gebhart/patrepeval huggingface dataset:
Factors Governing Selectivity of Dopamine Receptor Binding Compounds for D2R and D3R Subtypes (2021)

Targeting the D3 dopamine receptor (D3R) is a promising pharmacotherapeutic strategy for the treatment of many disorders. The structure of the D3R is similar to the D2 dopamine receptor (D2R), especially in the transmembrane spanning regions that form the orthosteric binding site, making it difficult to identify D3R selective pharmacotherapeutic agents. Here, we examine the molecular basis for the high affinity D3R binding and D3R vs D2R binding selectivity of substituted phenylpiperazine thiopheneamides. We show that removing the thiophenearylamide portion of the ligand consistently decreases the affinity of these ligands at D3R, while not affecting their affinity at the D2R. Our long (>10 μs) molecular dynamics simulations demonstrated that both dopamine receptor subtypes adopt two major conformations that we refer to as closed or open conformations, with D3R sampling the open conformation more frequently than D2R. The binding of ligands with conjoined orthosteric-allosteric binding moieties causes the closed conformation to populate more often in the trajectories. Also, significant differences were observed in the extracellular loops (ECL) of these two receptor subtypes leading to the identification of several residues that contribute differently to the ligand binding for the two receptors that could potentially contribute to ligand binding selectivity. Our observations also suggest that the displacement of ordered water in the binding pocket of D3R contributes to the affinity of the compounds containing an allosteric binding motif. These studies provide a better understanding of how a bitopic mode of engagement can determine ligands that bind selectively to D2 and D3 dopamine receptor subtypes.
Tri-gate bulk CMOS technology for improved SRAM scalability (2010)

A simple approach for manufacturing quasi-planar tri-gate bulk MOSFET structures is demonstrated and shown to be effective for reducing variation in 6T-SRAM read and write margins, in an early 28nm CMOS technology. With optimization of the pocket implant doses, quasi-planar bulk CMOS technology can facilitate voltage scaling. It also provides a means to achieve high yield with a notch-less 6T-SRAM cell layout, to facilitate area scaling.
Relaxation of scratch-induced surface deformation in silicate glasses: Role of densification and shear flow in lateral indentation experiments (2018)

Similar to normal indentation studies, structural compaction and shear flow occur also in the lateral deformation of glass surfaces through scratching. Here, we apply instrumented indentation with tangential displacement in order to study the elastic-plastic regime of scratch-deformation on silica, borosilicate and soda lime silicate glasses. We adopt the protocol of volume recovery analysis by high-temperature annealing to determine variations in geometry and volume of the scratch groove before and after the release of scratch-induced densification. While very similar relative recovery behavior is found for both normal indentation and scratch testing, inherent differences occur in the absolute presence of deformation modes across all three types of glass. In particular, caused by shear deformation at the apex of the employed Berkovich scratch tip, pronounced material pile-up occurs in scratching for normal loads which are about one order of magnitude below reference experiments of normal indentation. This leads to an increase in the effective friction coefficient and a non-trivial correlation between the scratch hardness and the normal hardness of glasses.
Immunochemistry and polypeptide composition of hepatitis B core antigen (HB/sub c/ Ag). [/sup 125/I tracer techniques] (1977)

Core particles were isolated from a nuclear extract of a hepatitis B-infected liver, labeled with /sup 125/I by using chloramine-T and further purified by rate zonal sedimentation on sucrose gradients. Iodinated HB/sub c/ Ag was used as a ligand in a sensitive double-antibody radioimmunoprecipitation (RIP) assay for antibody to HB/sub c/ Ag. The specificity of the RIP reaction was evaluated using defined anti-HB/sub c/ sera and paired sera from six well-documented cases of hepatitis B infection. The polypeptide composition of the iodinated antigen was examined by SDS-polyacrylamide gel electrophoresis of solubilized complexes of /sup 125/I-HB/sub c/ Ag and anti-HB/sub c/. Two major polypeptides with apparent m.w. of 17,000 and 35,000 daltons were observed and designated as cP-1 and cP-2, respectively.
The Second-Generation Exportin-1 Inhibitor KPT-8602 Demonstrates Potent Activity against Acute Lymphoblastic Leukemia (2016)

<b>Purpose:</b> Human exportin-1 (XPO1) is the key nuclear-cytoplasmic transport protein that exports different cargo proteins out of the nucleus. Inducing nuclear accumulation of these proteins by inhibiting XPO1 causes cancer cell death. First clinical validation of pharmacological inhibition of XPO1 was obtained with the Selective Inhibitor of Nuclear Export (SINE) compound selinexor (KPT-330) demonstrating activity in phase-II/IIb clinical trials when dosed 1 to 3 times weekly. The second-generation SINE compound KPT-8602 shows improved tolerability and can be dosed daily. Here, we investigate and validate the drug-target interaction of KPT-8602 and explore its activity against acute lymphoblastic leukemia (ALL).<b>Experimental Design:</b> We examined the effect of KPT-8602 on XPO1 function and XPO1-cargo as well as on a panel of leukemia cell lines. Mutant XPO1 leukemia cells were designed to validate KPT-8602's drug-target interaction. <i>In vivo</i>, anti-ALL activity was measured in a mouse ALL model and patient-derived ALL xenograft models.<b>Results:</b> KPT-8602 induced caspase-dependent apoptosis in a panel of leukemic cell lines <i>in vitro</i> Using CRISPR/Cas9 genome editing, we demonstrated the specificity of KPT-8602 for cysteine 528 in the cargo-binding groove of XPO1 and validated the drug target interaction. <i>In vivo</i>, KPT-8602 showed potent anti-leukemia activity in a mouse ALL model as well as in patient-derived T- and B-ALL xenograft models without affecting normal hematopoiesis.<b>Conclusions:</b> KPT-8602 is highly specific for XPO1 inhibition and demonstrates potent anti-leukemic activity supporting clinical application of the second-generation SINE compound for the treatment of ALL. <i>Clin Cancer Res; 23(10); 2528-41. ©2016 AACR</i>.
Packet Scheduling Algorithm to Improve Throughput and Fairness in SDM System Using Adaptive Antenna Array (2006)

This paper investigates several downlink packet scheduling algorithms in OFDM based systems for space division multiplexing (SDM) with adaptive antenna array beamforming. The packet scheduling algorithm, which generates directional beams toward accessing users in accordance with the priority based on received signal-to-interference plus noise power ratio (SINR) have been proposed. However, the algorithm can generate few directional beams due to the increase of inter beam interference. As a result, the improvement of overall capacity is limited. In this paper, we propose an algorithm to increase total throughput by increasing the number of directional beams. In our algorithm, difference of angle and interference among directional beams are considered. It is shown that the proposed algorithm can increase the sector throughput by 13 % as compared to the conventional SINR-priority based algorithm. Moreover, we investigate the effect to take into account the channel quality and waiting time of each user in the proposed algorithm from the viewpoint of the sector throughput and the fairness of transmission slot assignment probability. Simulation results show that the proposed algorithm with taking into account the received SINR averaged over the scheduled users improves the sector throughput by 5-10% as compared to the original proposed algorithm. It is also shown that, additionally taking into account the waiting time of the users, although the sector throughput is degraded by 12%, the number of users who have the transmission slot assignment probability of less than 0.1 is reduced by 26% compared to the original proposed algorithm
Location and topology of the fundamental gap in photonic crystals (2021)

The fundamental, or first, band gap is of unmatched importance in the study of photonic crystals. Here, we address precisely where this gap can be opened in the band structure of three-dimensional photonic crystals. Although strongly constrained by symmetry, this problem cannot be addressed directly with conventional band-symmetry analysis due to the existence of a photonic polarization vortex at zero frequency. We develop an approach for overcoming the associated symmetry singularity by incorporating fictitious, auxiliary longitudinal modes. Our strategy also enables us to extend recent developments in symmetry-based topological analysis to the fundamental gap of three-dimensional photonic crystals. Exploiting this, we systematically study the topology of the minimal fundamental gaps. This reveals the existence of topological gap-obstructions that push the fundamental gap higher than what a conventional analysis would suggest. Our work demonstrates that topology can play a crucial role in the opening of the fundamental photonic gap and informs future theoretical and experimental searches for conventional and topological band gaps in three-dimensional photonic crystals.
S49 Cells Endogenously Express Subtype 2 Somatostatin Receptors Which Couple to Increase Protein Tyrosine Phosphatase Activity in Membranes and Down-regulate Raf-1 Activity In Situ (1997)

S49 cells expressed type 2 somatostatin receptors (sstr2) by immunoblotting. Analysis by reverse transcription and polymerase chain reaction (RT-PCR) methodologies showed that S49 cells express predominantly sstr2A and sstr2B mRNAs; other subtypes were either not detected, in the case of sstr1, sstr3, sstr4, or variably detected, in the case of sstr5. No mutations were present in S49 cells at codon 12, 13, or 61 of the N-, K-, or H-ras genes. Nevertheless, randomly growing S49 cells contained Raf-1 activity by specific immune complex kinase assays. Treatment of S49 cells with somatostatin transiently inactivated the basal activity of Raf-1, but not that of B-Raf. Addition of somatostatin plus guanyl-5'-yl imidodiphosphate (GMPPNP) to S49 membranes stimulated PTPase activity. The concentration dependence for stimulation of PTPase activity correlated with high affinity binding of [125I-Tyr11]somatostatin-14. Both the effect of somatostatin to stimulate PTPase activity and to inactivate Raf-1 were abrogated by PTx. PTPase activity stimulated by somatostatin plus GMPPNP was recovered in a peak of high apparent M(r) (670,000) after solubilisation with Triton X-100 and Superose 6 chromatography. Furthermore, addition of activated, brain G alpha i/o subunits to fractions from control membranes stimulated PTPase activity in the high M(r) peak. Thus, S49 membranes contain a G-protein regulated PTPase (PTPase-G), and PTPase-G in these cells may reside in a high molecular weight complex.
Chain contribution to the Seebeck coefficient inYBa2Cu3O7−δ (1995)

Measurements of the Seebeck coefficient \ensuremath{\alpha}(T) and the resistivity R(T) of polycrystalline ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7\mathrm{\ensuremath{-}}\mathrm{\ensuremath{\delta}}}$ quenched from different temperatures ${\mathit{T}}_{\mathit{q}}$ and of polycrystalline (${\mathrm{Y}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{Ca}}_{\mathit{x}}$)(${\mathrm{Ba}}_{2\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{La}}_{\mathit{x}}$)${\mathrm{Cu}}_{3}$${\mathrm{O}}_{6.96\ifmmode\pm\else\textpm\fi{}0.01}$ were made to distinguish the contributions to \ensuremath{\alpha}(T) from the Cu(1)O chains and the ${\mathrm{CuO}}_{2}$ sheets. The ${\mathrm{CuO}}_{2}$ sheets give a positive contribution to \ensuremath{\alpha}(T) that is composed of a weakly temperature-dependent part ${\mathrm{\ensuremath{\alpha}}}_{0}$ that decreases sensitively with increasing oxidation and an enhancement part \ensuremath{\delta}\ensuremath{\alpha} that gives a broad maximum to \ensuremath{\alpha}(T) at a ${\mathit{T}}_{\mathrm{max}}$\ensuremath{\approxeq}140 \ifmmode^\circ\else\textdegree\fi{}C. These two features together have been shown to distinguish the superconductive compositions from the parent and overdoped compositions in other copper-oxide supeconductors. In fully oxidized ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{6.96}$, the contribution to \ensuremath{\alpha}(T) from the ${\mathrm{CuO}}_{2}$ sheets is obscured by a dominant, competitive negative contribution to \ensuremath{\alpha}(T) from the chains that has a similar, but negative, \ensuremath{\delta}\ensuremath{\alpha} enhancement.
Using force data to self-pace an instrumented treadmill and measure self-selected walking speed (2019)

Abstract Background Self-selected speed is an important functional index of walking. A self-pacing controller that reliably matches walking speed without additional hardware can be useful for measuring self-selected speed in a treadmill-based laboratory. Methods We adapted a previously proposed self-pacing controller for force-instrumented treadmills and validated its use for measuring self-selected speeds. We first evaluated the controller’s estimation of subject speed and position from the force-plates by comparing it to those from motion capture data. We then compared five tests of self-selected speed. Ten healthy adults completed a standard 10-meter walk test, a 150-meter walk test, a commonly used manual treadmill speed selection test, a two-minute self-paced treadmill test, and a 150-meter self-paced treadmill test. In each case, subjects were instructed to walk at or select their comfortable speed. We also assessed the time taken for a trial and a survey on comfort and ease of choosing a speed in all the tests. Results The self-pacing algorithm estimated subject speed and position accurately, with root mean square differences compared to motion capture of 0.023 m s −1 and 0.014 m, respectively. Self-selected speeds from both self-paced treadmill tests correlated well with those from the 10-meter walk test ( R &gt; 0.93, p &lt; 1 × 10 −13 ). Subjects walked slower on average in the self-paced treadmill tests (1.23 ± 0.27 m s −1 ) than in the 10-meter walk test (1.32 ± 0.18 m s −1 ) but the speed differences within subjects were consistent. These correlations and walking speeds are comparable to those from the manual treadmill speed selection test ( R = 0.89, p = 3 × 10 −11 ; 1.18 ± 0.24 m s −1 ). Comfort and ease of speed selection were similar in the self-paced tests and the manual speed selection test, but the self-paced tests required only about a third of the time to complete. Our results demonstrate that these self-paced treadmill tests can be a strong alternative to the commonly used manual treadmill speed selection test. Conclusions The self-paced force-instrumented treadmill well adapts to subject walking speed and reliably measures self-selected walking speeds. We provide the self-pacing software to facilitate use by gait researchers and clinicians.
Study of pellet formation of filamentous fungi Rhizopus oryzae using a multiple logistic regression model (2007)

Fungal pellet formation is an important topic of fermentation research. It has been reported that many factors such as agitation, medium nutrients, pH, polymer additives, and inoculum size influence the formation of fungal pellets. However, a few studies on the effects of all of these factors on fungal pellet formation have been reported. This paper conducted a comprehensive investigation using a completely randomized design (CRD) on a filamentous fungus, Rhizopus oryzae NRRL 395, in order to discover the effects of the above factors on fungal pellet formation. In addition, other factors, such as addition of biodegradable polymers and spore storage time that have not been reportedly studied were examined and their effects on pellet formation were investigated. A multiple logistic regression model was established to predict the probability of pellet formation using the above factors and their interactions as predictor variables. Model building and diagnostics were obtained using the Statistical Analysis System (SAS 9.0) program. The model developed in this study can be used to predict the pellet formation of other R. oryzae strains as well.
Time- and angle-resolved photoemission spectroscopy with optimized high-harmonic pulses using frequency-doubled Ti:Sapphire lasers (2014)

Time- and angle-resolved photoemission spectroscopy (trARPES) using femtosecond extreme ultraviolet high harmonics has recently emerged as a powerful tool for investigating ultrafast quasiparticle dynamics in correlated-electron materials. However, the full potential of this approach has not yet been achieved because, to date, high harmonics generated by 800 nm wavelength Ti:Sapphire lasers required a trade-off between photon flux, energy and time resolution. Photoemission spectroscopy requires a quasi-monochromatic output, but dispersive optical elements that select a single harmonic can significantly reduce the photon flux and time resolution. Here we show that 400 nm driven high harmonic extreme-ultraviolet trARPES is superior to using 800 nm laser drivers since it eliminates the need for any spectral selection, thereby increasing photon flux and energy resolution to <150 meV while preserving excellent time resolution of about 30 fs.
415/610GHz fT/fMAX SiGe HBTs Integrated in a 45nm PDSOI BiCMOS process (2022)

High Performance (HP) SiGe HBTs integrated in a 45nm PDSOI BiCMOS process with peak $f_{T}/f_{MAX}415/610$ GHz are reported here. These are the highest f <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MAX</inf> silicon devices demonstrated in any SOI platform. Measured $f_{T}/f_{MAX}$ at transmission line metal level for this HBT is 388/600GHz which gives significant performance benefit over CMOS in RF circuit designs. HBTs are integrated in a hybrid region on the wafer formed by removing the SOI and BOX with an epitaxial growth and planarization to form a co-planar top surface with the SOI. In addition to the HP HBTs and CMOS, the process also integrates a medium breakdown HBT with $f_{T}/BV_{CBO} =270$ GHz/5.6V and RF N/P FETs with $f_{T}/f_{MAX} =270/355$ GHz and 240/295 GHz. An early CML RO design has a gate delay of 1.76ps. Simple cascode power cells show > 23 dB gain at 70GHz and > 18 dB gain at 100GHz.
Nickel Overlayers Modify Precursor Gases To Pattern Forests of Carbon Nanotubes (2017)

We analyzed the effect of nickel overlayers positioned in close proximity (bridges) or in contact (stencils) with the catalytic layer on the growth of vertically aligned carbon nanotubes (VACNTs) using thermal chemical vapor deposition (CVD). We studied the physical–chemical mechanisms, namely, the interaction of the overlayer with the gases and with the catalyst. We demonstrate that nickel inhibits CNT growth by adsorbing carbon to form graphene and by interacting with the gas precursors, leading to their modification into species that do not nucleate and grow CNTs. We demonstrate that the effect of the nickel bridge extends to the length of its boundary layer. We tested overlayer patterns and showed that the patterns were replicated during CNT growth. This facile method is a valid alternative to pattern CNT forests without the need for complex lithography and lift-off of the catalyst in applications where lithographic precision is not required.
Butterfly Wing–Inspired Nanotechnology (2012)

This chapter discusses the butterfly-inspired nanotechnology as a good example to demonstrate how the hierarchical architecture of a butterfly wing affects the photonic function at nanoscale, how natural nanostructures inspire the design and fabrication of biomimetic photonic structures, and what the current and future applications of the butterfly wing–inspired nanotechnology. Most of the biomimetic hierarchical structures use natural butterfly wings as a template and are fabricated by various deposition and synthesis methods, such as chemical vapor deposition, solution casting, atomic layer deposition, soaking process, conformal-evaporated-film-by-rotation, sol-gel process, hydrothermal process, ultrasonication, and molding lithography. Although the silica wing is harder and more brittle than the natural butterfly wing, a pair of tweezers can more easily handle the silica wing. Laser direct-write in combination with particle-assisted laser nanofabrication, which can selectively and locally pattern, has demonstrated the potential to fabricate photonic crystal structures mimicking the natural butterfly wing scale.
Oxidative Stress in Dilated Cardiomyopathy Caused byMYBPC3Mutation (2015)

Cardiomyopathies can result from mutations in genes encoding sarcomere proteins including MYBPC3, which encodes cardiac myosin binding protein-C (cMyBP-C). However, whether oxidative stress is augmented due to contractile dysfunction and cardiomyocyte damage in MYBPC3-mutated cardiomyopathies has not been elucidated. To determine whether oxidative stress markers were elevated in MYBPC3-mutated cardiomyopathies, a previously characterized 3-month-old mouse model of dilated cardiomyopathy (DCM) expressing a homozygous MYBPC3 mutation (cMyBP-C((t/t))) was used, compared to wild-type (WT) mice. Echocardiography confirmed decreased percentage of fractional shortening in DCM versus WT hearts. Histopathological analysis indicated a significant increase in myocardial disarray and fibrosis while the second harmonic generation imaging revealed disorganized sarcomeric structure and myocyte damage in DCM hearts when compared to WT hearts. Intriguingly, DCM mouse heart homogenates had decreased glutathione (GSH/GSSG) ratio and increased protein carbonyl and lipid malondialdehyde content compared to WT heart homogenates, consistent with elevated oxidative stress. Importantly, a similar result was observed in human cardiomyopathy heart homogenate samples. These results were further supported by reduced signals for mitochondrial semiquinone radicals and Fe-S clusters in DCM mouse hearts measured using electron paramagnetic resonance spectroscopy. In conclusion, we demonstrate elevated oxidative stress in MYPBC3-mutated DCM mice, which may exacerbate the development of heart failure.
Tight-binding molecular-dynamics study of phonon anharmonic effects in silicon and diamond (1990)

The anharmonic effects on phonons in silicon and diamond have been studied by molecular-dynamics simulations using an empirical tight-binding Hamiltonian. One-phonon spectral intensities of the zone-center and zone-boundary (X) modes have been calculated through the Fourier transform of the velocity-velocity correlation functions. This scheme allows a quantitative and nonperturbative study of phonon frequency shift and phonon linewidth as a function of temperature. The results obtained are in good agreement with experimental data.