gebhart/patrepeval huggingface dataset:
Emission Polarization of Europium and Terbium Chelates (2003)

We measured the anisotropy of Tb3+ and Eu3+ in various chelate complexes bound with or without a carbostyril antenna. The anisotropy of the lanthanides depends on the chelate as well as whether the antenna is present. The anisotropy of Eu3+ bound to only a chelate is high while for Tb3+ the anisotropy is nearly zero. For Eu3+, the anisotropy decreases upon addition of the antenna, while for Tb3+ the anisotropy slightly increases once the antenna is attached. A theoretical model is discussed to account for the measured anisotropy of the Eu3+ bound to the chelate and how the addition of the antenna affects the anisotropy. While the transitions within Tb3+ are more complicated than those in Eu3+, the theoretical model is also extended to Tb3+ to explain qualitatively how the addition of the antenna affects the measured anisotropy of the terbium complex. Because of their low anisotropy, both Tb3+ and Eu3+, when bound to a chelate with an antenna, are ideal luminescent probes in resonance energy transfer experiments for measuring nanometer scale distances. Our results indicate that it may be possible to construct a probe with Eu3+ that retains its high anisotropy once the antenna is added to the chelate complex. This probe could measure rotational motion on the millisecond lifetime.
The 2′-5′ RNA Ligase of Escherichia coli (1996)

An RNA ligase previously detected in extracts of Escherichia coli is capable of joining Saccharomyces cerevisiae tRNA splicing intermediates in the absence of ATP to form a 2'-5' phosphodiester linkage (Greer, C., Javor, B., and Abelson, J. (1983) Cell 33, 899-906). This enzyme specifically ligates tRNA half-molecules containing nucleoside base modifications and shows a preference among different tRNA species. In order to investigate the function of this enzyme in RNA metabolism, the ligase was purified to homogeneity from E. coli lysate utilizing chromatographic techniques and separation of proteins by SDS-polyacrylamide gel electrophoresis. A single polypeptide of approximately 20 kilodaltons exhibited RNA ligase activity. The amino terminus of this protein was sequenced, and the open reading frame (ORF) encoding it was identified by a data base search. This ORF, which encodes a novel protein with a predicted molecular mass of 19.9 kDa, was amplified from E. coli genomic DNA and cloned. ORFs coding for highly similar proteins were detected in Methanococcus jannaschii and Bacillus stearothermophilus. The chromosomal gene encoding RNA ligase in E. coli was disrupted, abolishing ligase activity in cell lysates. Cells lacking ligase activity grew normally under laboratory conditions. However, moderate overexpression of the ligase protein led to slower growth rates and a temperature-sensitive phenotype in both wild-type and RNA ligase knockout strains. The RNA ligase reaction was studied in vitro using purified enzyme and was found to be reversible, indicating that this enzyme may perform cleavage or ligation in vivo.
“Living” free radical polymerization of macromonomers: Preparation of well defined graft copolymers (1997)

Abstract Well defined graft copolymers have been synthesized by a nitroxide‐mediated “living” free radical process using pre‐formed macromonomers. Analysis of the graft systems revealed that the macromonomer was efficiently incorporated into the polymeric backbone to give block copolymers of controlled molecular weight and narrow polydispersities. An added benefit of the “living” free radical process is that macromonomers, such as polylactide or polycaprolactone, which contain reactive functional groups can be used to form novel graft systems using this approach. Functionalized monomers or polymeric initiators were also used in the copolymerization mixture to give graft systems with a variety of functional groups attached to the backbone.
Biochemical role of the collagen-rich tumour microenvironment in pancreatic cancer progression (2011)

PDAC (pancreatic ductal adenocarcinoma) is among the most deadly of human malignances. A hallmark of the disease is a pronounced collagen-rich fibrotic extracellular matrix known as the desmoplastic reaction. Intriguingly, it is precisely these areas of fibrosis in which human PDAC tumours demonstrate increased expression of a key collagenase, MT1-MMP [membrane-type 1 MMP (matrix metalloproteinase); also known as MMP-14]. Furthermore, a cytokine known to mediate fibrosis in vivo, TGF-β1 (transforming growth factor-β1), is up-regulated in human PDAC tumours and can promote MT1-MMP expression. In the present review, we examine the regulation of PDAC progression through the interplay between type I collagen (the most common extracellular matrix present in human PDAC tumours), MT1-MMP and TGF-β1. Specifically, we examine the way in which signalling events through these pathways mediates invasion, regulates microRNAs and contributes to chemoresistance.
Rare Homologous Gene Targeting in Histoplasma capsulatum : Disruption of the URA5 Hc Gene by Allelic Replacement (1998)

URA5 genes encode orotidine-5'-monophosphate pyrophosphorylase (OMPpase), an enzyme involved in pyrimidine biosynthesis. We cloned the Histoplasma capsulatum URA5 gene (URA5Hc) by using a probe generated by PCR with inosine-rich primers based on relatively conserved sequences in OMPpases from other organisms. Transformation with this gene restored uracil prototrophy and OMPpase activity to UV-mutagenized ura5 strains of H. capsulatum. We attempted to target the genomic URA5 locus in this haploid organism to demonstrate homologous allelic replacement with transforming DNA, which has not been previously done in H. capsulatum and has been challenging in some other pathogenic fungi. Several strategies commonly used in Saccharomyces cerevisiae and other eukaryotes were unsuccessful, due to the frequent occurrence of ectopic integration, linear plasmid formation, and spontaneous resistance to 5-fluoroorotic acid, which is a selective agent for URA5 gene inactivation. Recent development of an efficient electrotransformation system and of a second selectable marker (hph, conferring hygromycin B resistance) for this fungus enabled us to achieve allelic replacement by using transformation with an insertionally inactivated Deltaura5Hc::hph plasmid, followed by dual selection with hygromycin B and 5-fluoroorotic acid, or by screening hygromycin B-resistant transformants for uracil auxotrophy. The relative frequency of homologous gene targeting was approximately one allelic replacement event per thousand transformants. This work demonstrates the feasibility but also the potential challenge of gene disruption in this organism. To our knowledge, it represents the first example of experimentally directed allelic replacement in H. capsulatum, or in any dimorphic systemic fungal pathogen of humans.
Effect of organic solvents on enzymatic production of cyclodextrins from unliquefied corn starch in an attrition bioreactor (1992)

Cyclodextrins were produced from unliquified corn starch in the presence of water-miscible organic solvents using cyclodextrin glycosyltransferase (CGTase) in an attrition bioreactor. The production yield was significantly increased by isopropanol and tertiary butanol, and maximum enhancement was observed to be about 40% by 5% tertiary butanol. Increase in the production of cyclodextrins by organic solvents seems to be due to the fact that organic solvents decreased the product inhibition of CGTase by forming an inclusion complex with cyclodextrins.
MicroUnity's MediaProcessor architecture (1996)

This media processor extends general-purpose computer systems for communicating and processing digital video, audio, data, and radio frequency signals at broadband rates.
Baff Mediates Survival of Peripheral Immature B Lymphocytes (2000)

B cell maturation is a very selective process that requires finely tuned differentiation and survival signals. B cell activation factor from the TNF family (BAFF) is a TNF family member that binds to B cells and potentiates B cell receptor (BCR)-mediated proliferation. A role for BAFF in B cell survival was suggested by the observation of reduced peripheral B cell numbers in mice treated with reagents blocking BAFF, and high Bcl-2 levels detected in B cells from BAFF transgenic (Tg) mice. We tested in vitro the survival effect of BAFF on lymphocytes derived from primary and secondary lymphoid organs. BAFF induced survival of a subset of splenic immature B cells, referred to as transitional type 2 (T2) B cells. BAFF treatment allowed T2 B cells to survive and differentiate into mature B cells in response to signals through the BCR. The T2 and the marginal zone (MZ) B cell compartments were particularly enlarged in BAFF Tg mice. Immature transitional B cells are targets for negative selection, a feature thought to promote self-tolerance. These findings support a model in which excessive BAFF-mediated survival of peripheral immature B cells contributes to the emergence and maturation of autoreactive B cells, skewed towards the MZ compartment. This work provides new clues on mechanisms regulating B cell maturation and tolerance.
Polymer self assembly in semiconductor microelectronics (2007)

We are inspired by the beauty and simplicity of self-organizing materials and the promise they hold for enabling continued improvements in semiconductor technology. Self assembly is the spontaneous arrangement of individual elements into regular patterns; under suitable conditions, certain materials self organize into useful nanometer-scale patterns of importance to high-performance microelectronics applications. Polymer self assembly is a nontraditional approach to patterning integrated circuit elements at dimensions and densities inaccessible to traditional lithography methods. We review here our efforts in IBM to develop and integrate self-assembly processes as high-resolution patterning alternatives and to demonstrate targeted applications in semiconductor device fabrication. We also provide a framework for understanding key requirements for the adoption of polymer self-assembly processes into semiconductor technology, as well as a discussion of the ultimate dimensional scalability of the technique.
Determination of Allele Frequency in Pooled DNA: Comparison of Three PCR-Based Methods (2005)

Determination of allele frequency in pooled DNA samples is a powerful and efficient tool for large-scale association studies. In this study, we tested and compared three PCR-based methods for accuracy, reproducibility, cost, and convenience. The methods compared were: (i) real-time PCR with allele-specific primers, (ii) real-time PCR with allele-specific TaqMan probes, and (iii) quantitative sequencing. Allele frequencies of three single nucleotide polymorphisms in three different genes were estimated from pooled DNA. The pools were made of genomic DNA samples from 96 cases with basal cell carcinoma of the skin and 96 healthy controls with known genotypes. In this study, the allele frequency estimation made by real-time PCR with allele-specific primers had the smallest median deviation (MD) from the real allele frequency with 1.12% (absolute percentage points) and was also the cheapest method. However; this method required the most time for optimization and showed the highest variation between replicates (SD = 6.47%). Quantitative sequencing, the simplest method, was found to have intermediate accuracies (MD = 1.44%, SD = 4.2%). Real-time PCR with TaqMan probes, a convenient but very expensive method, had an MD of 1.47% and the lowest variation between replicates (SD = 3.18%).
CuBICA: Independent Component Analysis by Simultaneous Third- and Fourth-Order Cumulant Diagonalization (2004)

CuBICA, which is an improved method for independent component analysis (ICA) based on the diagonalization of cumulant tensors is proposed. It is based on Comon's algorithm, but it takes third- and fourth-order cumulant tensors into account simultaneously. The underlying contrast function is also mathematically much simpler and has a more intuitive interpretation. It is therefore easier to optimize and approximate. A comparison with Comon's and three other ICA algorithms on different data sets demonstrates its performance.
Controlling Mechanical and Swelling Properties of Alginate Hydrogels Independently by Cross-Linker Type and Cross-Linking Density (2000)

ADVERTISEMENT RETURN TO ISSUEPREVNoteControlling Mechanical and Swelling Properties of Alginate Hydrogels Independently by Cross-Linker Type and Cross-Linking DensityKuen Yong Lee, Jon A. Rowley, Petra Eiselt, Erick M. Moy, Kamal H. Bouhadir, and David J. MooneyView Author Information Department of Biomedical Engineering, Chemical Engineering, Biologic & Materials Sciences, and Materials Science & Engineering, University of Michigan, Ann Arbor, Michigan 48109 Cite this: Macromolecules 2000, 33, 11, 4291–4294Publication Date (Web):April 22, 2000Publication History Received21 December 1999Revised23 March 2000Published online22 April 2000Published inissue 1 May 2000https://pubs.acs.org/doi/10.1021/ma9921347https://doi.org/10.1021/ma9921347brief-reportACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views11479Altmetric-Citations404LEARN 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 SUBJECTS:Absorption,Biopolymers,Hydrogels,Molecules,Nucleic acid structure Get e-Alerts
Urokinase-Type Plasminogen Activator and Its Inhibitor PAI-1: Predictors of Poor Response to Tamoxifen Therapy in Recurrent Breast Cancer (1995)

Measurement of primary breast tumor uPA levels may be useful in predicting the overall response of metastatic disease to tamoxifen therapy.
Polycystic Ovarian Syndrome: Evidence that Flutamide Restores Sensitivity of the Gonadotropin-Releasing Hormone Pulse Generator to Inhibition by Estradiol and Progesterone1 (2000)

Polycystic ovarian syndrome (PCOS) is a complex disorder with multiple abnormalities, including hyperandrogenism, ovulatory dysfunction, and altered gonadotropin secretion. The majority of patients have elevated LH levels in plasma and a persistent rapid frequency of LH (GnRH) pulse secretion, the mechanisms of which are unclear. Earlier work has suggested that the sensitivity of the GnRH pulse generator to inhibition by ovarian steroids is impaired. We performed a study to determine whether antiandrogen therapy with flutamide could enhance feedback inhibition by estradiol (E2) and progesterone (P) in women with PCOS. Ten anovulatory women with PCOS and nine normal controls (days 8-10 of the cycle) were studied on three occasions. During each admission, LH and FSH were determined every 10 min and E2, P, and testosterone (T) every 2 h for 13 h. After 12 h, GnRH (25 ng/kg) was given iv. After the first admission, patients were started on flutamide (250 mg twice daily), which was continued for the entire study. The second admission occurred on days 8-10 of the next menstrual cycle for normal controls and on study day 28 for PCOS patients. Subjects were then given E2 transdermally (mean plasma E2, 106+/-18 pg/mL) and P by vaginal suppository to obtain varied plasma concentrations of P (mean P, 4.4+/-0.5 ng/mL; range, 0.6-9.0 ng/mL), and a third study was performed 7 days later. At baseline women with PCOS had higher LH pulse amplitude, response to GnRH, T, androstenedione, and insulin and lower sex hormone-binding globulin concentrations (P < 0.05). Most hormonal parameters were not altered by 4 weeks of flutamide, except T in controls and E2 and FSH in PCOS patients, which were lower. Of note, flutamide alone had no effect on LH pulse frequency or amplitude, mean plasma LH, or LH responsiveness to exogenous GnRH. After the addition of E2 and P for 7 days, both PCOS patients and normal controls had similar reductions in LH pulse frequency (4.0+/-0.7 and 5.8+/-0.7 pulses/12 h, respectively). This contrasts with our earlier results in the absence of flutamide, where a plasma P level of less than 10 ng/mL had minimal effects on LH pulse frequency in women with PCOS, but was effective in controls. These results suggest that although the elevated LH pulse frequency in PCOS may in part reflect impaired sensitivity to E2 and P, continuing actions of hyperandrogenemia are important for sustaining the abnormal hypothalamic sensitivity to feedback inhibition by ovarian steroids.
Stable Cu2O nanocrystals grown on functionalized graphene sheets and room temperature H2S gas sensing with ultrahigh sensitivity (2012)

Stable Cu(2)O nanocrystals of around 3 nm were uniformly and densely grown on functionalized graphene sheets (FGS), which act as molecular templates instead of surfactants for controlled nucleation; the distribution density of nanocrystals can be easily controlled by FGS with different C/O ratios. The nanocomposite displays improved stability of the crystalline phase in wet air, which is attributed to finite-size effects that the high-symmetry crystalline phase is to be more stable at smaller size. Meanwhile, we conjecture that the oxygen adsorbed on the interfacial surface prefers to extract electrons from FGS, thus the interfacial bonding also makes a contribution in alleviating the process of corrosion to some extent. More importantly, the Cu(2)O-FGS nanocomposite based sensor realizes room temperature sensing to H(2)S with fantastic sensitivity (11%); even at the exposed concentration of 5 ppb, the relative resistance changes show good linearity with the logarithm of the concentration. The enhancement of sensitivity is attributed to the synergistic effect of Cu(2)O and FGS; on the one hand, surfactant-free capped Cu(2)O nanocrystals display higher surface activity to adsorb gas molecules, and on the other hand, FGS acting as conducting network presents greater electron transfer efficiency. These observations show that the Cu(2)O-FGS nanocomposite based sensors have potential applications for monitoring air pollution at room temperature with low cost and power consumption.
Homophilic Interactions between Cadherin Fragments at the Single Molecule Level: An AFM Study (2006)

We report measurements of the adhesion forces between single E-cadherin fragments anchored on solid surfaces. These fragments consist of the two outermost extracellular domains of the protein. The specificity of the measured rupture forces was demonstrated by Ca2+ exchange experiments. Two series of experiments were performed using two linkers of different rigidity and length. We find that the pull-off force is distributed with a maximum value independent of the linker and logarithmically dependent on the velocity of separation of the two surfaces. Our dynamical results are compatible with previous flow chamber experiments performed with the same fragments and can be compared from a different perspective with previously reported AFM experiments on the full-length extracellular domain of the VE-cadherin. Interestingly, using a rigid linker, we have been able for the first time to evidence the deformation of the cadherin molecule under mechanical stress, a piece of information not accessible with more classical grafting strategies.
Evaluation of K18-hACE2 Mice as a Model of SARS-CoV-2 Infection (2020)

Murine models of SARS-CoV-2 infection are critical for elucidating the biological pathways underlying COVID-19. Because human angiotensin-converting enzyme 2 (ACE2) is the receptor for SARS-CoV-2, mice expressing the human <i>ACE2</i> gene have shown promise as a potential model for COVID-19. Five mice from the transgenic mouse strain K18-<i>hACE2</i> were intranasally inoculated with SARS-CoV-2 Hong Kong/VM20001061/2020. Mice were followed twice daily for 5 days and scored for weight loss and clinical symptoms. Infected mice did not exhibit any signs of infection until day 4, when no other obvious clinical symptoms other than weight loss were observed. By day 5, all infected mice had lost around 10% of their original body weight but exhibited variable clinical symptoms. All infected mice showed high viral titers in the lungs as well as altered lung histology associated with proteinaceous debris in the alveolar space, interstitial inflammatory cell infiltration, and alveolar septal thickening. Overall, these results show that the K18-<i>hACE2</i> transgenic background can be used to establish symptomatic SARS-CoV-2 infection and can be a useful mouse model for COVID-19.
Fibrosis, a common pathway to organ failure: angiotensin II and tissue repair. (1997)

For heart, kidneys, lungs and liver alike, fibrosis represents a common pathway to their failure. Understanding pathophysiologic mechanisms involved in organ fibrosis are therefore of considerable interest, particularly given the potential for protective pharmacological strategies. Tissue repair involves inflammatory cells, including members of the monocyte/macrophage lineage, integral to initiating the repair process; and myofibroblasts, phenotypically transformed interstitial fibroblasts, responsible for collagen turnover and fibrous tissue formation. Each of these cellular events in the microenvironment of repair are associated with molecular events that lead to the de novo generation of angiotensin II (ANG II). In an autocrine/paracrine manner, this peptide regulates expression of TGF-beta 1 via angiotensin (AT1) receptor-ligand binding. It is this cytokine that contributes to phenotypic conversion of fibroblasts to myofibroblasts (myoFb) and regulates myofibroblast turnover of collagen. Angiotensin-converting enzyme (ACE) inhibition or AT1 receptor antagonism each prevent many of these molecular and cellular responses that eventuate in fibrosis and therefore have been found to be protective interventions.