gebhart/patrepeval huggingface dataset:
Optimization of Measurement Parameters and Performance Comparison for Analyst™ GT and Analyst HT or Acquest (2003)

The new Analyst™ GT is a multi-mode plate reader supporting all five leading technologies: fluorescence polarization (FP), fluorescence intensity, time-resolved fluorescence (TRF), absorbance and luminescence. It can be easily integrated into both workstation and robotic environments for HTS for all major non-radiometric applications. Analyst™ GT is based on second-generation SmartOptics™, a patented system that combines light sources, optical components and detectors together for fast high-precision measurements in 96-, 384-, and 1536-well microplates. Applications include kinase and photophase assays, receptor ligand binding assays, protease assays, cAMP, and cGMP, signal transduction, reporter gene assays and many others. In this study, we not only optimized measurement parameters on Analyst™ GT for all five modalities but also compared instrument settings and performance with the first generation Analyst HT and Acquest.
Poly(β-amino ester) Nanoparticle Delivery of TP53 Has Activity against Small Cell Lung Cancer In Vitro and In Vivo (2013)

Small cell lung cancer (SCLC) is an aggressive disease with one of the highest case-fatality rates among cancer. The recommended therapy for SCLCs has not changed significantly over the past 30 years; new therapeutic approaches are a critical need. TP53 is mutated in the majority of SCLC cases and its loss is required in transgenic mouse models of the disease. We synthesized an array of biodegradable poly(β-amino ester) (PBAE) polymers that self-assemble with DNA and assayed for transfection efficiency in the p53-mutant H446 SCLC cell line using high-throughput methodologies. Two of the top candidates were selected for further characterization and TP53 delivery in vitro and in vivo. Nanoparticle delivery of TP53 resulted in expression of exogenous p53, induction of p21, induction of apoptosis, and accumulation of cells in sub-G1 consistent with functional p53 activity. Intratumoral injection of subcutaneous H446 xenografts with polymers carrying TP53 caused marked tumor growth inhibition. This is the first demonstration of TP53 gene therapy in SCLC using nonviral polymeric nanoparticles. This technology may have general applicability as a novel anticancer strategy based on restoration of tumor suppressor gene function.
The Marinopyrroles, Antibiotics of an Unprecedented Structure Class from a Marine Streptomyces sp. (2008)

Cultivation of an obligate marine Streptomyces strain has furnished the marinopyrroles A and B, densely halogenated, axially chiral metabolites that contain an uncommon bispyrrole structure. X-ray analysis of marinopyrrole B showed that the natural product exists as an atropo-enantiomer with the M-configuration. Though configurationally stable at room temperature, M-(-)-marinopyrrole A can be racemized at elevated temperatures to yield the non-natural P-(+)-atropo-enantiomer. The marinopyrroles possess potent antibiotic activities against methicillin-resistant Staphylococcus aureus.
The Persistent Radical Effect In “Living” Radical Polymerization (1997)

A kinetic analysis is presented of “living” polymerizations initiated and controlled by reactions involving persistent radicals. It is shown how a simple self-regulation operates which is known as the persistent radical effect in other areas of radical chemistry. Predictive analytical formulas are derived for the time dependent concentrations of the radical intermediates and the dormant and the final polymer products. They are supported by numerical simulations and agree with experimental findings. In particular, we consider the initiation by homolysis of a stoichiometric initiator into a transient and a persistent radical in the absence and in the presence of self-initiation and the use of conventional initiators together with a persistent species.
Selective Rep-Cap Gene Amplification as a Mechanism for High-Titer Recombinant AAV Production from Stable Cell Lines (2000)

Gene transfer vectors based on adeno-associated virus mediate high-level, stable gene expression in a variety of postmitotic tissues; thus, there is interest in developing improved production systems. We previously described the generation of rAAV producer cell lines that, upon infection with adenovirus, yielded biologically active rAAV particles. In these studies we show that the adenovirus multiplicity of infection (m.o.i.) is a critical variable for efficient production of cell line-derived rAAV and can affect yields by over 200-fold. Moreover, a threshold level of adenovirus was found necessary for high-titer vector production. To define the possible factors responsible for adenovirus m.o.i. -dependent rAAV yields, we analyzed rep and cap expression as a function of adenovirus m.o.i. High-level AAV capsid protein synthesis was observed in rAAV producer cells at adenovirus m.o.i. > or =10. This prompted us to analyze the rep-cap copy number following adenovirus infection. We documented robust episomal DNA amplification (100-fold) of integrated rep-cap sequences. Interestingly, no amplification of rep-cap sequences was observed when the sequences (in plasmid form) were transfected into adenovirus-infected HeLa cells. These data suggest that adenovirus-dependent rep-cap gene amplification is a critical process responsible for efficient rAAV synthesis in stable cell lines.
Single-shot chirped-pulse spectral interferometry used to measure the femtosecond ionization dynamics of air (2000)

A novel interferometry technique is presented by which, in one shot, one can measure phase changes with a resolution of tens of femtoseconds while extending the measurement over picoseconds or even longer. The method is based on spectral (frequency-domain) interferometry with a pair of linearly chirped pules as probes. With this technique we obtained single-shot measurements of the rapid phase changes induced by optical field ionization of air. This allowed us to calculate the time profile of the electron density created by an intense short laser pulse.
Thromboangiitis Obliterans (Buerger's Disease) (2000)

Thromboangiitis obliterans (Buerger's disease) is a nonatherosclerotic segmental inflammatory disease that most commonly affects the small and medium-sized arteries, veins, and nerves of the arms and legs.1 Von Winiwarter first described a patient with thromboangiitis obliterans in 1879.2 Twenty-nine years later, Leo Buerger provided a detailed and accurate description of the pathological findings in 11 amputated limbs.3 Thromboangiitis obliterans differs from other forms of vasculitis in some important ways. Pathologically, there is a highly cellular and inflammatory thrombus with relative sparing of the blood-vessel wall. The acute-phase reactants (as assessed by the Westergren sedimentation rate and serum C-reactive protein level) . . .
Bacterial contamination of stethoscopes on the intensive care unit (2009)

We assessed how often bedside stethoscopes in our intensive care unit were cleaned and whether they became colonised with potentially pathogenic bacteria. On two separate days the 12 nurses attending the bedspaces were questioned about frequency of stethoscope cleaning on the unit and the bedside stethoscopes were swabbed before and after cleaning to identify colonising organisms. Twenty-two health care providers entering the unit were asked the same questions and had their personal stethoscopes swabbed. All 32 non-medical staff cleaned their stethoscopes at least every day; however only three out of the 12 medical staff cleaned this often. Out of 24 intensive care unit bedside stethoscopes tested, two diaphragms and five earpieces were colonised with pathogenic bacteria. MRSA cultured from one earpiece persisted after cleaning. Three out of the 22 personal stethoscope diaphragms and five earpieces were colonised with pathogens. After cleaning, two diaphragms and two earpieces were still colonised, demonstrating the importance of regular cleaning.
Photoacoustic study of the photochemistry of adsorbed indigoid dyes (1982)

The photochemistry of thioindigo, 6,6'-diethoxythioindigo, and N,N'-diacetylindigo adsorbed on alumina has been investigated. The results are compared with those obtained in solution. Unsubstituted thioindigo can be isomerized at the surface. In contrast to the findings in solution the cis isomer is stabilized at the surface and cannot be backconverted. If thioindigo is substituted in 6,6'-positions, only the trans form is found in the surface spectrum, and no trans ? cis photoisomerization is observed. The results on N,N'-diacetyl-indigo indicate that this compound decomposes at the surface. The spectrum obtained is identical to that of indigo.
Analysis of Lyso-Globotriaosylsphingosine in Dried Blood Spots (2013)

Recently, lyso-globotriaosylsphingosine (lyso-Gb3) was found to be elevated in plasma of treatment naive male patients and some female patients with Fabry Disease (FD). This study tested whether lyso-Gb3 could be analyzed in dried blood spots (DBS) from filter cards and whether concentrations are elevated in newborn infants with FD. Lyso-Gb3 concentrations were analyzed in DBS following extraction using a novel HPLC-mass spectrometry (MS)/MS method. Lyso-Gb3 levels in DBS were above the lower limit of quantitation (0.28 ng/mL) in 5/17 newborn FD infants (16 males; range: 1.02-8.81 ng/mL), but in none of the newborn controls, in all 13 patients (4 males) with classic FD (range: 2.06-54.1 ng/mL), in 125/159 Taiwanese individuals with symptomatic or asymptomatic FD who carry the late onset α-galactosidase A (GLA) mutation c.936+919G>A (IVS4+919G>A) (3.75±0.69 ng/mL; range: 0.418-3.97 ng/mL) and in 20/29 healthy controls (0.77±0.24 ng/mL; range: 0.507-1.4 ng/mL). The HPLC-MS/MS method for analysis of lyso-Gb3 is robust and yields reproducible results in DBS in patients with FD. However, concentrations of lyso-Gb3 were below the limit of quantitation in most newborn infants with FD rendering this approach not suitable for newborn screening. In addition, most females with the late onset mutation have undetectable lyso-Gb3 concentrations.
Ethenolysis Reactions Catalyzed by Imido Alkylidene Monoaryloxide Monopyrrolide (MAP) Complexes of Molybdenum (2009)

Monoaryloxide-pyrrolide (MAP) olefin metathesis catalysts of molybdenum that contain a chiral bitetralin-based aryloxide ligand are efficient for ethenolysis of methyl oleate, cyclooctene, and cyclopentene. Ethenolysis of 5000 equiv of methyl oleate produced 1-decene (1D) and methyl-9-decenoate (M9D) with a selectivity of >99%, yields up to 95%, and a TON (turnover number) of 4750 in 15 h. Tungstacyclobutane catalysts gave yields approximately half those of molybdenum catalysts, either at room temperature or at 50 degrees C, although selectivity was still >99%. Ethenolysis of 30,000 equiv of cyclooctene to 1,9-decadiene could be carried out with a TON of 22,500 at 20 atm (75% yield), while ethenolysis of 10,000 equiv of cyclopentene to 1,6-heptadiene could be carried out with a TON of 5800 at 20 atm (58% yield). There is no reason to propose that the efficiency of ethenolysis has been maximized with the most successful catalyst reported here.
A novel regulation of PD-1 ligands on mesenchymal stromal cells through MMP-mediated proteolytic cleavage (2015)

Whether fibroblasts regulate immune response is a crucial issue in the modulation of inflammatory responses. Herein, we demonstrate that foreskin fibroblasts (FFs) potently inhibit CD3<sup>+</sup> T cell proliferation through a mechanism involving early apoptosis of activated T cells. Using blocking antibodies, we demonstrate that the inhibition of T cell proliferation occurs through cell-to-cell interactions implicating PD-1 receptor expressed on T cells and its ligands, PD-L1 and PD-L2, on fibroblasts. Dual PD-1 ligand neutralization is required to abrogate (i) binding of the PD-1-Fc fusion protein, (ii) early apoptosis of T cells, and (iii) inhibition of T cell proliferation. Of utmost importance, we provide the first evidence that PD-1 ligand expression is regulated through proteolytic cleavage by endogenous matrix metalloproteinases (MMPs) without transcriptional alteration during culture-time. Using (i) different purified enzymatic activities, (ii) MMP-specific inhibitors, and (iii) recombinant human MMP-9 and MMP-13, we demonstrated that in contrast to CD80/CD86, PD-L1 was selectively cleaved by MMP-13, while PD-L2 was sensitive to broader MMP activities. Their cleavage by exogenous MMP-9 and MMP-13 with loss of PD-1 binding domain resulted in the reversion of apoptotic signals on mitogen-activated CD3<sup>+</sup> T cells. We suggest that MMP-dependent cleavage of PD-1 ligands on fibroblasts may limit their immunosuppressive capacity and thus contribute to the exacerbation of inflammation in tissues. In contrast, carcinoma-associated fibroblasts appear PD-1 ligand-depleted through MMP activity that may impair physical deletion of exhausted defective memory T cells through apoptosis and facilitate their regulatory functions. These observations should be considered when using the powerful PD-1/PD-L1 blocking immunotherapies.
Purification and characterization of human recombinant IgE-Fc fragments that bind to the human high affinity IgE receptor (1993)

The Fc-region of immunoglobulin E (IgE) comprising C epsilon 2, C epsilon 3, and C epsilon 4 domains is sufficient for binding to the alpha chain of the high affinity IgE-Fc receptor (Fc epsilon RI alpha). In order to identify the smallest Fc fragment capable of binding to the Fc epsilon RI alpha with high affinity, various regions of the IgE-Fc molecule were expressed in COS cells and investigated for their ability to bind Fc epsilon RI alpha. The smallest fragment that showed Fc epsilon RI alpha binding activity spans amino acids 329-547 and lacks the entire C epsilon 2 domain. Two active fragments, viz. Fc epsilon(315-547) (containing Cys328 which is responsible for interchain S-S bonding) and Fc epsilon(329-547), have been overexpressed in CHO cells and purified to homogeneity. The purified proteins bind to the Fc epsilon RI alpha with high affinity, similar to native IgE. SDS-polyacrylamide gel electrophoresis analyses indicate that Fc epsilon(315-547) is an S-S-linked dimer of apparent molecular mass of 68 kDa. Fc epsilon(329-547) appears on SDS-gel as three distinct bands at approximately 32 kDa, both under reducing and nonreducing conditions. However, size exclusion chromatography and analytical ultracentrifugation studies suggest that Fc epsilon(329-547) also remains associated as a dimer. The presence of N-linked glycosylation was detected in both proteins. The deglycosylated form of Fc epsilon(315-547) was isolated after Endo F/N-glycosidase F digestion and demonstrated to have binding activity comparable to that of the mock-digested protein. These results suggest that the presence of N-linked sugars is not necessary for Fc epsilon RI alpha binding. Both proteins blocked the release of histamine from RBL cells expressing human Fc epsilon RI alpha in a dose-dependent manner. The availability of these recombinant IgE-Fc proteins will be helpful in elucidating the key epitopes essential for the binding of IgE to its high affinity receptor.
The Mithramycin Gene Cluster of Streptomyces argillaceus Contains a Positive Regulatory Gene and Two Repeated DNA Sequences That Are Located at Both Ends of the Cluster (1999)

Sequencing of a 4.3-kb DNA region from the chromosome of Streptomyces argillaceus, a mithramycin producer, revealed the presence of two open reading frames (ORFs). The first one (orfA) codes for a protein that resembles several transport proteins. The second one (mtmR) codes for a protein similar to positive regulators involved in antibiotic biosynthesis (DnrI, SnoA, ActII-orf4, CcaR, and RedD) belonging to the Streptomyces antibiotic regulatory protein (SARP) family. Both ORFs are separated by a 1.9-kb, apparently noncoding region. Replacement of the mtmR region by an antibiotic resistance cassette completely abolished mithramycin biosynthesis. Expression of mtmR in a high-copy-number vector in S. argillaceus caused a 16-fold increase in mithramycin production. The mtmR gene restored actinorhodin production in Streptomyces coelicolor JF1 mutant, in which the actinorhodin-specific activator ActII-orf4 is inactive, and also stimulated actinorhodin production by Streptomyces lividans TK21. A 241-bp region located 1.9 kb upstream of mtmR was found to be repeated approximately 50 kb downstream of mtmR at the other end of the mithramycin gene cluster. A model to explain a possible route for the acquisition of the mithramycin gene cluster by S. argillaceus is proposed.
Dectin-1 Interaction with Tetraspanin CD37 Inhibits IL-6 Production (2007)

C-type lectins are pattern-recognition receptors important for pathogen binding and uptake by APCs. Evidence is accumulating that integration of incoming cellular signals in APCs is regulated by grouping of receptors and signaling molecules into organized membrane complexes, such as lipid rafts and tetraspanin microdomains. In this study, we demonstrate that C-type lectin dectin-1 functionally interacts with leukocyte-specific tetraspanin CD37. Dectin-1 and CD37 colocalize on the surface of human APCs. Importantly, macrophages of CD37-deficient (CD37(-/-)) mice express decreased dectin-1 membrane levels, due to increased dectin-1 internalization. Furthermore, transfection of CD37 into a macrophage cell line elevated endogenous dectin-1 surface expression. Although CD37 deficiency does not affect dectin-1-mediated phagocytosis, we observed a striking 10-fold increase of dectin-1-induced IL-6 production in CD37(-/-) macrophages compared with wild-type cells, despite reduced dectin-1 cell surface expression. Importantly, the observed increase in IL-6 production was specific for dectin-1, because signaling via other pattern-recognition receptors was unaffected in CD37(-/-) macrophages and because the dectin-1 ligand curdlan was used. Taken together, these findings show that tetraspanin CD37 is important for dectin-1 stabilization in APC membranes and controls dectin-1-mediated IL-6 production.
High accuracy computation with linear analog optical systems: a critical study (1986)

High accuracy optical processors based on the algorithm of digital multiplication by analog convolution (DMAC) are studied for ultimate performance limitations. Variations of optical processors that perform high accuracy vector–vector inner products are studied in abstract and with specific examples. It is concluded that the use of linear analog optical processors in performing digital computations with DMAC leads to impractical requirements for the accuracy of analog optical systems and the complexity of postprocessing electronics.
Reawakening fetal hemoglobin: prospects for new therapies for the β-globin disorders (2012)

The level of fetal hemoglobin (HbF) modifies the severity of the common β-globin disorders. Knowledge of the normal mechanisms that repress HbF in the adult stage has remained limited until recently despite nearly 3 decades of molecular investigation, in part because of imperfect model systems. Recent studies have provided new insights into the developmental regulation of globin genes and identified specific transcription factors and epigenetic regulators responsible for physiologic silencing of HbF. Most prominent among these regulators is BCL11A, a transcriptional repressor that inhibits adult-stage HbF expression. KLF1 and c-Myb are additional critical HbF-regulating erythroid transcription factors more broadly involved in erythroid gene expression programs. Chromatin modifiers, including histone deacetylases and DNA methyltransferases, also play key roles in orchestrating appropriate globin gene expression. Taken together, these discoveries present novel therapeutic targets for further consideration. Although substantial hurdles remain, opportunities are now rich for the rational design of HbF inducers.
Immunotherapy with HER-2 and VEGF peptide mimics plus metronomic paclitaxel causes superior antineoplastic effects in transplantable and transgenic mouse models of human breast cancer (2012)

HER-2 and the vascular endothelial factor receptor (VEGF) represent validated targets for the therapy of multiple tumor types and inhibitors of these receptors have gained increasing importance in the clinic. In this context, novel bioactive agents associated with better therapeutic outcomes and improved safety profile are urgently required. Specifically engineered HER-2- and VEGF-derived peptides in combination with low-dose chemotherapy might provide a substantial impact on tumor metastasis and cancer progression. We tested the antitumor effects of HER-2 and VEGF peptide mimics in combination with metronomic paclitaxel in both PyMT and Balb/c murine model challenged with TUBO cells. The combination of low-dose paclitaxel and HER-2 or VEGF peptide mimics had greater inhibitory effects than either agent alone. Peptide treatment caused virtually no cardiotoxic effects, while paclitaxel and the anti-HER-2 antibody trastuzumab (Herceptin), exerted consistent cardiotoxicity. The combination regimen also promoted significant reductions in tumor burden and prolonged survival rates in both transgenic and transplantable tumor models. Tumor weights were significantly reduced in mice treated with HER-2 peptides alone, and even more in animals that received HER-2 peptide with low-dose paclitaxel, which alone had no significant effects on tumor growth in the transgenic model. Specifically engineered native peptide sequences from HER-2 and VEGF used in combination with metronomic paclitaxel demonstrate enhanced anticancer efficacy and an encouraging safety profile. This novel approach to targeted therapy may offer new avenues for the treatment of breast cancer and other solid tumors that overexpress HER-2 and VEGF.
Co‐localization of N‐acetyl‐aspartyl‐glutamate in central cholinergic, noradrenergic, and serotonergic neurons (1987)

Abstract An immunohistochemical technique for simultaneously visualizing two different antigens has been used to investigate the presence of the acidic dipeptide, N‐acetyl‐aspartyl‐glutamate (NAAG), in cholinergic, noradrenergic‐adrenergic, and serotonergic neurons within CNS. The brain slices were processed sequentially with purified antisera against NAAG and then monoclonal antibody against choline acetyltransferase (ChAT), a marker for cholinergic neurons, or antiserum against dopamine‐β‐hydroxylase (DBH), a marker of noradrenergic‐adrenergic neurons, or antiserum against serotonin (5HT). Both antigens were revealed by the peroxidase reaction but with different chromogens, which are easily distinguishable. An intense double staining of NAAG‐like immunoreactivity (NAAG‐LI) and ChAT was observed in the motoneurons of the spinal cord as well as in the several motor components of cranial nerve nuclei including facial, ambiguus, and trigeminal nuclei. A partial colocalization of NAAG‐LI and ChAT was evident in the perikarya of the basal forebrain cholinergic system, whereas cholinergic neurons of the medial septum exhibited only sporadic staining for NAAG‐LI. A complete coexistence of NAAG‐LI and DBH was observed in the locus coeruleus. Most of the other noradrenergic and adrenergic cell groups of the medulla region exhibited substantial co‐localization with the exception of the A2 cell group, which was virtually devoid of NAAG‐LI. In the dorsal raphe, only a low percentage of serotonergic neurons stained for NAAG‐LI. The co‐existence of NAAG‐LI and serotonin was more evident in the neurons of the median raphe, although the majority of cells failed to show double staining. In the raphe pallidus and raphe magnus, the co‐existence with NAAG‐LI remained partial but involved a large percentage of serotonergic neurons. These results suggest a more widespread neuronal function of NAAG in addition to its proposed role as putative neurotransmitter in a subgroup of glutamatergic neurons.