor using reticulated polyvinyl formal (PVF) resin as a supporting material. Long-term (up to 1 week) perfusion culture experiments using the packed-bed reactor (20 mm i.d.) loaded with 500 PVF resin cubes (mean pore size 250 mum, 2 x 2 x 2 mm), together with conventional monolayer culture experiments as controls, were performed in serum-free or serum-containing medium. Ammonium metabolism and urea synthesis activities were evaluated quantitatively based on reaction kinetic analyses. Initial rates of ammonium metabolism and urea-N synthesis, as well as GPT enzyme activities, were adopted as indexes of the metabolic performance of the reactor and activities of the cultured hepatocytes.When serum-free medium was used in the perfusion cultures, ammonium metabolic and urea-N synthetic rates showed significant decay with elapse of the culture period, being less than 10% of those measured on day 1. This loss of activity was more prominent in the perfusion culture than in the monolayer cultures using this medium. In contrast, when serum-containing medium was used, approximately 50% of these activities obtained on day 1 were maintained even at the end of the cultures both in the perfusion and monolayer culture experiments.We concluded that the packed-bed reactor using PVF resin enabled high-density culture of hepatocytes, and showed a satisfactory ability to maintain the metabolic function of immobilized hepatocytes for relatively long periods of up to 1 week. This type of reactor is thus considered to represent a breakthrough in overcoming the difficulties involved in the development of a hybridtype artificial liver support system. (c) 1994 John Wiley & Sons, Inc.
Cerebral blood flow increase in cancer patients by applying cervical spinal cord stimulation (2007)

Introduction. Generally, high-grade gliomas and head and neck tumors have decreased loco-regional blood flow resulting in reduced delivery of chemotherapy and oxygen, as well as an increases in radiation resistance to radiotherapy. The aim of this study was to analyze the effect of cervical spinal cord electrical stimulation (cSCS) on cerebral blood flow in patients with those tumors.
Palladium-Catalyzed Heck Reaction on 1-Alkoxy-1,3-dienes:  A Regioselective γ-Arylation of α,β-Unsaturated Carbonyl Compounds (2003)

[reaction: see text] alpha,beta-Unsaturated acetals afford, in the presence of the LIC-KOR superbase, 1-alkoxybuta-1,3-dienes. These substrates cross couple with aryl derivatives in the presence of Pd catalyst (Heck conditions) in a regio- and stereoselective mode. With dialkyl acetals, the reaction affords arylated dienes; on the other hand, in the case of 1,3-dioxane derivatives, the final outcome of the process formally corresponds to the direct gamma-arylation reaction of the starting alpha,beta-unsaturated material.
Molybdenum disulfide nanoporous membranes for water desalination (2016)

We demonstrate molybdenum disulfide (MoS2) as a nano porous membrane for water desalination. By performing extensive molecular dynamics simulations, we find that a nanopore in a single-layer MoS2 can effectively reject salt ions and allow transport of water at a high rate. More than 88% of ions are rejected by membranes having pore areas ranging from 20 to 60 A^2. Water flux through the nanoporous MoS2 membrane is found to be 2 to 5 orders of magnitude greater than that of other known nanoporous membranes (MFI-type zeolite, commercial polymeric seawater Reverse Osmosis (RO), brackish RO, Nanofiltration and High-flux RO). Pore chemistry and architecture are shown to play a significant role in modulating the water flux. MoS2 pores with only molybdenum atoms on their edges give rise to higher fluxes which are about 70% greater than that of graphene nanopores. These observations are explained by the permeation coefficients, energy barriers, water density and velocity distributions in the pores. Our findings pave way towards identifying efficient membranes for water desalination.