gebhart/patrepeval huggingface dataset:
The Design, Synthesis and Conformation of Some New<i>β</i>-Hairpin Mimetics: Novel Reagents for Drug and Vaccine Discovery (2000)

Syntheses and conformational studies are presented of some novel templates for use in the construction of β-hairpin mimetics. The templates are relatively rigid molecules that constrain the backbone conformation of an attached peptide loop into the β-region of φ/ψ-space. They include diketopiperazines incorporating substituted proline derivatives, as well as heterochiral diproline units, which can be incorporated efficiently into cyclic peptide β-hairpin mimetics by solid-phase methods. Potential applications of β-hairpin mimetics in drug and synthetic vaccine discovery are discussed.
Targeting of magnolin on ERKs inhibits Ras/ERKs/RSK2-signaling-mediated neoplastic cell transformation (2013)

Mitogen-activated protein kinases play a key role in cell proliferation, cell cycle progression and cell transformation, and activated Ras/extracellular signal-regulated kinases (ERKs)/ribosomal S6 kinase 2 (RSK2) signaling pathways have been widely identified in many solid tumors. In this study, we found that magnolin, a compound found in the Magnolia species, directly targeted and inhibited ERK1 and ERK2 kinase activities with IC50 values of 87 and 16.5 nM by competing with adenosine triphosphate in an active pocket. Further, we demonstrated that magnolin inhibited epidermal growth factor (EGF)-induced p90RSKs phosphorylation at Thr359/Ser363, but not ERKs phosphorylation at Thr202/Tyr204, and this resulted in inhibition of cell proliferation by suppression of the G1/S cell cycle transition. Additionally, p38 kinases, Jun N-terminal kinases and Akts were not involved in the magnolin-mediated inhibitory signaling. Magnolin targeting of ERK1 and 2 activities suppressed the phosphorylation of RSK2 and downstream target proteins including ATF1 and c-Jun and AP-1, a dimer of Jun/Fos, and the transactivation activities of ATF1 and AP-1. Notably, ERKs inhibition by magnolin suppressed EGF-induced anchorage-independent cell transformation and colony growth of Ras(G12V)-harboring A549 human lung cancer cells and NIH3T3 cells stably expressing Ras(G12V) in soft agar. Taken together, these results demonstrated that magnolin might be a naturally occurring chemoprevention and therapeutic agent capable of inhibiting cell proliferation and transformation by targeting ERK1 and ERK2.
Molecular Mimicry Revisited: Gut Bacteria and Multiple Sclerosis (2006)

Molecular mimicry is a possible explanation for autoimmune side effects of microorganism infections. Protein sequences from a particular microorganism are compared to known autoimmune immunogens. For diseases such as multiple sclerosis (MS), where the infectious agent is unknown, guesses to its identity are made. Mimics are assumed to be rare. This study takes a radically different approach. Reported sequences from all known human bacterial and viral agents were searched for autoimmune immunogen mimics. Three encephalitogenic peptides, whose autoimmune requirements have been studied extensively, were selected for comparison. Mimics were seen in a wide variety of organisms. For each immunogen, the mimics were found predominantly in nonpathogenic gut bacteria. Since the three immunogens used in this study are related to MS, it is suggested that a microorganism responsible for autoimmune activity in MS could be a normally occurring gut bacterium. This would explain many of the peculiar MS epidemiological data and why no infective agent has been identified for MS and supports recently found MS gut metabolism abnormalities.
Measles Virus Attenuation Associated with Transcriptional Impediment and a Few Amino Acid Changes in the Polymerase and Accessory Proteins (1998)

Measles virus (MV) isolated in B95a cells, a marmoset B-cell line, retains full pathogenicity for cynomolgus monkeys, while its derivative obtained by adaptation to the growth in Vero cells, a monkey kidney cell line, loses the pathogenic potential (F. Kobune, H. Sakata, and A. Sugiura, J. Virol. 64:700-705, 1990). Here, we show with a pair of strains, a fresh isolate (9301B) in B95a cells and its Vero cell-adapted form (9301V), that the in vivo attenuation parallels the decrease of replication and syncytium-inducing capabilities in the original B95a cells and that these in vitro phenotypes are attributable to impediment of transcription, which is already obvious at the level of primary transcription catalyzed by the virion-associated RNA polymerase. On the other hand, cell fusion assays detected no functional difference between the glycoproteins of the two viruses. Essentially the same transcriptional impediment with reduced syncytium induction following Vero cell adaptation was found with two other pairs of strains that had been similarly prepared. Nucleotide sequence comparison between the 9301B and 9301V viruses revealed that a few (at most five) amino acid changes, which sporadically took place in the polymerase (L and P proteins) and/or accessory V and C proteins, were responsible for the in vitro and in vivo attenuation through adaptation to growth in Vero cells.
Appearance-and-Relation Networks for Video Classification (2018)

Spatiotemporal feature learning in videos is a fundamental problem in computer vision. This paper presents a new architecture, termed as Appearance-and-Relation Network (ARTNet), to learn video representation in an end-to-end manner. ARTNets are constructed by stacking multiple generic building blocks, called as SMART, whose goal is to simultaneously model appearance and relation from RGB input in a separate and explicit manner. Specifically, SMART blocks decouple the spatiotemporal learning module into an appearance branch for spatial modeling and a relation branch for temporal modeling. The appearance branch is implemented based on the linear combination of pixels or filter responses in each frame, while the relation branch is designed based on the multiplicative interactions between pixels or filter responses across multiple frames. We perform experiments on three action recognition benchmarks: Kinetics, UCF101, and HMDB51, demonstrating that SMART blocks obtain an evident improvement over 3D convolutions for spatiotemporal feature learning. Under the same training setting, ARTNets achieve superior performance on these three datasets to the existing state-of-the-art methods.1
Perspective on Solvent Use in the Pharmaceutical Industry (2006)

Solvent use consistently accounts for between 80 and 90% of mass utilization in a typical pharmaceutical/fine chemicals (non-polymer) batch chemical operation. Moreover, within these operations, solvents play a dominant role in the overall toxicity profile of any given process; i.e. on a mass basis, solvents account for the largest proportion of chemicals of concern used in the process. However, for the typical synthetic organic chemist, solvents are just a medium in which a reaction takes place; the interest is in the reactivity and building of a molecule, not in the means by which this is carried out. So, in a typical retrosynthetic analysis, solvent and solvent-reactant interactions, separability, and particle engineering are generally not included. The best means in which this reaction can take place is also not considered; i.e., the reaction space, configuration, order of addition, heat/mass transfer, etc., is generally not considered. This publication presents a case for greater awareness of solvent issues in batch chemical operations typically found in the pharmaceutical industry.
False‐positive coliform reaction mediated by <i>Aeromonas</i> in the Colilert defined substrate technology system (1998)

The Colilert defined substrate technology system allows specific, one-step detection of both coliforms and Escherichia coli while claiming to suppress the influence of non-coliform heterotrophs. The Colilert assay was examined in order to determine whether organisms from the genus Aeromonas could interfere and cause production of a false-positive coliform result as aquatic Aeromonas are known to constitute a fraction of the heterotrophic population found in drinking water. Results obtained clearly demonstrate that Aeromonas sp. can elicit a positive coliform type reaction at very low densities. Cell suspensions as low as 1 x 10(1) cells 10 ml-1 were observed to yield a positive reaction using Colilert reagent 4 weeks short of shelf-life expiry. Use of aged Colilert for monitoring water quality could lead to overestimation of coliforms as Aeromonas have been identified in many treated drinking water supplies.
CRYSTAL SRTUCTURE OF POLYIMIDES. APPLICATION OF MOLECULAR SIMULATION TECHNIQUE TO CALCULATE THE CRYSTAL STRUCTURE (1994)

A review is given on the application of molecular simulation technique to calculate the crystal structure of polyimides showing some selected examples, which include a comparison between molecular sumulation technique and X-ray diffraction analysis of the rigid-rod aromatic heterocyclic polyimide, a structural characterization of an ordered aromatic polyimide, ‘Kapton’, and an X-ray structural analysis of a thermoplastic polyimide.
APIs and Protocols For Convergent Network Services (2002)

The Telecom companies are looking to converged services to replace the lost revenue they used to get from long distance and simple access charges. APIs (Application Programming Interfaces) are the crucial tool used for creating these services. 

* Detailed coverage of JAIN (Java Integrated Networks) and Parlay, the first open APIs released 
* Provides software basics for telecom professionals 
* Thoroughly details object-oriented environments 
* Endorsed by the creators of JAIN and parlay
Table of contents

Preface
Chapter 1: Introduction
Chapter 2: Software for Managers
Chapter 3: The Java Programming Language
Chapter 4: XML: The Extensible Makeup Language
Chapter 5: Distributed Computing
Chapter 6: Directories
Chapter 7: Telephony for Programmers
Chapter 8: IP Telephony
Chapter 9: Session Initiation Protocol (SIP)
Chapter 10: Going Further with SIP
Chapter 11: Web-Oriented Service Technology
Chapter 12: JTAPI
Chapter 13: JAIN
Chapter 14: Parlay
Appendix A: Acronyms
Appendix B: Web References
Bibliography
Index
Frequency domain near‐infrared spectroscopy of the uterine cervix during cervical ripening (2007)

Our results show that FD-NIRS is a promising diagnostic tool to detect changes in cervical concentrations of hemoglobin and water. A severe tissue edema, probably due to a hormone-induced inflammatory process, seems to be important for cervical ripening. The reduction in total hemoglobin is likely to be a consequence of the increased water content of the tissue resulting in a dramatic increase of the distance between vessels. We propose this technology to assess the cervical ripening and eventually to predict preterm labor.
SHEWMAC: an end-of-line SPC scheme for joint monitoring of process mean and variance (2003)

Under the effects of multiple-stream and sequence-disorder, process change caused by one machine at an in-line step may result in changes in both the mean and variance of end-of-line wafer acceptance test (WAT) data sequence. To speed up trend detection of WAT data without resorting to an intensive computing power, an end-of line SHEWMAC scheme is proposed, which combines a Shewhart, an exponentially weighted moving average (EWMA), and an exponentially weighted moving Cpk (EWMC) charts for jointly monitoring the mean and variance of wafer lot average sequence from WAT data. In view of the wide ranges of process conditions and low volume of each product in a foundry fab, a data normalization technique is adopted to aggregate data of similar products and a new design method is developed to generate a robust set of scheme parameters. Simulation and field data validation show that SHEWMAC is superior to the combined Shewhart-EWMA scheme in shift detection speed and is complementary to the in-line SPC.
Case management in a wound care program. (1997)

Patients who need wound care can present a complex challenge in the current managed care environment. Managing health care benefits and financial and socioeconomic factors that impact wound healing are as crucial to wound healing as providing aggressive wound care. Case management is used to describe the strategies involved in coordinating patient care to achieve optimal clinical and financial outcomes and ensure quality and continuity of care. In this article, the author illustrates how case management plays an integral part in a wound care program. The article features tips on how to effectively use limited financial resources that burden many patients who need wound care, includes ways to approach physicians when current wound care is not effective, and focuses on early discharge planning and a multidisciplinary team approach to ensure optimal clinical and financial outcomes. To help sharpen skills, included at the end of the article is a Case Study Challenge and tools to use in practice: Case Management Plans for Wound Patients.
Pharmacokinetics of Scopolamine During Caesarean Section (1990)

Departments of Anesthesiology, Clinical Pharmacology and Pharmacology, University of Turku, Turku, Finland
HYBRID REVERBERATION ALGORITHM USING TRUNCATED IMPULSE RESPONSE CONVOLUTION AND RECURSIVE FILTERING (2001)

of a Master’s Research Project at the University of Miami. Research project supervised by Professor William Pirkle. No. of pages in text: 79 Artificial reverberation can be developed by convolving an input signal with the specific impulse response of an acoustic space. This computationally exhaustive method achieves superb reverberation, but is often abandoned for simpler filtering methods. Since it is only the length of the impulse response that determines the computational cost and resolution, a new hybrid algorithm is developed that borrows from the original impulse response easing the computational burden. A truncated impulse response can still convey the rich energy of the space while a digital filter bank can model the late echoes and reverberation tail. This more efficient algorithm will use a reduced length block convolution and recursive filter network to achieve similar high quality reverberation.
Linear- and Angular-Shaped Naphthodithiophenes: Selective Synthesis, Properties, and Application to Organic Field-Effect Transistors (2011)

A straightforward synthetic approach that exploits linear- and angular-shaped naphthodithiophenes (NDTs) being potential as new core structures for organic semiconductors is described. The newly established synthetic procedure involves two important steps; one is the chemoselective Sonogashira coupling reaction on the trifluoromethanesulfonyloxy site over the bromine site enabling selective formation of o-bromoethynylbenzene substructures on the naphthalene core, and the other is a facile ring closing reaction of fused-thiophene rings from the o-bromoethynylbenzene substructures. As a result, three isomeric NDTs, naphtho[2,3-b:6,7-b']dithiophene, naphtho[2,3-b:7,6-b']dithiophenes, and naphtho[2,1-b:6,5-b']dithiophene, are selectively synthesized. Electrochemical and optical measurements of the parent NDTs indicated that the shape of the molecules plays an important role in determining the electronic structure of the compounds; the linear-shaped NDTs formally isoelectronic with naphthacene have lower oxidation potentials and more red-shifted absorption bands than those of the angular-shaped NDTs isoelectronic with chrysene. On the contrary, the performance of the thin-film-based field-effect transistors (FETs) using the dioctyl or diphenyl derivatives were much influenced by the symmetry of the molecules; centrosymmetric derivatives tend to give higher mobility (up to 1.5 cm(2) V(-1) s(-1)) than axisymmetric ones (∼0.06 cm(2) V(-1) s(-1)), implying that the intermolecular orbital overlap in the solid state is influenced by the symmetry of the molecules. These results indicate that the present NDT cores, in particular the linear-shaped, centrosymmetric naphtho[2,3-b:6,7-b']dithiophene, are promising building blocks for the development of organic semiconducting materials.
Light Microscopic Evidence of Hair Cell Regeneration After Gentamicin Toxicity in Chick Cochlea (1987)

This study examines the temporal pattern of hair cell loss in the chick basilar papilla following ten days of gentamicin administration in hatchling chicks. Chicks were subsequently killed at ages 11, 18, 25, and 32 days. The basilar papillae were embedded in plastic and serially sectioned for light microscopic analysis. Hair cell counts were obtained at 100-microM intervals throughout the length of the papilla. Significant hair cell loss was documented basally in the 11-day-old chicks, and spread apically over time to maximal loss in the 18-day-old animals. Relative to the control chicks, there was a 36% hair cell loss in these animals. Interestingly, there appears to be a progressive partial recovery of the normal hair cell counts in the 25- and 32-day-old animals.
Guiding and bending of acoustic waves in highly confined phononic crystal waveguides (2004)

We demonstrate experimentally the guiding and the bending of acoustic waves in highly confined waveguides formed by removing rods from a periodic two-dimensional lattice of steel cylinders immersed in water. Full transmission is observed for a one-period-wide straight waveguide within the full band gap of the perfect phononic crystal. However, when the waveguide width is doubled, destructive interference causes the transmission to vanish in the center of the passband. Waveguiding over a wide frequency range is obtained for a one-period-wide waveguide with two sharp 90° bends. Finite-difference time-domain computations are found to be in good agreement with the measurements.
Synthesis and characterization of CuGaTe2 films prepared by three source co-evaporation technique (2002)

Optical and microstructural properties of polycrystalline CuGaTe2 films deposited by three source co-evaporation technique are presented. Two characteristic bandgaps were detected at 1.24 and 1.69 eV corresponding to allowed direct transition and forbidden direct transition respectively. Microstructure was studied by x-ray diffraction (XRD) and SEM/TEM. Harris texture analysis of the XRD data indicated (112) to be the predominant orientation for stoichiometric composition of CuGaTe2 films with Cu/Ga~1.0 whereas (204) orientation was most predominant for the off-stoichiometric films having excess Cu or excess Ga. Variation of Urbach tail width with Cu/Ga ratio was studied. The films had a rough surface, and the surface roughness of the films obtained from diffused reflectance measurement indicated a variation within 32-58 nm.
Air Traffic Complexity: Towards an Intrinsic Metric (2000)

International audience
Molecular Basis of the Mixed Lineage Leukemia-Menin Interaction (2010)

Chromosomal translocations targeting the mixed lineage leukemia (MLL) gene result in MLL fusion proteins that are found in aggressive human acute leukemias. Disruption of MLL by such translocations leads to overexpression of Hox genes, resulting in a blockage of hematopoietic differentiation that ultimately leads to leukemia. Menin, which directly binds MLL, has been identified as an essential oncogenic co-factor required for the leukemogenic activity of MLL fusion proteins. Here, we characterize the molecular basis of the MLL-menin interaction. Using (13)C-detected NMR experiments, we have mapped the residues within the intrinsically unstructured fragment of MLL that are required for binding to menin. Interestingly, we found that MLL interacts with menin with a nanomolar affinity (K(d) ∼ 10 nM) through two motifs, MBM1 and MBM2 (menin binding motifs 1 and 2). These motifs are located within the N-terminal 43-amino acid fragment of MLL, and the MBM1 represents a high affinity binding motif. Using alanine scanning mutagenesis of MBM1, we found that the hydrophobic residues Phe(9), Pro(10), and Pro(13) are most critical for binding. Furthermore, based on exchange-transferred nuclear Overhauser effect measurements, we established that MBM1 binds to menin in an extended conformation. In a series of competition experiments we showed that a peptide corresponding to MBM1 efficiently dissociates the menin-MLL complex. Altogether, our work establishes the molecular basis of the menin interaction with MLL and MLL fusion proteins and provides the necessary foundation for development of small molecule inhibitors targeting this interaction in leukemias with MLL translocations.
Regulatory Dysfunction of the Interleukin-7 Receptor in CD4 and CD8 Lymphocytes From HIV-Infected Patients-Effects of Antiretroviral Therapy (2006)

Despite an increase in plasma IL-7 levels, the CD4 T-cell pool decrease progressively in HIV-infected patients. Here we report on our tests to check the hypothesis that defects in the IL-7 receptor system might be involved in this phenomenon. The cell surface expression of CD127 was measured ex vivo in CD4 and CD8 T lymphocytes drawn from 3 groups of HIV patients. IL-7 function was also followed in vitro by measuring IL-7-driven T-cell proliferation, the induction of the CD25 activation marker, and overexpression of the antiapoptotic molecule Bcl-2. Untreated viremic patients showed a slight but significant decrease in CD127 expression on the surface of their CD4 lymphocytes. By contrast, CD127 expression was substantially altered on the surface of CD8 T lymphocytes taken from untreated viremic patients. IL-7-induced overexpression of the antiapoptotic molecule Bcl-2 was dramatically altered in viremic patients, whereas IL-7-dependent CD25 induction and T-cell proliferation were reduced. Highly active antiretroviral therapy partially corrected these defects in patients with an undetectable viral load and CD4 counts of more than 400 cells/microL. The effects of HAART were less pronounced in patients with undetectable VL but low CD4 counts (<250 cells/microL). The IL-7 receptor is dysfunctional in the CD4 and CD8 lymphocytes of HIV-infected patients. This may be due to abnormal activation of the immune system in HIV-infected patients and may contribute to the reduced CD4 count and the altered function of the CD8 compartment.
High-power grating-coupled surface emitters (1989)

Surface-emitting lasers with second-order gratings for output coupling have been demonstrated to emit 2-8 W pulsed, with a differential efficiency of 20%. The radiation pattern resulting from the interference of two grating regions indicates coherent operation, and a single longitudinal mode output.
73-GHz self-aligned SiGe-base bipolar transistors with phosphorus-doped polysilicon emitters (1992)

The authors report a thermal-cycle emitter process using phosphorus for the fabrication of self-aligned SiGe-base heterojunction bipolar transistors. The low thermal cycle results in extremely, narrow basewidths and preservation of lightly doped spacers in both the emitter-base and base-collector junctions for improved breakdown. Transistors with 35-nm basewidths were obtained with low emitter-base reverse leakage and a peak cutoff frequency of 73 GHz for an intrinsic base sheet resistance of 16 k Omega / Square Operator . Minimum NTL (nonthreshold logic) and ECL (emitter-coupled logic) gate delays of 28 and 34 ps, respectively were obtained with these devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>