gebhart/patrepeval huggingface dataset:
EFFECTIVE LONG-TERM IMMUNOSUPPRESSION MAINTAINED BY LOW CYCLOSPORINE LEVELS IN PRIMARY CADAVERIC RENAL TRANSPLANT RECIPIENTS (1987)

Nephrotoxicity and cost are the major problems in the use of cyclosporine (CsA) in renal transplantation. Thus, maintenance of CsA levels at the lower limits of the therapeutic range is desirable. The lowest CsA level effective in preventing rejection while avoiding nephrotoxicity has not been defined. We report on 44 primary cadaveric renal transplant recipients treated with a protocol that involved a progressive reduction in the trough CsA levels. CsA was initiated at an oral dose of 15 mg/kg, and this dose was adjusted to achieve serum trough levels, as measured by radioimmunoassay, of 150-200 ng/ml during the first month, 100-150 ng/ml during the second month, 75-100 ng/ml during the third month, and 50-75 ng/ml thereafter. Patient and graft survival at 18 months were 94% and 83.6%, respectively. The mean daily CsA doses were 6.7 +/- 3.1 mg/kg at 6 months, 5.5 +/- 3.2 mg/kg at 12 months, and 4.7 +/- 2.4 mg/kg at 18 months. Corresponding trough serum CsA levels were 94 +/- 59 ng/ml, 64 +/- 22 ng/ml, and 44 +/- 21 ng/ml at 6, 12, and 18 months, respectively. Mean serum creatinine concentrations were 1.8 +/- 0.6 mg/dl at 6 months, 1.7 +/- 0.5 mg/dl at 12 months, and 1.6 +/- 0.5 mg/dl at 18 months. The mean serum creatinine concentration at 18 months was not significantly different from that of 18 conventionally treated primary cadaveric renal transplant recipients (1.6 +/- 0.5 vs. 1.4 +/- 0.4 mg/dl, P = .31). A total of 67% of patients did not have any rejection episodes under this protocol, while 71% of patients never developed CsA nephrotoxicity. No patient was taken off CsA for progressive nephrotoxicity. We conclude that trough serum CsA levels of 50-75 ng/ml, as measured by radioimmunoassay, are sufficient to maintain effective immunosuppression in the long-term management of primary cadaveric renal transplant recipients. These values are much lower than previously recommended, and this approach ameliorates chronic CsA nephrotoxicity.
ChemInform Abstract: A Facile Synthesis of N‐Benzylallylglycine. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
DNase I sensitivity of the α2(I) collagen gene: correlation with its expression but not with its methylation pattern (1984)

The chromatin structure of the chick alpha 2(I) collagen gene was probed with DNase I. Because our previous work strongly suggested that the 5' end of this gene is not methylated whereas the rest of the gene is methylated whether or not the gene is expressed, we compared the relative DNase I sensitivity of the methylated and unmethylated segments. Both regions demonstrate similar relative DNase I sensitivities within a given tissue. In chromatin of chick embryo fibroblasts, we find a DNase I hypersensitive site which maps between 100 and 300 bp preceding the start of transcription. This site is not found in brain chromatin but is present in chick embryo fibroblasts transformed by Rous Sarcoma virus although the rate of transcription of the alpha 2(I) collagen gene is greatly reduced in these cells. Hence, the mechanism responsible for the large decrease in alpha 2(I) collagen gene expression in RSV transformed cells is different from the mechanism that is responsible for the presence of a DNase I hypersensitive site in the promoter. Furthermore, changes in the DNase I sensitivity of the chromatin of the alpha 2(I) collagen promoter occur without changes in the methylation pattern of the gene.
Making Progress through Molecular Attacks on Cancer (2005)

The success of kinase inhibitor therapy in chronic myeloid leukemia (CML) has validated the long-held thesis in the cancer research community that a precise molecular understanding of cancer can directly affect cancer therapy. Now that several years have passed since the approval of imatinib/Gleevec for CML treatment, we have a greater appreciation for the challenges involved in effectively deploying these agents in the clinic. In this paper, I review recent events in the treatment of CML and highlight early applications of kinase inhibitor therapy to other diseases such as glioblastoma. I conclude with a vision that it may be possible, through analysis of tumor proteins secreted into serum, to track distinct molecular features of various cancers in order to select appropriate molecularly targeted therapy and measure treatment response. This new science of cancer biomarkers could radically transform the conduct of clinical trials and speed the evaluation of new molecularly targeted agents.
8. H (2002)

PreviousNext No AccessEncyclopedic Dictionary of Applied Geophysics, Fourth edition8. HAuthors: Robert E. SheriffRobert E. SheriffProfessor, University of Houstonhttps://doi.org/10.1190/1.9781560802969.chh SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.9781560802969.chhFiguresReferencesRelatedDetails Encyclopedic Dictionary of Applied Geophysics, Fourth editionISBN (print):978-1-56080-118-4ISBN (online):978-1-56080-296-9Copyright: 2002 Pages: 442 publication data© 2002 All rights reserved. No part of this publication may be reproduced or distributed in any form or by any means without written permission of the publisherPublisher:Society of Exploration Geophysicists HistoryPublished in print: 01 Jan 2002 CITATION INFORMATION Robert E. Sheriff, (2002), "8. H," Geophysical References Series : 171-184. https://doi.org/10.1190/1.9781560802969.chh Plain-Language Summary PDF DownloadLoading ...
The synthesis of [3H]L-734,217, an orally active fibrinogen receptor antagonist (1996)

The synthesis of [3H]L-734,217, 1b, an orally active fibrinogen receptor antagonist, is described. The conversion of 3-amino crotonate 6 to [3H]L-734,217 was carried out via a two step sequence of catalytic tritiation followed by basic hydrolysis. Deuterium model reactions showed that the reduction of 6 with PtO2 occurred via hydrogen transfer from the solvent (ethanol or acetic acid) leading to poor isotope incorporation. When this reduction was conducted in methanol with 10% Pd/C, good isotope incorporation resulted. Ultimately, [3H]L-734,217 was formed with a specific activity of 42 Ci/mmol.
Co-oxidation of octane and benzaldehyde using molecular oxygen with Au–Pd/carbon prepared by sol-immobilisation (2015)

Oxidation of octane in the presence of benzaldehyde over a AuPd catalysts leads to the formation of octyl benzoate.
Molecular and Atomic Hydrogen Diffusion Behavior by Reaction Kinetic Analysis in Projection Range of Hydrocarbon Molecular Ion for CMOS Image Sensors (2019)

In this study, two types of hydrogen diffusion behavior in the projection range of a hydrocarbon molecular ion after high‐temperature heat treatment for the passivation of interface state defects at SiO 2 /Si interface of the CMOS image sensor is presented. The hydrogen peak concentration in the hydrocarbon ion projection range is observed by secondary ion mass spectrometry analysis after silicon epitaxial growth and the subsequent high‐temperature heat treatment. Moreover, the hydrogen peak concentration strongly depends on heat treatment time after epitaxial growth and the subsequent heat treatment. Two dissociation activation energies by reaction kinetic analysis using the results of the time dependence of hydrogen diffusion behavior are also determined. Assuming two dissociation reactions, the activation energy from the projection range of a hydrocarbon molecular ion is derived. The results of reaction kinetic analysis show that the dissociation activation energies are 0.79 eV for molecular hydrogen and 0.42 eV for atomic hydrogen. The dissociation activation energy of 0.79 eV indicates molecular hydrogen diffusion activation energy, whereas that of 0.42 eV indicates atomic hydrogen diffusion from the projection range of a hydrocarbon molecular ion. Therefore, it is believed that the molecular and atomic hydrogen diffusion behavior of the hydrocarbon molecular ion implanted silicon epitaxial wafers can contribute to the effective reduction in the density of interface state defects at the SiO 2 /Si interface.
Overcoming the Diffraction Limit Using Multiple Light Scattering in a Highly Disordered Medium (2011)

We report that disordered media made of randomly distributed nanoparticles can be used to overcome the diffraction limit of a conventional imaging system. By developing a method to extract the original image information from the multiple scattering induced by the turbid media, we dramatically increase a numerical aperture of the imaging system. As a result, the resolution is enhanced by more than 5 times over the diffraction limit, and the field of view is extended over the physical area of the camera. Our technique lays the foundation to use a turbid medium as a far-field superlens.
Gradient Design for High‐Energy and High‐Power Batteries (2022)

Charge transport is a key process that dominates battery performance, and the microstructures of the cathode, anode, and electrolyte play a central role in guiding ion and/or electron transport inside the battery. Rational design of key battery components with varying microstructure along the charge-transport direction to realize optimal local charge-transport dynamics can compensate for reaction polarization, which accelerates electrochemical reaction kinetics. Here, the principles of charge-transport mechanisms and their decisive role in battery performance are presented, followed by a discussion of the correlation between charge-transport regulation and battery microstructure design. The design strategies of the gradient cathodes, lithium-metal anodes, and solid-state electrolytes are summarized. Future directions and perspectives of gradient design are provided at the end to enable practically accessible high-energy and high-power-density batteries.
Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments (2001)

The observation of light metal ions in nucleic acids crystals is generally a fortuitous event. Sodium ions in particular are notoriously difficult to detect because their X-ray scattering contributions are virtually identical to those of water and Na(+.)O distances are only slightly shorter than strong hydrogen bonds between well-ordered water molecules. We demonstrate here that replacement of Na(+) by K(+), Rb(+) or Cs(+) and precise measurements of anomalous differences in intensities provide a particularly sensitive method for detecting alkali metal ion-binding sites in nucleic acid crystals. Not only can alkali metal ions be readily located in such structures, but the presence of Rb(+) or Cs(+) also allows structure determination by the single wavelength anomalous diffraction technique. Besides allowing identification of high occupancy binding sites, the combination of high resolution and anomalous diffraction data established here can also pinpoint binding sites that feature only partial occupancy. Conversely, high resolution of the data alone does not necessarily allow differentiation between water and partially ordered metal ions, as demonstrated with the crystal structure of a DNA duplex determined to a resolution of 0.6 A.
Time-resolved pump-probe experiments with 0.1 micron resolution (2002)

We report picosecond time-resolved pump-probe experiments using a reflection near-field scanning optical microscope. The sample was a laterally-patterned gold nanostructure. Strain-induced reflectivity changes as low as /spl Delta/R/R=10/sup -4/ could be detected in the near-field.
Hydrothermal synthesis of doped ZnO and its application in photodegradation of toxic amaranth dye (2008)

Likewise, the results of the transmittance indicate that the optical energy bandgap is constant for all reactions with a value about 3.29 eV.
Study of the Surface Chemical Reactions of Thiophene with Ag/Titania by the Complementary Temperature-Programmed Electron Spin Resonance, Temperature-Programmed Desorption, and X-ray Photoelectron Spectroscopy: Adsorption, Desorption, and Sorbent Regeneration Mechanisms (2010)

Reaction of thiophene with the ultradeep desulfurization sorbent Ag/titania under ambient conditions was studied by the multiple complementary temperature-programmed techniques: electron spin resonance (ESR), high-vacuum temperature-programmed desorption (HV-TPD), high-vacuum temperature-programmed reaction spectroscopy (HV-TPRS) and by X-ray photoelectron spectroscopy (XPS). Sorption of thiophene at 25−75 °C proceeds via strong molecular adsorption. Decomposition of the adsorption complex “Ag/titania + thiophene” occurs in a stage-wise fashion. At ∼75 to 175 °C, the adsorption complex decomposes without reaction with molecular oxygen. Adsorbed thiophene molecularly desorbs at ∼90 °C (desorption energy = 105 kJ/mol). At ∼75 to 175 °C, the nonoxidative pyrolysis of the adsorption complex with the C−S scission and desorption of butadiene proceeds. At ∼225 to 525 °C, molecular oxygen participates in thermal decomposition of the adsorption complex to form SO2. Under the deficiency of O2, the hydrogen-lean “coke” CxHy (x ≫ y) is formed. The combination of temperature-programmed ESR, TPD/TPRS, and XPS is well-suited to investigate the molecular-level mechanisms of adsorption, desorption, and surface chemical reactions of the sulfur-containing adsorbates.
Image-guided high intensity focused ultrasound annular array for hemostasis and tumor treatment (2005)

To develop and characterize an ultrasound-guided high intensity focused ultrasound (HIFU) array, an 11-element annular phased array (aperture of 3.5×6.0 cm, focal depth of 3.0–6.0 cm, frequency of 3 MHz) was coupled to an imaging probe (C9-5, Philips). LabView software was developed to control driving electronics and image guidance. Radiation force balance measurements, Schlieren imaging, and hydrophone field mapping were performed. Lesions were produced in gel phantoms, and ex vivo porcine liver and human cancerous uterus. The lesions were formed beginning at a focal depth of 6.0 cm and moving by 0.5 cm increments to 3.0 cm, and vice versa, with the overall treatment time of 2 min. The transducer had efficiency of 38%, with intensities of up to 6200 W/cm2 at the natural focus of 5 cm, in water. The 6 dB focal area varied from 0.4 mm2 (at 3 cm) to 1.5 mm2 (at 6 cm). The 3 to 6 cm tissue lesions were 2.7±0.5 cm in length, compared to 4.1±0.3 cm for the 6 to 3 cm lesions. The average lesion width was 1 cm. Image-guided HIFU array may enable treatment of large tumor volumes and hemorrhage control at different depths inside the body.
Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli (2016)

Abstract The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as non-coding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU, but the remaining thirteen “recalcitrant” AGRs required diversification to identify viable alternatives. Successful replacement codons tended to conserve local ribosomal binding site-like motifs and local mRNA secondary structure, sometimes at the expense of amino acid identity. Based on these observations, we empirically defined metrics for a multi-dimensional “safe replacement zone” (SRZ) within which alternative codons are more likely to be viable. To further evaluate synonymous and non-synonymous alternatives to essential AGRs, we implemented a CRISPR/Cas9-based method to deplete a diversified population of a wild type allele, allowing us to exhaustively evaluate the fitness impact of all 64 codon alternatives. Using this method, we confirmed relevance of the SRZ by tracking codon fitness over time in 14 different genes, finding that codons that fall outside the SRZ are rapidly depleted from a growing population. Our unbiased and systematic strategy for identifying unpredicted design flaws in synthetic genomes and for elucidating rules governing codon choice will be crucial for designing genomes exhibiting radically altered genetic codes. Significance Statement This work presents the genome-wide replacement of all rare AGR arginine codons in the essential genes of Escherichia coli with synonymous CGN alternatives. Synonymous codon substitutions can lethally impact non-coding function by disrupting mRNA secondary structure and ribosomal binding site-like motifs. Here we quantitatively define the range of tolerable deviation in these metrics and use this relationship to provide critical insight into codon choice in recoded genomes. This work demonstrates that genome-wide removal of AGR is likely to be possible, and provides a framework for designing genomes with radically altered genetic codes.
Caenorhabditis Elegans Segmentation Using Texture-Based Models for Motility Phenotyping (2014)

With widening interests in using model organisms for reverse genetic approaches and biomimmetic microrobotics, motility phenotyping of the nematode Caenorhabditis elegans is expanding across a growing array of locomotive environments. One ongoing bottleneck lies in providing users with automatic nematode segmentations of C. elegans in image sequences featuring complex and dynamic visual cues, a first and necessary step prior to extracting motility phenotypes. Here, we propose to tackle such automatic segmentation challenges by introducing a novel texture factor model (TFM). Our approach revolves around the use of combined intensity- and texture-based features integrated within a probabilistic framework. This strategy first provides a coarse nematode segmentation from which a Markov random field model is used to refine the segmentation by inferring pixels belonging to the nematode using an approximate inference technique. Finally, informative priors can then be estimated and integrated in our framework to provide coherent segmentations across image sequences. We validate our TFM method across a wide range of motility environments. Not only does TFM assure comparative performances to existing segmentation methods on traditional environments featuring static backgrounds, it importantly provides state-of-the-art C. elegans segmentations for dynamic environments such as the recently introduced wet granular media. We show how such segmentations may be used to compute nematode "skeletons" from which motility phenotypes can then be extracted. Overall, our TFM method provides users with a tangible solution to tackle the growing needs of C. elegans segmentation in challenging motility environments.
Theoretical Study of Light Refraction in (2007)

A rigorous theory for solving general 3-D photonic crystal refraction problem is developed. The power flow direction and transmission intensity of each mode refracted at a periodic surface are rigorously analyzed and determined from matrix equations. We further illustrate how to apply our method to design a low-index-contrast 3-D superprism structure that exhibits efficient transmission over a wide angular scanning range at wave- lengths near 1550 nm. Index Terms—Light refraction, superprism, 3-D photonic crys- tals (PCs), transmission.
Session #5: Round Table - Jerome Jourquin, Moderator (2020)

Dr. Jerome Jourquin joined Susan G. Komen® in January of 2011 as a member of the team managing the money provided to breast cancer researchers around the world. In 2015, he started managing the Komen Scholars, a group of breast cancer research and advocacy leaders guiding Komen as advisors. Since 2019, he became Senior Manager, Data Science, a position in which he oversees Komen’s Big Data for Breast Cancer (BD4BC) Initiative that aims at using big data to fuel scientific discoveries and accelerate the delivery of equitable, patient-focused care. Committed to the Nashville community where he is based, Dr. Jourquin sits on Komen Central Tennessee’s More Than Pink Walk® Planning Committee and is the treasurer of the Alliance Française of Nashville. Prior to joining Komen, Dr. Jourquin completed in 2010 a Masters in Bioinformatics at Vanderbilt University, where he developed GLAD4U (http://bioinfo.vanderbilt.edu/glad4u/), a National Library of Medicine-awarded web-service designed tobuild prioritized gene lists based on user queries. With a particular interest in data mining and data sharing, Dr. Jourquin was also part of a multidisciplinary team of experimentalists, mathematicians, engineers, and bioinformaticists studying breast cancer invasion at Vanderbilt. Dr. Jourquin, a French native, earned a Ph.D. in Neurosciences from the University of Aix-Marseilles (2003) and a Master in Cell Biology and Animal Physiology from the University of Paris 7 –Denis Diderot (1997). In addition to authoring a book chapter on laminins and cancer, his research studies have been published in various scientific journals.
Deterministic Nanotexturing by Directional Photofluidization Lithography (2011)

Directional photofluidization lithography enables deterministic large-area nanotexturing of periodic surface reliefs with precisely controlled structural complexity. The proposed nanotexturing technique demonstrates a hidden potential of micro- and nanofabrication methods, which allows for manipulation of the photonic and interface properties of nanotextured surfaces. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Direct Visualization of Glucose Phosphorylation with a Cationic Polythiophene (2008)

ATP-dependent phosphorylation of glucose catalyzed by hexokinase can be detected in real time by a homogeneous visual inspection based on a water-soluble cationic polythiophene derivative (CPT) that responds to the presence of ATP. The color of CPT solutions changes from pink-red in the presence of ATP to yellow when ATP is converted to ADP following the glucose phosphorylation by hexokinase.