gebhart/patrepeval huggingface dataset:
Correction: Interaction of Pyrrolobenzodiazepine (PBD) Ligands with Parallel Intermolecular G-Quadruplex Complex Using Spectroscopy and ESI-MS (2012)

Studies on ligand interaction with quadruplex DNA, and their role in stabilizing the complex at concentration prevailing under physiological condition, has attained high interest. Electrospray ionization mass spectrometry (ESI-MS) and spectroscopic studies in solution were used to evaluate the interaction of PBD and TMPyP4 ligands, stoichiometry and selectivity to G-quadruplex DNA. Two synthetic ligands from PBD family, namely pyrene-linked pyrrolo[2,1-c][1,4]benzodiazepine hybrid (PBD1), mixed imine-amide pyrrolobenzodiazepine dimer (PBD2) and 5,10,15,20-tetrakis(N-methyl-4pyridyl)porphyrin (TMPyP4) were studied. G-rich single-stranded oligonucleotide d(59GGGGTTGGGG39) designated as d(T 2 G 8 ), from the telomeric region of Tetrahymena Glaucoma, was considered for the interaction with ligands. ESI-MS and spectroscopic methods viz., circular dichroism (CD), UV-Visible, and fluorescence were employed to investigate the Gquadruplex structures formed by d(T 2 G 8 ) sequence and its interaction with PBD and TMPyP4 ligands. From ESI-MS spectra, it is evident that the majority of quadruplexes exist as d(T 2 G 8 ) 2 and d(T 2 G 8 ) 4 forms possessing two to ten cations in the centre, thereby stabilizing the complex. CD band of PBD1 and PBD2 showed hypo and hyperchromicity, on interaction with quadruplex DNA, indicating unfolding and stabilization of quadruplex DNA complex, respectively. UV-Visible and fluorescence experiments suggest that PBD1 bind externally where as PBD2 intercalate moderately and bind externally to Gquadruplex DNA. Further, melting experiments using SYBR Green indicate that PBD1 unfolds and PBD2 stabilizes the Gquadruplex complex. ITC experiments using d(T 2 G 8 ) quadruplex with PBD ligands reveal that PBD1 and PBD2 prefer external/loop binding and external/intercalative binding to quadruplex DNA, respectively. From experimental results it is clear that the interaction of PBD2 and TMPyP4 impart higher stability to the quadruplex complex.
Comparative evaluation of sutures and non-penetrating metal clips for vascular reconstruction (1995)

The immediate inflammatory response following aortic reconstruction with two types of sealed Dacron grafts was studied in a prospective, randomized manner. C-reactive protein (CRP) levels were measured before surgery and on days 2 and 8 postoperatively. In the collagen-sealed group (n = 10) CRP levels were 10 ± 9.6, 180.2 ± 48.3, and 54.3 ± 34.3 mg/L, respectively. In the gelatin-impregnated group (n = 10) the values were 10.5 ± 8.7, 200.7 ± 27.3, and 80.3 ± 30.2 mg/L, respectively. The slight differences were not significant according to the analysis of variance test for repeated measurements. These findings suggest that implantation of a knitted Dacron graft sealed with collagen does not lead to a higher inflammatory reaction compared with a gelatin-sealed graft.
Simulation of power evolution and control dynamics in optical transport systems (2005)

The design and analysis of control strategies for high-capacity, reconfigurable optical transmission systems require an understanding of optical system dynamics involving the time-dependent interaction of many components. This paper describes system simulation software that couples continuous physical-layer models of optical transmission components with discrete models for events such as channel add/drops. The simulator computes detailed time traces of signal and noise power propagation along a line system consisting of multiple controlled transmission elements and monitoring devices in response to a particular discrete event. Examples are given illustrating the rich variety of experimentation modes the software supports, including the evaluation of control algorithms, systematic exploration of design parameters, and investigation of cost reduction plans. Details of the development effort are presented, illustrating the contributions of the optical physicists, applied mathematicians, system engineers, and computer scientists who were involved in this collaborative project.
Accelerated Line Search for Coordinate Descent Optimization (2006)

Iterative reconstruction (IR) methods show promise for image quality improvements in helical X-ray CT. Coordinate descent methods have good convergence properties for these problems, but include a one-dimensional, nonlinear optimization for each voxel's update. This paper presents two methods for speeding computation by replacing the 1D line search with one-step updates. Both methods greatly reduce this portion of IR computation, at no loss of convergence speed as measured by full iteration count. Experimental examples include both phantom and clinical CT scans.
Multiple Proton Implantations into Silicon: A Combined EBIC and SRP Study (2013)

Protons with energies of 1 MeV and 2.5 MeV were implanted into a p -doped silicon wafer and then the wafer was annealed at 350 °C for one hour. This resulted in two n -doped layers in the otherwise p -doped sample. The carrier concentration was measured using spreading resistance profiling while the positions of the four pn -junctions were measured using electron beam induced current measurements. The carrier concentration is not limited by the available hydrogen but by the concentration of suitable radiation induced defects.
Additive pulse compression mode-locking of fiber lasers (1991)

By exploiting the unique combination of an active medium and nonlinearity in a single-mode Nd3+ fiber laser, we demonstrate self-sustained generation of pedestal-free bandwidth-limited pulses as short as 125 fs (Fig. 1) at a wavelength of 1.064 μm by additive pulse-compression mode locking (APCM). The pulse bandwidth of 9.4 nm (Fig. 2) is larger than the homogeneous linewidth of the Nd3+-laser, which demonstrates that the homogeneous linewidth is not a limiting factor for ultrashort pulse generation in glass lasers. The operation principle of APCM is similar to an optimized version of additive pulse modelocking (APM)1 (or the soliton laser2) combined with soliton shaping (SS).3
Dy-doped selenide glass for 1.3-μm optical fiber amplifiers (2002)

Summary form only given. Dy/sup 3+/-doped materials have been proposed for optical fibre amplifiers at 1.3 μm. Dy/sup 3+/ has several advantages over Pr/sup 3+/-based amplifiers for 1.3-μm telecommunication applications. First, numerous pump bands exist in the near-IR for populating the (/sup 6/H/sub 9/2/, /sup 6/F/sub 11/2/) level. Secondly, these pump bands have absorption coefficients >10 times that of the Pr/sup 3+/ /sup 1/G/sub q/ level in the same host.
Large-area, single-transverse-mode semiconductor laser with diffraction-limited super-Gaussian output (1995)

An external cavity semiconductor laser that incorporates a large-area amplifier has been successfully stabilized into a single transverse mode over the 600 μm width of the amplifier. Single-transverse-mode operation is achieved by using the combination of a diffractive mode-selecting mirror and an aperture. 2.8 W of stable diffraction-limited output power is achieved.
Reactions of potent mutagens, 3-amino-1-methyl-5H-pyrido[4,3-b]indole (Trp-P-2) and 2-amino-6-methyl-dipyrido[1,2-a:3',2'-d]imidazole (Glu-P-1) with nucleic acid. (1980)

Two potent mutagens, 3-amino-1-methyl-5H-pyrido[4,3-b]indole (Trp-P-2), isolated from a tryptophan pyrolysate, and 2-amino-6-methyldipyrido[1,2-a:3',2'-d]imidazole (Glu-P-1), isolated from a glutamic acid pyrolysate, modified calf thymus DNA in the presence of rat liver microsomes. The major base modified by Trp-P-2 was identified wih 3-(3-guanyl)amino-1-methyl-5H-pyrido[4,3-b]indole. The major base modified by Glu-P-1 was identified with 2-(8-guanyl)amino-6-methyldipyrido[1,2-a:3',2'-d]imidazole. N-acetoxy-Glu-P-1 efficiently modified DNA without microsomes.
Prospective, multicenter study of P4HB (Phasix™) mesh for hernia repair in cohort at risk for complications: 3-Year follow-up (2020)

Long-term outcomes following ventral hernia repair with P4HB mesh demonstrate low recurrence rates at 3-year (36-month) postoperative time frame with no patients developing late mesh complications or requiring mesh removal. 5-year (60-month) follow-up is ongoing.
Techniques of the modeling, measurement and reduction of common mode noise for a multi-winding switching transformer (2017)

The reduction of common mode (CM) noise for isolated converters has been a popular research topic. This paper proposed a generalized two-capacitor modeling technique for switching transformers with multiple windings and complicated winding structures. Based on the proposed model, a Flyback transformer with multiple winding structures is investigated. A new measurement technique to characterize and evaluate switching transformer's CM noise performance is developed. Only a signal generator and an oscilloscope are needed for the measurement and no any in-circuit tests are needed. The technique can help to quickly design and evaluate transformers for CM noise reduction in mass testing and production. CM noise reduction techniques including balance capacitor technique, core shielding technique and winding design technique are developed based on the developed two-capacitor model and measurement technique. Experimental results verify the proposed model and the developed CM noise reduction techniques.
Freezing behavior of single sulfuric acid aerosols suspended in a quadrupole trap (1997)

The freezing properties of sulfuric acid droplets were studied by suspending single 20‐ to 30‐μm‐diameter particles in a quadrupole trap and cooling them to stratospheric temperatures (≥191.5 K). Each particle's dc balance voltage was measured to determine the particle composition as a function of temperature and map out the particle's trajectory relative to the sulfuric acid phase diagram. Angularly resolved optical scattering patterns were monitored to detect freezing events. Particles cooled through the sulfuric acid tetrahydrate region (35–70 wt % H 2 SO 4 ) did not freeze and remained spherical liquid droplets for several hours. Only particles cooled through the ice‐liquid equilibrium region (&lt;35 wt% H 2 SO 4 ) showed evidence of freezing. This supports previous experimental and field observations that stratospheric sulfuric acid aerosols are likely to remain liquid to within a few degrees of the ice frost point.
Binding of RPR260243 at the intracellular side of the hERG1 channel pore domain slows closure of the helix bundle crossing gate (2023)

The opening and closing of voltage-dependent potassium channels is dependent on a tight coupling between movement of the voltage sensing S4 segments and the activation gate. A specific interaction between intracellular amino- and carboxyl-termini is required for the characteristically slow rate of channel closure (deactivation) of hERG1 channels. Compounds that increase hERG1 channel currents represent a novel approach for prevention of arrhythmia associated with prolonged ventricular repolarization. RPR260243 (RPR), a quinoline oxo-propyl piperidine derivative, inhibits inactivation and dramatically slows the rate of hERG1 channel deactivation. Here we report that similar to its effect on wild-type channels, RPR greatly slows the deactivation rate of hERG1 channels missing their amino-termini, or of split channels lacking a covalent link between the voltage sensor domain and the pore domain. By contrast, RPR did not slow deactivation of C-terminal truncated hERG1 channels or D540K hERG1 mutant channels activated by hyperpolarization. Together, these findings indicate that ability of RPR to slow deactivation requires an intact C-terminus, does not slow deactivation by stabilizing an interaction involving the amino-terminus or require a covalent link between the voltage sensor and pore domains. All-atom molecular dynamics simulations using the cryo-EM structure of the hERG1 channel revealed that RPR binds to a pocket located at the intracellular ends of helices S5 and S6 of a single subunit. The slowing of channel deactivation by RPR may be mediated by disruption of normal S5-S6 interactions.
Powerful CarbonCarbon Bond Forming Reactions Based on a Novel Radical Exchange Process (2006)

Xanthates and related derivatives have proved to be extremely useful for both inter- and intramolecular radical additions. The broad applicability of the intermolecular addition to un-activated olefins opens tremendous opportunities for synthesis, since various functional groups can be brought together under mild conditions and complex structures can be rapidly assembled. The presence of the xanthate in the product is also a powerful asset for further modifications, by both radical and non-radical pathways. Of special importance is the access to highly substituted aromatic and heteroaromatic derivatives and the synthesis of block polymers through a controlled radical polymerisation mediated by various thiocarbonylthio group containing agents (RAFT and MADIX processes).
Multi-Parameter Performance Modeling using Symbolic Regression (2019)

Performance modeling is becoming critically important due to the need for design-space exploration on emerging exascale architectures. Existing modeling and prediction approaches are either restricted by a limited number of parameters, or provide extreme tradeoffs between simulation performance and modeling accuracy that are not ideal for exascale simulations. At one extreme are low-level discrete-event simulators, which provide high accuracy, but are prohibitively slow for largescale simulations. At the opposite extreme are abstract modeling approaches that are sufficiently fast, but tend to support a limited number of parameters, while also lacking accuracy due to machine-specific behaviors that deviate from anticipated models. In this paper, we improve upon existing abstract modeling approaches by leveraging symbolic regression to automatically discover an underlying multi-parameter model of the system and application that captures difficult-to-understand behaviors. For three High Performance Computing (HPC) applications running on Vulcan, we show that symbolic regression provided modeling accuracies that were 3.5×, 4.6×, and 6.2× better than analytical models developed using linear regression.
Intraocular lens resolution in air and water (1987)

The resolution of 96 polymethylmethacrylate intraocular lenses with convexo-plano optics, ranging in power from 13 to 27 diopters, was measured in air and water. The resolution of each lens was expressed in linear units of resolving power, which is the maximum number of line-pairs that can be resolved per millimeter, as described in the current ANSI Standard Z80.7-1984. There was no clearly defined relationship between linear resolving power measured in air and that measured in water. Measurements on high power lenses (greater than 20 diopters) indicate that it is possible for an intraocular lens to meet the current 100 line-pair per millimeter standard for resolution and still be a limiting factor in a patient's best attainable visual acuity. An alternative method for evaluating lens resolution is to determine the resolution efficiency (the relative percentage performance of a lens compared to a diffraction-limited lens of the same dioptric power). Using these units, a consistent and predictable relationship from air to water was demonstrated. Our findings confirm that if a minimum standard of 30% resolution efficiency in air is established, in contrast to linear resolving power, the lens will perform near its diffraction limit when implanted in the eye. For intraocular lenses of materials other than polymethylmethacrylate, a minimum resolution efficiency in air other than 30% may be required.
P1‐277: SPECT IMAGING FOR AMYLOID PLAQUES WITH A NOVEL RADIOIODINATED LIGAND IN AN ALZHEIMER'S DISEASE MODEL (2014)

Non-invasive determination for amyloid- b peptide (A b) deposition has important significance for early diagnosis and medical intervention to Alzheimer's disease (AD). Until now, however, little single photon emission computed tomography (SPECT) imaging agents have successfully detected A b deposition in the living brains. In the present study, we have developed a serial of imidazopyridine derivatives for SPECT imaging. Five compounds with imidazopyridine structure were synthesized and the affinity to human A b fibrils were evaluated with IC50 for binding of [125 I]IMPY. The compounds with high affinity were selected for further development. The detectability of Ab deposition was investigated by in-vitro autoradiography and in-vivo SPECT imaging in AD model mouse (Tg2576), and compared with positron emission tomography (PET) imaging with [11 C]PiB in the same individuals. Two of newly developed compounds, compound 1 and 5, showed higher affinity to synthetic human A b 1-40 fibrils than well-known amyloid imaging agent IMPY. Further metabolite analysis has detected brain-permeable radioactive metabolites of 125 I-labeled compound 1and IMPY, a well-known ligand for SPECT imaging, while no radioactive metabolite from 125 I-labeled compound 5([125 I]compound 5) was detectable. In vitro autoradiography has clearly demonstrated that there was overt specific binding of [125 I] compound 5 in temporal cortex region of AD enriched with A b plaques. Moreover, ex vivo autoradiographic analysis showed that measurement with [125 I] compound 5 has higher sensibility for detecting A b accumulation than with [125 I]IMPY, in Tg2576 mouse. SPECT imaging with [123 I] compound 5 has also successfully detected A b deposition in the living aged Tg2576 mice, and furthermore showed strong correlation in quantitative analysis for A b plaques detection with positron emission tomography (PET) imaging with [11 C]PiB, implying that [123 I] compound 5 has detectability at least equivalent to [11 C]PiB for A b deposition. [123 I] compound 5 has demonstrated high potential as SPECT ligand for further clinical application.
Interface Extensions for TCP-ENO (2016)

TCP-ENO negotiates encryption at the transport layer. It also defines
a few parameters that are intended to be used or configured by
applications. This document specifies operating system interfaces for
access to these TCP-ENO parameters. We describe the interfaces in
terms of socket options, the de facto standard API for adjusting per-
connection behavior in TCP/IP, and sysctl, a popular mechanism for
setting global defaults. Operating systems that lack socket or sysctl
functionality can implement similar interfaces in their native
frameworks, but should ideally adapt their interfaces from those
presented in this document.
Intraoperative optical coherence tomography for assessing human lymph nodes for metastatic cancer (2016)

Intraoperative OCT has strong potential to supplement current post-operative histopathology with real-time in situ assessment of LNs to preserve both non-cancerous nodes and their lymphatic vessels, and thus reduce the associated risks and complications from surgical disruption of lymphoid structures following biopsy.
Mechanical forces alter zyxin unbinding kinetics within focal adhesions of living cells (2005)

The formation of focal adhesions that mediate alterations of cell shape and movement is controlled by a mechanochemical mechanism in which cytoskeletal tensional forces drive changes in molecular assembly; however, little is known about the molecular biophysical basis of this response. Here, we describe a method to measure the unbinding rate constant k(OFF) of individual GFP-labeled focal adhesion molecules in living cells by modifying the fluorescence recovery after photobleaching (FRAP) technique and combining it with mathematical modeling. Using this method, we show that decreasing cellular traction forces on focal adhesions by three different techniques--chemical inhibition of cytoskeletal tension generation, laser incision of an associated actin stress fiber, or use of compliant extracellular matrices--increases the k(OFF) of the focal adhesion protein zyxin. In contrast, the k(OFF) of another adhesion protein, vinculin, remains unchanged after tension dissipation. Mathematical models also demonstrate that these force-dependent increases in zyxin's k(OFF) that occur over seconds are sufficient to quantitatively predict large-scale focal adhesion disassembly that occurs physiologically over many minutes. These findings demonstrate that the molecular binding kinetics of some, but not all, focal adhesion proteins are sensitive to mechanical force, and suggest that force-dependent changes in this biophysical parameter may govern the supramolecular events that underlie focal adhesion remodeling in living cells.
Systemically Administered TLR7/8 Agonist and Antigen-Conjugated Nanogels Govern Immune Responses against Tumors (2022)

The generation of specific humoral and cellular immune responses plays a pivotal role in the development of effective vaccines against tumors. Especially the presence of antigen-specific, cytotoxic T cells influences the outcome of therapeutic cancer vaccinations. Different strategies, ranging from delivering antigen-encoding mRNAs to peptides or full antigens, are accessible but often suffer from insufficient immunogenicity and require immune-boosting adjuvants as well as carrier platforms to ensure stability and adequate retention. Here, we introduce a pH-responsive nanogel platform as a two-component antitumor vaccine that is safe for intravenous application and elicits robust immune responses <i>in vitro</i> and <i>in vivo</i>. The underlying chemical design allows for straightforward covalent attachment of a model antigen (ovalbumin) and an immune adjuvant (imidazoquinoline-type TLR7/8 agonist) onto the same nanocarrier system. In addition to eliciting antigen-specific T and B cell responses that outperform mixtures of individual components, our two-component nanovaccine leads in prophylactic and therapeutic studies to an antigen-specific growth reduction of different tumors expressing ovalbumin intracellularly or on their surface. Regarding the versatile opportunities for functionalization, our nanogels are promising for the development of highly customized and potent nanovaccines.
ChemInform Abstract: Zeolites as Base Catalysts: Condensation of Benzaldehyde Derivatives with Activated Methylenic Compounds on Germanium‐Substituted Faujasite. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.