gebhart/patrepeval huggingface dataset:
Photogeneration and Reactivity of Naphthoquinone Methides as Purine Selective DNA Alkylating Agents (2010)

A one-step protecting-group-free synthesis of both 6-hydroxy-naphthalene-2-carbaldehyde and the bifunctional binaphthalenyl derivative afforded 6-hydroxymethylnaphthalen-2-ol, 6-methylaminomethyl-naphthalen-2-ol, [(2-hydroxy-3-naphthyl)methyl]trimethyl ammonium iodide, and a small library of bifunctional binol analogues in good yields. Irradiation of naphthol quaternary ammonium salt and binol-derivatives (X = OH, NHR, NMe(3)(+), OCOCH(3), and L-proline) at 310 and 360 nm resulted in the photogeneration of the 2,6-naphthoquinone-6-methide (NQM) and binol quinone methide analogues (BQMs) by a water-mediated excited-state proton transfer (ESPT). The hydration, the mono- and bis-alkylation reactions of morpholine and 2-ethanethiol, as N and S prototype nucleophiles, by the transient NQM (λ(max) 310, 330 nm) and BQMs (λ(max) 360 nm) were investigated in water by product distribution analysis and laser flash photolysis (LFP). Both the photogeneration and the reactivity of NQM and BQMs exhibited striking differences. BQMs were at least 2 orders of magnitude more reactive than NQM, and they were generated much more efficiently from a greater variety of photoprecursors including the hydroxymethyl, quaternary ammonium salt and several binol-amino acids. On the contrary, the only efficient precursor of NQM was the quaternary ammonium salt. All water-soluble BQM precursors were further investigated for their ability to alkylate and cross-link plasmid DNA and oligonucleotides by gel electrophoresis: the BQMs were more efficient than the isomeric o-BQM (binol quinone methide analogue of 2,3-naphthoquinone-3-methide). Sequence analysis by gel electrophoresis, HPLC, and MS showed that the alkylation occurred at purines, with a preference for guanine. In particular, a BQM was able to alkylate N7 of guanines resulting in depurination at the oligonucleotide level, and ribose loss at the nucleotide level. The photoreactivity of BQM precursors translated into photocytotoxic and cytotoxic effects on two human cancer cell lines: in particular, one compound showed promising selectivity index on both cell lines.
Amniotic membrane transplantation for severe neurotrophic corneal ulcers (2000)

Amniotic membrane transplantation can be considered an effective alternative for treating severe neurotrophic corneal ulcers.
An Unusually Fast Nucleophilic Aromatic Displacement Reaction: The Gas‐Phase Reaction of Fluoride Ions with Nitrobenzene (2004)

Quick reactions: The gas-phase nucleophilic displacement reaction of fluoride ions with nitrobenzene proceeds with a rate constant close to the collision limit. The calculated energy profile indicates that the reaction proceeds by an out-of-plane attack, with the Meisenheimer complex being the local transition state for the reaction (see picture).
Human Kidney-Derived Cells Ameliorate Acute Kidney Injury Without Engrafting into Renal Tissue (2017)

Previous studies have suggested that CD133<sup>+</sup> cells isolated from human kidney biopsies have the potential to ameliorate injury following intravenous (IV) administration in rodent models of kidney disease by integrating into damaged renal tissue and generating specialized renal cells. However, whether renal engraftment of CD133<sup>+</sup> cells is a prerequisite for ameliorating injury has not yet been unequivocally resolved. Here, we have established a cisplatin-induced nephropathy model in immunodeficient rats to assess the efficacy of CD133<sup>+</sup> human kidney cells in restoring renal health, and to determine the fate of these cells after systemic administration. Specifically, following IV administration, we evaluated the impact of the CD133<sup>+</sup> cells on renal function by undertaking longitudinal measurements of the glomerular filtration rate using a novel transcutaneous device. Using histological assays, we assessed whether the human kidney cells could promote renal regeneration, and if this was related to their ability to integrate into the damaged kidneys. Our results show that both CD133<sup>+</sup> and CD133<sup>-</sup> cells improve renal function and promote renal regeneration to a similar degree. However, this was not associated with engraftment of the cells into the kidneys. Instead, after IV administration, both cell types were exclusively located in the lungs, and had disappeared by 24 hours. Our data therefore indicate that renal repair is not mediated by CD133<sup>+</sup> cells homing to the kidneys and generating specialized renal cells. Instead, renal repair is likely to be mediated by paracrine or endocrine factors. Stem Cells Translational Medicine 2017;6:1373-1384.
Progressive Growing of GANs for Improved Quality, Stability, and Variation (2017)

We describe a new training methodology for generative adversarial networks. The key idea is to grow both the generator and discriminator progressively: starting from a low resolution, we add new layers that model increasingly fine details as training progresses. This both speeds the training up and greatly stabilizes it, allowing us to produce images of unprecedented quality, e.g., CelebA images at 1024^2. We also propose a simple way to increase the variation in generated images, and achieve a record inception score of 8.80 in unsupervised CIFAR10. Additionally, we describe several implementation details that are important for discouraging unhealthy competition between the generator and discriminator. Finally, we suggest a new metric for evaluating GAN results, both in terms of image quality and variation. As an additional contribution, we construct a higher-quality version of the CelebA dataset.
Exchange of surface proteins impacts on viral vector cellular specificity and transduction characteristics: the retina as a model (2001)

Recombinant vectors based on adeno-associated virus (AAV) or human immunodeficiency 1 (lentivirus) are promising tools for long term in vivo gene delivery. Their design allows the exchange of capsids or envelopes, respectively, theoretically providing the opportunity to transduce a range of cell types. We constructed AAV vectors encoding enhanced green fluorescent protein (EGFP) within an AAV serotype 2 (AAV2) genome contained in an AAV2, five or one capsid (called AAV2/2, AAV2/5 and AAV2/1, respectively). Similarly we produced lentiviral vectors, encoding the same expression cassette present in the AAV vectors, pseudotyped with proteins from vesicular stomatitis virus glycoprotein (VSVG) or Mokola envelopes. Transduction characteristics of these vectors were evaluated in the murine retina following subretinal or intravitreal administration. The time of onset of transgene expression and the targeted cell types differed between the various recombinants. Onset of transgene expression was 3-4 days for lentiviral vectors and AAV2/1. In contrast, onset was at 2-4 weeks for AAV2/5 and AAV2/2, respectively. After subretinal injection, both lenti-VSVG and AAV2/5 transduced the retinal pigment epithelium (RPE) and photoreceptors efficiently whereas transgene expression was restricted to RPE cells using lenti with the Mokola envelope or AAV2/1. After intravitreal administration, only AAV2/2 and lenti-VSVG transduced the inner retina. Vector-mediated fluorescence was detected in the retina for over 12 weeks for all of the vectors. We conclude that pseudotyping provides a useful means to manipulate viral vector cell targeting specificity as well as retinal transduction characteristics of vectors containing the same genome.
Biogenic Amines as Hygienic Quality Indicators of Tuna. Relationships with Microbial Counts, ATP-Related Compounds, Volatile Amines, and Organoleptic Changes (1997)

Changes in 10 biogenic amines throughout tuna storage at 0, 8, and 20 °C were studied. ATP-related compounds, volatile amines, microbial counts, and organoleptic assessment were also monitored. No statistical differences were found for those parameters between samples from different anatomical areas. Similar evolution profiles were observed for biogenic amines at the three temperatures, although the highest amounts were achieved, in general, in samples stored at 20 °C. Histamine was the prevailing biogenic amine throughout storage, and the defect action level of 50 μg/g was surpassed in samples stored at 8 or 20 °C before organoleptic rejection. A great increase in cadaverine and tyramine and a slight increase in putrescine were also observed. Formation of histamine, tyramine, and cadaverine seems to be related to mesophilic flora, Enterobacteriaceae and coliforms. Hygienic quality estimation by means of trimethylamine values and IMP ratio yielded inconsistent results in samples corresponding to the limit of organoleptic acceptance. In accordance with the results of this work, we proposed for tuna assessment the use of an index calculated from the sum of the contents of histamine, tyramine, cadaverine, and putrescine which showed good correlations with both time of storage and organoleptic assessment. Keywords: Biogenic amines; histamine; tuna spoilage; ATP-related compounds; volatile amines
CCAAT Enhancer Binding Protein-α (C/EBPα) Determines Myeloid Versus Erythroid Cell Fate in Multipotential Progenitors. (2004)

Abstract C/EBPα is a bZip transcription factor, which is required for granulocyte development, and loss of C/EBPα function is associated with the development of acute myelogenous leukemia and myelodysplastic syndrome. While the precise mechanisms that regulate cell fate decisions during hematopoietic development are largely unknown, expression of transcription factors (PU.1 and GATA-1) can induce lineage conversion. In this regard, C/EBPα can drive the differentiation of B cells into macrophages, and bi-potential cell lines into granulocytes at the expense of macrophages. C/EBPα can also promote the transdifferentiation of myoblasts into adipocytes. We have recently found that there are increased numbers of erythroid cells in the fetal liver of C/EBPα −/ − mice. Also, C/EBPα is expressed in more primitive progenitor cells than granulocyte/macrophage progenitors (GMP) including hematopoietic stem cells. Therefore, we initiated experiments to evaluate whether C/EBPα has a functional role in regulating cell fate decisions in progenitors more primitive than GMP where it may promote a myeloid versus erythroid cell fate decision. To test this hypothesis, we over-expressed C/EBPα using retroviral vectors in 1) bone marrow cells (BMC) and evaluated their growth and differentiation in vitro, and in vivo when transplanted into mice; 2) purified multipotential progenitors with erythroid and myeloid potential, and erythroid restricted progenitors; and 3) murine erythroid leukemia (MEL) cells. We found that there was a marked decrease in erythroid lineage cells and an increase in myeloid cells in mice transplanted with BMC that over-expressed C/EBPα. We also observed a decrease in erythroid cell growth in vitro with BMC that expressed C/EBPα. Furthermore, when infected with retroviral vectors that express C/EBPα, erythroid restricted progenitors acquired myeloid cell morphology and myeloid specific cell surface markers. In addition, MEL cells that over-express C/EBPα showed increased myeloid gene expression including GM-CSFR, PR3 and myeloid specific esterase, while they showed decreased expression of β-globin and Epo receptor (EpoR) which is required for erythroid cell differentiation and survival. We detected high levels of EpoR in C/EBPα −/ − suggesting an inverse relationship between C/EBPα and EpoR expression. Thus, C/EBPα is a dual function transcription factor that can repress erythroid specific genes while enhancing myeloid lineage gene expression. Consequently, C/EBPα acts as a switch to drive hematopoietic progenitor cells toward myeloid cell development at the expense of erythroid maturation, and can reprogram erythroid cells into myeloid cells. # Funded in part by DHHS #NO1-CO-12400
Capture of human monoclonal antibodies from cell culture supernatant by ion exchange media exhibiting high charge density (1998)

A shortcut purification sequence for therapeutic proteins should consist of three steps: capture, purification, and polishing. Special emphasis has been put on direct capture of human monoclonal antibodies from culture supernatants with ion-exchangers avoiding pretreatment steps such as desalting, dilution, and other means to reduce the ionic strength. CM-HyperD, a cation-exchanger composed of an inorganic macroporous support filled with a viscoelastic gel with a high charge density was used. Capture of monoclonal antibodies from clarified hybridoma cell culture grown in media supplemented with fetal calf serum was investigated. Screening of different pH conditions and buffers for the load step showed that monoclonal antibodies were efficiently bound by CM-HyperD at pH 4.0 and 5.0 at an ionic strength equivalent to culture supernatant. Combination of negative purification with Q-Sepharose FF and capturing with CM-HyperD gave sufficient yield and resolution. Implementation of wash steps with higher conductivity did not improve the purity, but decreased the yield. Interestingly, high flow rates improved the purity. When antibodies were captured from serumfree culture supernatant the antibody could be eluted in a single peak with substantial reduction of contaminants. Capturing of antibodies by ion-exchange sorbents from culture supernatant is possible despite the high salt content.
Enhanced Downlink MU-CoMP Schemes for TD-LTE-Advanced (2010)

As one of the key technologies in TD-LTE-Advanced downlink system, MIMO-OFDMA (Multi-Input and Multi-Output Orthogonal Frequency Division Multiplexing Access) achieves high system throughput by using multiple antennas at both the transmitter and receiver while eliminating intra-cell interference by utilizing closely-spaced orthogonal sub-carriers. Nonetheless, the inter-cell interference among several UEs remains unsolved. Therefore CoMP(Coordinated Muti-Point transmission/reception) is introduced to solve this problem. This paper studies different MU(Multi User) CoMP schemes based on two different coordinated topologies and transparent/non-transparent MU(Multi User)-MIMO. The simulation results shows the CoMP schemes achieve different gains in average sector throughput and 5% edge-user throughput as compared to the performance of conventional pre-coding scheme.
Human receptor kinetics and lung tissue retention of the enhanced-affinity glucocorticoid fluticasone furoate (2007)

Fluticasone furoate (FF)--USAN approved name, a new topically active glucocorticoid has been recently identified. The aim of this study was to characterise the binding affinity of this compound to the human lung glucocorticoid receptor in relation to other glucocorticoids. Additionally, we sought to determine the binding behaviour of fluticasone furoate to human lung tissue. The glucocorticoid receptor binding kinetics of fluticasone furoate revealed a remarkably fast association and a slow dissociation resulting in a relative receptor affinity (RRA) of 2989 +/- 135 with reference to dexamethasone (RRA: 100 +/- 5). Thus, the RRA of FF exceeds the RRAs of all currently clinically used corticosteroids such as mometasone furoate (MF; RRA 2244), fluticasone propionate (FP; RRA 1775), ciclesonide's active metabolite (RRA 1212 - rat receptor data) or budesonide (RRA 855). FP and FF displayed pronounced retention in human lung tissue in vitro. Lowest tissue binding was found for MF. There was no indication of instability or chemical modification of FF in human lung tissue. These advantageous binding attributes may contribute to a highly efficacious profile for FF as a topical treatment for inflammatory disorders of the respiratory tract.
Clinical utility and patient perspectives on the use of extended half-life rFIXFc in the management of hemophilia B (2014)

Hemophilia B is an X-linked genetic disease caused by mutation of the gene for coagulation protein factor IX (FIX), with an incidence of approximately once every 30,000 male births in all populations and ethnic groups. When severe, the disease leads to spontaneous life threatening bleeding episodes. When untreated, most patients die from bleeding complications before 25 years of age. Current therapy requires frequent intravenous infusions of therapeutic recombinant or plasma-derived protein concentrates containing FIX. Most patients administer the infusions at home every few days, and must limit their physical activities to avoid abnormal bleeding when the FIX activity levels are below normal. After completing the pivotal Phase III clinical trial, a new therapeutic FIX preparation that has been engineered for an extended half-life in circulation, received regulatory approval in March 2014 in Canada and the US. This new FIX represents a major therapeutic advance for patients with hemophilia B. The half-life is prolonged due to fusion of the native FIX molecule with the normal constant region of immunoglobulin G. This fusion molecule then follows the normal immunoglobulin recirculation pathways through endothelial cells, resulting in prolonged times in circulation. In the clinical trials, over 150 patients successfully used eftrenonacog alfa regularly for more than 1 year to prevent spontaneous bleeding, to successfully treat any bleeding episodes, and to provide effective coagulation for major surgery. All infusions were well tolerated and effective, with no inhibitors detected and no safety concerns. This promising therapy should allow patients to use fewer infusions to maintain appropriate FIX activity levels in all clinical settings.
Computer‐aided diagnosis scheme for histological classification of clustered microcalcifications on magnification mammograms (2004)

The histological classification of clustered microcalcifications on mammograms can be difficult, and thus often require biopsy or follow-up. Our purpose in this study was to develop a computer-aided diagnosis scheme for identifying the histological classification of clustered microcalcifications on magnification mammograms in order to assist the radiologists' interpretation as a "second opinion." Our database consisted of 58 magnification mammograms, which included 35 malignant clustered microcalcifications (9 invasive carcinomas, 12 noninvasive carcinomas of the comedo type, and 14 noninvasive carcinomas of the noncomedo type) and 23 benign clustered microcalcifications (17 mastopathies and 6 fibroadenomas). The histological classifications of all clustered microcalcifications were proved by pathologic diagnosis. The clustered microcalcifications were first segmented by use of a novel filter bank and a thresholding technique. Five objective features on clustered microcalcifications were determined by taking into account subjective features that experienced the radiologists commonly use to identify possible histological classifications. The Bayes decision rule with five objective features was employed for distinguishing between five histological classifications. The classification accuracies for distinguishing between three malignant histological classifications were 77.8% (7/9) for invasive carcinoma, 75.0% (9/12) for noninvasive carcinoma of the comedo type, and 92.9% (13/14) for noninvasive carcinoma of the noncomedo type. The classification accuracies for distinguishing between two benign histological classifications were 94.1% (16/17) for mastopathy, and 100.0% (6/6) for fibroadenoma. This computerized method would be useful in assisting radiologists in their assessments of clustered microcalcifications.
Synthesis of hydrogen permselective silicon dioxide, titanium dioxide, aluminum oxide, and boron oxide membranes from the chloride precursors (1991)

Hydrogen-permselective membranes were synthesized by chemical vapor deposition of SiO_2, TiO_2, Al_2O_3, and B_2O_3 layers within the pores of Vycor tubes. The deposition involved reaction of SiCl_4, etc., with water at 100-800 °C depending on the chloride and the reaction geometry. Permselective SiO_2 layers could be formed in either the one-sided or the two-sided (opposing reactants) geometry, while deposition of TiO_2 and Al_2O_3 layers was achieved only in the two-sided geometry. The permeation coefficients at 450 °C were 0.3 and 0.1 cm^3/(cm^2•min•atm) for SiO_2 membranes produced in the one-sided and two-sided geometries, respectively. The H_2:N_2 permeation ratios were 1000-5000. The TiO_2 and Al_2O_3 membranes had somewhat lower permeation coefficients and H_2:N_2 ratios. The membranes were characterized by scanning electron microscopy (SEM) and electron microprobe analysis (EMA). A reaction mechanism is suggested involving heterogeneous reactions of chloride and water molecules with hydroxyl and chloride groups in the growing deposit layer.
Cluster Composition Distributions of Pure Ethanol: Influence of Water and Ion–Molecule Reactions Revealed by Liquid-Ionization Tandem Mass Spectrometry (2013)

Studies of clusters in condensed phase at atmospheric pressure are very important for understanding the properties and structures of liquids. Liquid-ionization (LPI) mass spectrometry is useful to study hydrogen-bonded clusters at the liquid surface and in a gas phase. An improved ion source connected to a tandem mass spectrometer provides detailed information about clusters. Mass spectra of pure ethanol (99.5%) observed by the first mass analyzer (Q1) showed neat ethanol cluster ions (C2H5OH) m H(+) with m up to 10 and hydrate ions (C2H5OH) m (H2O) n H(+) with m larger than 7 and n=1, such as those with m-n=8-1 and 9-1. When the flow rate of ethanol (liquid) was increased, large ethanol cluster ions with m larger than 25 were observed by the second mass analyzer (Q3). It is interesting to note that neat ethanol cluster ions are more abundant than corresponding (with the same m) hydrate ions (n=1), and major hydrate ions contain only one molecule of water. Results indicate that ion-molecule reactions occur between Q1 and Q3, because such mass spectra have never been observed by Q1. Various results indicate that neat ethanol clusters exist at the liquid surface and are ionized to give cluster ions.
Database machines: have they a future? (1987)

Abstract The concept of a Database Machine had its origins in the early research on associative storage systems carried out in the 1960s. In particular, it was realised that, since data was being continuously scanned in any fixed head drum or disk device, it should be possible to make a form of associative memory by incorporating appropriate matching logic in the data channels. Many studies were carried out by research groups in Europe and North America but, although the concept appeared promising, the prevailing electronic technology of the period made the building of such a machine impractical at the time.
710: A Novel Cell Source for Urologic Tissue Reconstruction (2007)

You have accessJournal of UrologyPodium 23, Monday, May 21, 2007, 8:00 - 10:00 am1 Apr 2007710: A Novel Cell Source for Urologic Tissue Reconstruction Yuan Yuan Zhang, Elena McNeill, Shay Saker, James J. Yoo, and Anthony Atala Yuan Yuan ZhangYuan Yuan Zhang More articles by this author , Elena McNeillElena McNeill More articles by this author , Shay SakerShay Saker More articles by this author , James J. YooJames J. Yoo More articles by this author , and Anthony AtalaAnthony Atala More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)30950-9AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "710: A Novel Cell Source for Urologic Tissue Reconstruction." The Journal of Urology, 177(4S), p. 238 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 177Issue 4SApril 2007Page: 238 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Yuan Yuan Zhang More articles by this author Elena McNeill More articles by this author Shay Saker More articles by this author James J. Yoo More articles by this author Anthony Atala More articles by this author Expand All Advertisement PDF downloadLoading ...