gebhart/patrepeval huggingface dataset:
Binding and fusion of Autographa californica nucleopolyhedrovirus to cultured insect cells. (1997)

Binding of baculoviruses to insect cells and fusion of the virus envelope to cell membranes are early events suggested to be affected by baculovirus enhancins. The binding of Autographa californica nucleopolyhedrovirus (AcMNPV) to the Spodoptera frugiperda cell line Sf21 and the fusion of the virus envelope to cell membranes were characterized. Virus binding assays demonstrated that AcMNPV budded virus (BV) bound to specific binding sites on Sf21 cells with an avidity of 2.3 x 10(10) M(-1). The cells displayed 3.1 x 10(3) specific binding sites per cell in a confluent monolayer. In addition, the effects of pH, buffer composition and cation concentration on the binding were examined. Using a fluorescent probe (R18) and fluorescence microscopy, the fusion of AcMNPV BV envelope to the cell membrane was directly visualized in living cells. It has been reported that Trichoplusia ni nucleopolyhedrovirus enters Sf21 cells by membrane fusion at the cell surface; however, the present studies confirmed the well established concept that adsorptive endocytosis is the major entry pathway for baculovirus BV infection. Membrane fusion kinetics and fluorescence microscopy demonstrated and verified that the envelope-cell membrane fusion was triggered by acidification. The effect of a T. ni granulovirus enhancin on virus binding and membrane fusion was examined, and no increase in activity was observed.
4‐4: Invited Paper: An End‐To‐End Virtual Reality Live Streaming Solution (2017)

In this paper, we present an end‐to‐end solution for Virtual Reality Live Streaming of live events such as sports and concerts in near real‐time. The technologies and innovations are in domains such as capture, production, distribution, and end‐user consumption, and also in the interfaces. The solution, called Intel True VR, is ground breaking because the end result is a brand new media and a completely new viewing experience for fans at home. VR live streaming, powered by solutions such as True VR, are poised to be a significant portion of the Immersive Media market.
A Point of Inflection and Reflection on Systems Chemical Biology (2019)

For the past several decades, chemical biologists have been leveraging chemical principles for understanding biology, tackling disease, and biomanufacturing, while systems biologists have holistically applied computation and genome-scale experimental tools to the same problems. About a decade ago, the benefit of combining the philosophies of chemical biology with systems biology into systems chemical biology was advocated, with the potential to systematically understand the way small molecules affect biological systems. Recently, there has been an explosion in new technologies that permit massive expansion in the scale of biological experimentation, increase access to more diverse chemical space, and enable powerful computational interpretation of large datasets. Fueled by these rapidly increasing capabilities, systems chemical biology is now at an inflection point, poised to enter a new era of more holistic and integrated scientific discovery. Systems chemical biology is primed to reveal an integrated understanding of fundamental biology and to discover new chemical probes to comprehensively dissect and systematically understand that biology, thereby providing a path to novel strategies for discovering therapeutics, designing drug combinations, avoiding toxicity, and harnessing beneficial polypharmacology. In this Review, we examine the emergence of new capabilities driving us to this inflection point in systems chemical biology, and highlight holistic approaches and opportunities that are arising from integrating chemical biology with a systems-level understanding of the intersection of biology and chemistry.
Phase Retrieval in Optical Imaging (2017)

The problem of phase retrieval, namely – the recovery of a function given the magnitude of its Fourier transform - arises in various fields of science and engineering, including electron microscopy, crystallography, astronomy, and optical imaging. Due to the loss of Fourier phase information, this problem is generally ill-posed. We review several modern methods for treating the phase retrieval problem and illustrate their use in optical imaging.
Expression of the myc proto-oncogenes in developing human fetal brain. (1990)

We have analysed c-myc, N-myc and L-myc gene expression in developing human fetal brain by Northern hybridization, RNAase protection and in situ hybridization. The unique zonal organization of the developing fetal brain allows a particularly good assessment of the coupling of myc gene expression to cell proliferation and differentiation in vivo. By Northern and in situ hybridization, L-myc as well as c-myc and N-myc transcripts in the brain were found in the post-mitotic cortical and intermediate layers, as well as in the mitotically active layers containing the neuroepithelial precursor cells. Consistent results were also obtained for L-myc using RNAase protection analysis. Both the 3.6 and 3.8kb forms of the L-myc mRNA, resulting from alternative splicing of intron I, were detected in layers of neuroectodermal origin, but not in the meninges or choroid plexus. We also extended L-myc expression and splicing analyses to other developing human fetal tissues. L-myc mRNA was expressed in several other fetal tissues, particularly in fetal skin. Predominantly intron I containing L-myc mRNA was observed in fetal striated and cardiac muscle. Thus, L-myc is expressed in a wider spectrum of developing tissues than previously known. Our findings also, show that L-myc as well as N-myc and c-myc expression is uncoupled from cell division in developing brain.
A simple high-speed digital receiver (2002)

Summary form only given. Here we demonstrate a simple optical receiver that overcomes the bit rate limits due to post-detection amplification with the use of a high current p-i-n photodiode and an erbium-doped fiber amplifier (EDFA) to yield over 1.9 volts peak-to-peak (p-p) output directly form the photodetector, in contrast to a 150-mV output previously reported.
Abstract 4352: Discovery of the first cell-active inhibitors of poly(ADP Ribose) glycohydrolase through high-throughput screening and computational approaches (2016)

Abstract DNA repair is a critical process for the survival and normal proliferation of healthy cells. However, given the enhanced levels of cellular stress and genomic instability, these repair processes are even more critical to the survival of malignant cells, where rates of DNA damage are considerably increased. Given this, inhibitors of DNA damage repair have seen a resurgence of interest in recent years in an effort to exploit tumour cell vulnerabilities. One such example of this approach has resulted in the recent approval of the PARP inhibitor olaparib (Lynparza™) for women with advanced ovarian cancer associated with defective BRCA genes. Olaparib acts against the poly(ADP-ribose)polymerase (PARP) enzymes, more recently re-defined as the ARTD (Diphtheria toxin-like human ADP-ribosyltransferase) enzyme class. Whilst PARP is widely known to play critical and well-understood roles in DNA repair, poly(ADP ribose) glycohydrolase (PARG) is less well known but equally essential for effective DNA repair, degrading PAR chains and facilitating effective DNA repair. However, its inhibition may offer several key advantages over PARP inhibition. Most critically, whilst there are 18 isoforms, there exists only a single PARG protein, offering a specific point of therapeutic intervention. However, due to the open nature of the PARG binding cleft and the nature of the binding site, this protein has been considered to be difficult to inhibit with small, drug-like small molecules, particularly in the cellular context. This poster will describe our efforts to overcome these challenges against this challenging target and report our early successes achieved through innovative computational chemistry strategies. These efforts have delivered several credible, drug-like startpoints for further medicinal chemistry optimisation. Citation Format: Bohdan Waszkowycz, Dominic James, Steven Durant, Nicola Hamilton, Cliff Jones, Stuart Jones, Allan Jordan, Alan Lau, Alison MGonagle, Mark O’Connor, Kate Smith, Alex Stowell, Julie Tucker, Ian Waddell, Donald Ogilvie. Discovery of the first cell-active inhibitors of poly(ADP Ribose) glycohydrolase through high-throughput screening and computational approaches. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4352.
Development of Hexadecyloxypropyl Tenofovir (CMX157) for Treatment of Infection Caused by Wild-Type and Nucleoside/Nucleotide-Resistant HIV (2010)

CMX157 is a lipid (1-0-hexadecyloxypropyl) conjugate of the acyclic nucleotide analog tenofovir (TFV) with activity against both wild-type and antiretroviral drug-resistant HIV strains, including multidrug nucleoside/nucleotide analog-resistant viruses. CMX157 was consistently >300-fold more active than tenofovir against multiple viruses in several different cell systems. CMX157 was active against all major subtypes of HIV-1 and HIV-2 in fresh human peripheral blood mononuclear cells (PBMCs) and against all HIV-1 strains evaluated in monocyte-derived macrophages, with 50% effective concentrations (EC(50)s) ranging between 0.20 and 7.2 nM. The lower CMX157 EC(50)s can be attributed to better cellular uptake of CMX157, resulting in higher intracellular levels of the active antiviral anabolite, TFV-diphosphate (TFV-PP), inside target cells. CMX157 produced >30-fold higher levels of TFV-PP in human PBMCs exposed to physiologically relevant concentrations of the compounds than did TFV. Unlike conventional prodrugs, including TFV disoproxil fumarate (Viread), CMX157 remains intact in plasma, facilitating uptake by target cells and decreasing relative systemic exposure to TFV. There was no detectable antagonism with CMX157 in combination with any marketed antiretroviral drug, and it possessed an excellent in vitro cytotoxicity profile. CMX157 is a promising clinical candidate to treat wild-type and antiretroviral drug-resistant HIV, including strains that fail to respond to all currently available nucleoside/nucleotide reverse transcriptase inhibitors.
Differential Binding of Somatostatin Agonists to Somatostatin Receptors in Brain and Adenohypophysis (1987)

In order to improve our understanding of the ligand specificity of somatostatin (SRIF) receptors in pituitary and brain, and to identify analogs that bind to one type exclusively, we compared several new SRIF analogs for competitive binding to pituitary and cerebral cortex membranes. Binding of [125I-Tyr11]SRIF to hypophysis and brain was of high affinity [KD = 0.76 nM (0.2-1.3) and 0.37 nM(0.1-0.8), mean (95% confidence limits)] and was characteristic of binding to one class of sites in both tissues. Competition by several SRIF analogs for such radioligand binding demonstrated that ligand specificity of adenohypophysial receptors was distinctly different from that of cerebral cortex. Two cyclic octapeptides (sequence; see text) bound to pituitary SRIF receptors with high affinity [Ki = 0.85 nM (0.5-1.2) and 0.35 nM (-0.3-0.9)] and were potent inhibitors of GH secretion from primary cultured pituitary cells [EC50 = 0.009 nM (0-0.02) and 0.017 nM (0.01-0.02), respectively]. However, these selective peptides did not compete (Ki much greater than 1 microM) for radioligand binding to brain. Amidation of the C-terminal end appeared to strikingly alter brain SRIF receptor recognition of the substituted ligand. Indeed, such amidation of the parent peptide, (sequence; see text) resulted in a reduced ability to displace labeled ligand from brain sites [Ki = 165.3 nM (47.6-282.9) to 842.2 nM (603.9-1,081)] but did not affect competition for pituitary receptors. Our results indicate that anterior pituitary SRIF receptors (SRIFa) have ligand specificities which are clearly different from those of their brain counterparts (SRIFb).(ABSTRACT TRUNCATED AT 250 WORDS)
Broadband energy-efficient optical modulation by hybrid integration of silicon nanophotonics and organic electro-optic polymer (2015)

Silicon-organic hybrid integrated devices have emerging applications ranging from high-speed optical interconnects to photonic electromagnetic-field sensors. Silicon slot photonic crystal waveguides (PCWs) filled with electro-optic (EO) polymers combine the slow-light effect in PCWs with the high polarizability of EO polymers, which promises the realization of high-performance optical modulators. In this paper, a broadband, power-efficient, low-dispersion, and compact optical modulator based on an EO polymer filled silicon slot PCW is presented. A small voltage-length product of V<sub>&pi;</sub>×L=0.282V×mm is achieved, corresponding to an unprecedented record-high effective in-device EO coefficient (r<sub>33</sub>) of 1230pm/V. Assisted by a backside gate voltage, the modulation response up to 50GHz is observed, with a 3-dB bandwidth of 15GHz, and the estimated energy consumption is 94.4fJ/bit at 10Gbit/s. Furthermore, lattice-shifted PCWs are utilized to enhance the optical bandwidth by a factor of ~10X over other modulators based on non-band-engineered PCWs and ring-resonators.
The Anatomical Relationship Between the Dorsal Cutaneous Branch of the Ulnar Nerve and the Ulnar Styloid Process with Variations in Forearm Position (2016)

We recommend making a skin incision on the ulnar side around the styloid process with the forearm in supination or neutral position was another method to avoid injury of DCBUN.
SU‐E‐T‐346: Validation of Beam Accuracy of a Gated Spot‐Scanning Proton Therapy System with Real‐Time Tumor‐Tracking at Hokkaido University (2014)

Purpose: At Hokkaido University, we have developed a gated spot scanning proton beam therapy system with real‐time tumor‐tracking under collaborative work with Hitachi Ltd. This system has the ability to gate proton beams from the synchrotron, turning the beam on only when the actual positions of inserted fiducial markers monitored by two fluoroscopic X‐ray systems are within the planned positions [Shirato, 2012]. In this research, we validated the accuracy of the proton beams while utilizing external gating signals. Methods: The accuracy of spot positions, spot dose, absolute dose at the center of the SOBP, and range were measured while utilizing external gating signals. The following external gating signals were generated by an arbitrary waveform generator: (1) ON at all times (without gating), (2) an OFF period of 4 s followed by an ON period of 1 s, (3) two ON periods of 0.5 s with a 0.15 s OFF interval, (4) signals recorded during the treatment of real‐time tumor‐tracking X‐ray therapy in Hokkaido University. The spot positions and spot dose were measured by beam monitors in the nozzle. The ranges were measured with a multi‐layer ion chamber made by Hitachi Ltd. The absolute dose was measured with a Farmer ionization chamber and a RFA300 water phantom system. Results: The maximum error of the beam position in the isocenter plane was 0.8 mm without the gating signal and 1.0 mm with the gating signal. The maximum error of the spot dose was 0.0029 MU, below the criterion of 0.0032 MU. The maximum error of the absolute dose was 0.4% and the maximum variation of the range was 0.1 mm. Conclusion: It was confirmed with measurements of the beam that the accuracy of the proton beam met the criteria with external gating signals. This research was supported by the Cabinet Office, Government of Japan and the Japan Society for the Promotion of Science (JSPS) through the Funding Program for World‐Leading Innovative R&amp;D on Science and Technology (FIRST Program), initiated by the Council for Science and Technology Policy (CSTP).
Sparsity-cognizant overlapping co-clustering for behavior inference in social networks (2010)

Co-clustering can be viewed as a two-way (bilinear) factorization of a large data matrix into dense/uniform and possibly overlapping sub-matrix factors (co-clusters). This combinatorially complex problem emerges in several applications, including behavior inference tasks encountered with social networks. Existing co-clustering schemes do not exploit the fact that overlapping factors are often sparse, meaning that their dimension is considerably smaller than that of the data matrix. Based on plaid models which allow for overlapping submatrices, the present paper develops a sparsity-cognizant overlapping co-clustering (SOC) approach. Numerical tests demonstrate the ability of the novel SOC scheme to globally detect multiple overlapping co-clusters, outperforming the original plaid model algorithms which rely on greedy search and ignore sparsity.
Comparison of Figures-of-Merit of N and P SiC Schottky Diodes with Ni Schottky Contacts at High Temperatures (2002)

The current–voltage characteristics and the figures-of-merit [(VBD)2/Ron] and [Iforward,2V/Ireverse,100V] of N and P type SiC Schottky diodes are compared in a temperature range of 300–700 K. While the FOM [(VBD)2/Ron] of N-type diodes are always greater than that of P-type diodes due to the significant reduction in the breakdown voltage of P-type diodes with temperature, the FOM [Iforward,2V/Ireverse,200V] for P-diodes is higher than that for N- diodes, since the reverse leakage current of the P-diodes is considerably lower than that of N-diodes, due to the higher barrier height of Ni Schottky contacts on P-type SiC. Also, it is observed that the P-diodes have a lower on-resistance at elevated temperatures than N-diodes, due to the significant increase in hole concentration with temperature. All the above results were obtained from theoretical simulations using ATLAS device modeling software and MathCAD.
Ability-Based Design (2011)

Current approaches to accessible computing share a common goal of making technology accessible to users with disabilities. Perhaps because of this goal, they may also share a tendency to centralize disability rather than ability. We present a refinement to these approaches called ability-based design that consists of focusing on ability throughout the design process in an effort to create systems that leverage the full range of human potential. Just as user-centered design shifted the focus of interactive system design from systems to users, ability-based design attempts to shift the focus of accessible design from disability to ability. Although prior approaches to accessible computing may consider users’ abilities to some extent, ability-based design makes ability its central focus. We offer seven ability-based design principles and describe the projects that inspired their formulation. We also present a research agenda for ability-based design.
Importance of Annealing Step on Dielectric Constant of ZrO2 Layer of MIM Capacitors with Al2O3/ZrO2 and ZrO2/Al2O3 Stack Structures (2021)

Several stack structures such as 1st ZrO2/Al2O3/2nd ZrO2 (ZAZ), 1st TiO2/Al2O3/2nd TiO2 (TAT), and 1st ZrO2/(Ta/Nb)Ox-Al2O3/2nd ZrO2 (ZTNAZ) as insulator of DRAM capacitor with metal-insulator-metal (MIM) structure have been widely investigated [1-4]. ZAZ is one of the most candidate structure because ZrO2 has relatively high-dielectric-constant (high-k) value (>30) and wide band gap (~5.8 eV) [1,2]. An amorphous Al2O3 interlayer acts as blocking layer to suppress the leakage current through the grain boundaries of ZrO2 layer. An annealing process was generally carried out after ZAZ deposition or TiN/ZAZ/TiN fabrication. The effects of annealing step on k-values of 1st ZrO2 and 2nd ZrO2 layers are not fully understood. In this study, we investigate k-values of ZrO2 layer of TiN MIM capacitors with Al2O3/ZrO2 (AZ) and ZrO2/Al2O3 (ZA) insulators fabricated by post-deposition annealing (PDA) after AZ and ZA insulators deposition or post-metallization annealing (PMA) after TiN top electrode (TE-TiN) deposition.
Revealing the quantum nature of a free electron in an attosecond laser pulse (2018)

Free electrons interacting with the frequency comb of an attosecond laser pulse follow intricate quantum dynamics. We present an analytic treatment of the interaction and use it to shape the electron energy spectrum.
Editorial: targeting aberrant hepatic inflammation for treatment of non‐alcoholic steatohepatitis—authors' reply (2022)

LINKED CONTENT This article is linked to Safadi et al papers. To view these articles, visit https://doi.org/10.1111/apt.16664 and https://doi.org/10.1111/apt.16748
ChemInform Abstract: A Novel Series of Matrix Metalloproteinase Inhibitors for the Treatment of Inflammatory Disorders. (1997)

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.
Ultra wide band (UWB) compatibility with IMT-2000: time for a transform or noisy neighbours? (2003)

UWB history and regulation is summarized. Interference impact to 3G is quantified using two alternative methods: coupling loss and 'geometry factor'. To avoid reduction of capacity or coverage of 3G networks some alternative proposals for UWB operating bands are made.
Multi-type Electronic Interactions in Precursor Solutions of Molecular Doped P3HT Polymer (2023)

Spin casting of molecular doped polymer solution mixtures is one of the commonly used methods to obtain conductive organic semiconductor films. In spin-casted films, electronic interaction among the dopant and polymer is one of the crucial factors that dictate the doping efficiency. Here, we investigate excitonic couplings using ultrafast two-dimensional electronic spectroscopy to examine the different types of electronic interaction in ion pairs of the prototype F4TCNQ doped P3HT polymer system in precursor solution mixture for spin-casting. Off-diagonal peaks in 2D spectra clearly establish the excitonic coupling between P3HT+ and F4TCNQ− ions in solution. The observed excitonic coupling is the direct manifestation of Coulombic interaction amongst the ion-pair. The excited state lifetime of F4TCNQ− in ion-pairs shows biexponential decay: 30 fs and 200 fs, which hints towards the presence of heterogeneous population with different interaction strengths. To examine the nature of these different types of interactions in solution mixture, we study the system using molecular dynamics simulations on a fully solvated model employing the generalized Amber force field. We retrieve three dominant interaction modes of F4TCNQ anions with P3HT: side-chain, π-stack and slipped stack. To quantify these interactions, we complement our studies with electronic structure calculations, which reveal the excitonic coupling strengths of: ∼75 cm−1 for side-chain, ∼150 cm−1 for π-π-stack, and ∼69 cm−1 for slipped stack. These various interaction modes provide information on the key geometries of the seed structures in precursor solution mixtures, which may determine the final structures in spin-casted films. The insights gained from our study may guide new strategies to control and ultimately tune the Coulomb interactions in polymer-dopant solutions.