gebhart/patrepeval huggingface dataset:
Interfacial Cavity Filling To Optimize CD4–Mimetic Miniprotein Interactions with HIV-1 Surface Glycoprotein (2013)

Ligand affinities can be optimized by interfacial cavity filling. A hollow (Phe43 cavity) between HIV-1 surface glycoprotein (gp120) and cluster of differentiation 4 (CD4) receptor extends beyond residue phenylalanine 43 of CD4 and cannot be fully accessed by natural amino acids. To increase HIV-1 gp120 affinity for a family of CD4-mimetic miniproteins (miniCD4s), we targeted the gp120 Phe43 cavity with 11 non-natural phenylalanine derivatives, introduced into a miniCD4 named M48 (1). The best derivative, named M48U12 (13), bound HIV-1 YU2 gp120 with 8 pM affinity and showed potent HIV-1 neutralization. It contained a methylcyclohexyl derivative of 4-aminophenylalanine, and its cocrystal structure with gp120 revealed the cyclohexane ring buried within the gp120 hydrophobic core but able to assume multiple orientations in the binding pocket, and the aniline nitrogen potentially providing a focus for further improvement. Altogether, the results provide a framework for filling the interfacial Phe43 cavity to enhance miniCD4 affinity.
Squalamine treatment of human tumors in nu/nu mice enhances platinum-based chemotherapies. (2001)

Squalamine, an antiangiogenic aminosterol, is presently undergoing Phase II clinical trials in cancer patients. To broaden our understanding of the clinical potential for squalamine, this agent was evaluated in nu/nu mouse xenograft models using the chemoresistant MV-522 human non-small cell lung carcinoma and the SD human neuroblastoma lines. Squalamine was studied alone and in combination with either cisplatin or paclitaxel plus carboplatin. Squalamine alone produced a modest MV-522 tumor growth inhibition (TGI) and yielded a TGI with cisplatin that was better than cisplatin alone. Squalamine also significantly enhanced the activity of paclitaxel/carboplatin combination therapy in the MV-522 tumor model. Squalamine similarly improved the effectiveness of cisplatin in producing TGI when screened against the SD human neuroblastoma xenograft. Xenograft tumor shrinkage was seen for the MV-522 tumor in combination treatments including squalamine, whereas no tumor shrinkage was seen when squalamine was omitted from the treatment regimen. To gain a greater understanding of the mechanism by which squalamine inhibited tumor growth in the xenograft studies, in vitro experiments were carried out with vascular endothelial growth factor-stimulated human umbilical vein endothelial cells in culture exposed to squalamine. Squalamine treatment was found to retard two cellular events necessary for angiogenesis, inducing disorganization of F-actin stress fibers and causing a concomitant reduction of detectable cell the surface molecular endothelial cadherin (VE-cadherin). We propose that the augmentation by squalamine of cytotoxicity from platinum-based therapies is attributable to interference by squalamine with the ability of stimuli to promote endothelial cell movement and cell-cell communication necessary for growth of new blood vessels in xenografts after chemotherapeutic injury to the tumor.
Wideband repetition rate tunability of ultrashort pulse generation using MZ-modulator-based flat comb generator and DF-DDF (2008)

We have demonstrated wideband frequency-tunable ultrashort pulse generation using a Mach-Zehnder-modulator-based flat comb generator (MZ-FCG) and a dispersion- flattened dispersion-decreasing fiber. Continuous wave lights were converted to ultraflat comb signals by the MZ-FCG. The comb signals were formed into picosecond pulse trains by chirp compensation, and they are compressed into femtosecond ones by a soliton compression technique. Pulse trains of 200 fs width were successfully generated in a repetition rate range of 5–17 GHz. Our pulse source is very simple configuration and possesses high stability and low timing jitter.
Microwave to millimeter-wave electrodynamic response and applications of semiconductor nanostructures: LDRD project 67025 final report. (2006)

Solid-state lighting (SSL) technologies, based on semiconductor light emitting devices, have the potential to reduce worldwide electricity consumption by more than 10%, which could significantly reduce U.S. dependence on imported energy and improve energy security. The III-nitride (AlGaInN) materials system forms the foundation for white SSL and could cover a wide spectral range from the deep UV to the infrared. For this LDRD program, we have investigated the synthesis of single-crystalline III-nitride nanowires and heterostructure nanowires, which may possess unique optoelectronic properties. These novel structures could ultimately lead to the development of novel and highly efficient SSL nanodevice applications. GaN and III-nitride core-shell heterostructure nanowires were successfully synthesized by metal organic chemical vapor deposition (MOCVD) on two-inch wafer substrates. The effect of process conditions on nanowire growth was investigated, and characterization of the structural, optical, and electrical properties of the nanowires was also performed.
Verification of carrier noise diffusion technique using a zero-sequence voltage at zero-speed drive (2017)

This paper proposes a reducing technique of carrier noise of PWM inverters without increasing the carrier frequency during zero-speed drive of a permanent magnet motor. The feature of the proposed technique is that the frequency component of the carrier noise is diffused by zero-sequence voltage. In particular, the zero-sequence voltage is randomized by the M-sequence signal and added to the voltage references. The proposed technique decides the output range of the zero-sequence voltage by calculating through the relationship of d-axis voltage and q-axis voltage, and adds the random zero-sequence voltage within the above range. Experimental results show the spectra of the carrier noise are diffused when the large zero-sequence voltage is added by using the proposed technique and the period of the M-sequence signal is more than 511. As the result, the carrier noise is reduced by the effect of spectrum whitening.
Moisture-Insensitive Polycarbosilane Films with Superior Mechanical Properties (2012)

We report cross-linked polycarbosilane (CLPCS) films with superior mechanical properties and insensitivity to moisture. CLPCS are prepared by spin-coating and thermal curing of hexylene-bridged disilacyclobutane (DSCB) rings. The resulting films are siloxane-free and hydrophobic, and present good thermal stability and a low dielectric constant of k = 2.5 without the presence of supermicropores and mesopores. The elastic stiffness and fracture resistance of the films substantially exceed those of traditional porous organosilicate glasses because of their unique molecular structure. Moreover, the films show a remarkable insensitivity to moisture attack, which cannot be achieved by traditional organosilicate glasses containing siloxane bonds. These advantages make the films promising candidates for replacing traditional organosilicate glasses currently used in numerous applications, and for use in emerging nanoscience and energy applications that need protection from moisture and harsh environments.
ChemInform Abstract: Synthesis of 1D‐3‐Deoxy‐, 1D‐2,3‐Dideoxy‐, and 1D‐2,3,6‐Trideoxy‐myo‐ inositol 1,4,5‐Trisphosphate from Quebrachitol, Their Binding Affinities, and Calcium Release Activity. (1993)

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.
Abstract C042: Inhibition of Dihydroorotate Dehydrogenase (DHODH) by RP7214 attenuates growth and promotes differentiation of AML cell lines (2019)

Abstract Background: Dihydroorotate dehydrogenase (DHODH), a rate limiting enzyme in pyrimidine synthesis, is overexpressed in certain cancers; blockade of which impedes tumor cell proliferation via cell cycle arrest. RP7214 is a novel and potent DHODH inhibitor that inhibited DHODH activity in enzyme and PHA induced HWB/PBMC proliferation with IC50 and EC50 values of 7.8 &amp; 2.5/0.60 nM respectively. The objective of this study was to evaluate the single-agent activity of RP7214 on AML cell differentiation and growth. Methods: Viability of representative AML cell lines (U937, HL-60, THP-1, and KG-1) following incubation with RP7214 for 72 h as well as rescue in the presence of 300 µM Uridine was determined in an MTT-based assay. For differentiation experiments, THP-1 cells were incubated with RP7214 in complete media for 72 h. RNA was isolated, reverse transcribed to cDNA, and real-time PCR was performed to analyze CD11b gene expression. In addition, cell surface expression of CD11b in THP-1 cells incubated with RP7214 and the effect-reversal in presence of Uridine was evaluated by flow cytometry. Apoptosis and cell cycle were determined following incubation with RP7214 for 72 and 48 h respectively. Results: RP7214 inhibited AML cell proliferation in all the four cell lines tested with GI50 ranging from 2.4 to 7.6 µM. Addition of 300 µM Uridine caused a rightward shift with GI50 &amp;gt;10 µM. RT-PCR analysis indicated an 80-fold increase in mRNA expression of the differentiation marker CD11b in THP-1 cells treated with 3 µM RP7214. Similarly, expression of the CD11b marker on THP-1 cell surface was enhanced by 40% following incubation with 5 µM compound; effect of which was reduced to 15% in the presence of 300 µM Uridine. RP7214 dose-dependently induced apoptosis (30-50% at 3 µM) and arrested cycle progression in the “S-phase” (40-45% at 3 µM) in U937 and THP-1 cells. Conclusions: Results demonstrate the utility of RP7214 as a potent DHODH inhibitor in AML acting via suppression of cellular pyrimidine pools and promoting differentiation to fully mature cells. The compound is currently being evaluated in IND-enabling tolerability studies with Phase-1 trial in AML expected to commence in 2020. Citation Format: Srikant Viswanadha, Satyanarayana Eleswarapu, Swaroop Vakkalanka. Inhibition of Dihydroorotate Dehydrogenase (DHODH) by RP7214 attenuates growth and promotes differentiation of AML cell lines [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C042. doi:10.1158/1535-7163.TARG-19-C042
A Novel Nuclear Protein Interacts With the Symbiotic DMI3 Calcium- and Calmodulin-Dependent Protein Kinase of Medicago truncatula (2007)

Many higher plants establish symbiotic relationships with arbuscular mycorrhizal (AM) fungi that improve their ability to acquire nutrients from the soil. In addition to establishing AM symbiosis, legumes also enter into a nitrogen-fixing symbiosis with bacteria known as rhizobia that results in the formation of root nodules. Several genes involved in the perception and transduction of bacterial symbiotic signals named "Nod factors" have been cloned recently in model legumes through forward genetic approaches. Among them, DMI3 (Doesn't Make Infections 3) is a calcium- and calmodulin-dependent kinase required for the establishment of both nodulation and AM symbiosis. We have identified, by a yeast two-hybrid system, a novel protein interacting with DMI3 named IPD3 (Interacting Protein of DMI3). IPD3 is predicted to interact with DMI3 through a C-terminal coiled-coil domain. Chimeric IPD3::GFP is localized to the nucleus of transformed Medicago truncatula root cells, in which split yellow fluorescent protein assays suggest that IPD3 and DMI3 physically interact in Nicotiana benthamiana. Like DMI3, IPD3 is extremely well conserved among the angiosperms and is absent from Arabidopsis. Despite this high level of conservation, none of the homologous proteins have a demonstrated biological or biochemical function. This work provides the first evidence of the involvement of IPD3 in a nuclear interaction with DMI3.
A low-cost, ultra sensitive hand-held system for explosive detection using piezo-resistive micro-cantilevers (2011)

This paper presents a hand-held explosive detector system based on piezo-resistive cantilever sensors. A novel signal conditioning scheme comprising current excitation method with modified half bridge configuration, is implemented to measure as low as 20 ppb variations in the sensor resistance. The proposed circuit is insensitive to thermoelectric and stray noise effects as well as to temperature changes with minimum SNR value of 20 dB which is better than previously reported values. The hand held system comprises micro-cantilever sensor, analog signal conditioning module, sigma-delta ADC, digital modules along with digital output displayed on the LCD. The micro-cantilevers feature a special coating like 6-Marcaptonicotonic acid (6-MNA) or 4-mercaptobenzoic acid (4-MBA) on one side of the cantilever. The selective reaction takes place with TNT and RDX molecules (the target analyte molecules) on the functionalized cantilever surface with special coating. This reaction changes the resistance of the piezo-resistive sensor. On-chip implementation of one of the techniques is presented while some other methods are realized using discrete components. The objective is to explore different techniques for converting cantilever deflection into a measurable quantity and challenges ahead of converting explosive detector system into a complete SoC. These challenges are also discussed in the paper.
2.56&#x00D7;10<sup>17</sup> Hz/s frequency chirp signal generation using DSB-SC optical modulation without optical filters (2011)

The narrowband frequency chirped signal was generated by the frequency sweeper with the bandwidth of 200 MHz and duration of 100 ns, and then, the multiplier upconverted the signal to the bandwidth of 6.4 GHz. The electrical signal was launched into the HER modulator through the driver amplifier. For frequency doubled signal generation, the modulator was operated under a double-sideband suppressed carrier (DSB-SC) modulation condition. The optical signal source was a semiconductor laser diode (LD) operated at a wavelength of 1550 nm. The modulated optical signal was detected by a photodiode (PD).
Ligand Tuning of Localized Surface Plasmon Resonances in Antimony-Doped Tin Oxide Nanocrystals (2022)

Aliovalent-doped metal oxide nanocrystals exhibiting localized surface plasmons (LSPRs) are applied in systems that require reflection/scattering/absorption in infrared and optical transparency in visible. Indium tin oxide (ITO) is currently leading the field, but indium resources are known to be very restricted. Antimony-doped tin oxide (ATO) is a cheap candidate to substitute the ITO, but it exhibits less advantageous electronic properties and limited control of the LSPRs. To date, LSPR tuning in ATO NCs has been achieved electrochemically and by aliovalent doping, with a significant decrease in doping efficiency with an increasing doping level. Here, we synthesize plasmonic ATO nanocrystals (NCs) via a solvothermal route and demonstrate ligand exchange to tune the LSPR energies. Attachment of ligands acting as Lewis acids and bases results in LSPR peak shifts with a doping efficiency overcoming those by aliovalent doping. Thus, this strategy is of potential interest for plasmon implementations, which are of potential interest for infrared upconversion, smart glazing, heat absorbers, or thermal barriers.
Prevalence of cataract surgery and post-surgical visual outcomes in an urban Asian population: the Singapore Malay Eye Study (2008)

Five per cent of the sample of the Malay population aged 40-80 years in Singapore had cataract surgery. One in ten had post-operative best-corrected visual acuity of 20/60 or worse, largely related to concomitant retinal diseases.
Concatenated codes over fading dispersive channels (2003)

Concatenated codes using short RS (Reed-Solomon) codes with CI (channel erasure information) and different outer codes are compared. It is shown that CI improves the performance of RS codes over fading dispersive channels at small values of signal-to-noise ratios (SNR<10). The improvement obtained by concatenation is significant for underspread channels. For overspread channels, less improvement is observed. In general, concatenation is recommended if small error rates are desired. This technique is effective at lower SNR because symbols are more likely to be unreliable in that range due to higher noise levels.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
In-line miniature 3D-printed pressure-cycled ventilator maintains respiratory homeostasis in swine with induced acute pulmonary injury (2022)

The COVID-19 pandemic demonstrated the need for inexpensive, easy-to-use, rapidly mass-produced resuscitation devices that could be quickly distributed in areas of critical need. In-line miniature ventilators based on principles of fluidics ventilate patients by automatically oscillating between forced inspiration and assisted expiration as airway pressure changes, requiring only a continuous supply of pressurized oxygen. Here, we designed three miniature ventilator models to operate in specific pressure ranges along a continuum of clinical lung injury (mild, moderate, and severe injury). Three-dimensional (3D)-printed prototype devices evaluated in a lung simulator generated airway pressures, tidal volumes, and minute ventilation within the targeted range for the state of lung disease each was designed to support. In testing in domestic swine before and after induction of pulmonary injury, the ventilators for mild and moderate injury met the design criteria when matched with the appropriate degree of lung injury. Although the ventilator for severe injury provided the specified design pressures, respiratory rate was elevated with reduced minute ventilation, a result of lung compliance below design parameters. Respiratory rate reflected how well each ventilator matched the injury state of the lungs and could guide selection of ventilator models in clinical use. This simple device could help mitigate shortages of conventional ventilators during pandemics and other disasters requiring rapid access to advanced airway management, or in transport applications for hands-free ventilation.
Capillary electrophoresis fourier transform ion cyclotron resonance mass spectrometry with sustained off-resonance irradiation for the characterization of protein and peptide mixtures (1994)

A new approach to protein and peptide analysis that involves the coupling of on-line capillary electrophoresis-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry with a variation of sustained off-resonance irradiation is described. With this technique, multiple irradiation frequencies are broadcast simultaneously, which yields fragmentation of species at different mass-to-charge ratio values from the same waveform. In conjunction with capillary electrophoresis, this technique can provide sequence information from small amounts of proteins or peptides in complex mixtures. Initial results obtained from a mixture of gramicidin S (1141 u), bee venom melittin (2845 u), and equine apomyoglobin (16,951 u) are presented.
Precomputed Radiance Transfer for Reflectance and Lighting Estimation (2020)

Decomposing scenes into reflectance and lighting is an important task for applications such as relighting, image matching or content creation. Advanced light transport effects like occlusion and indirect lighting are often ignored, leading to subpar decompositions in which the albedo needs to compensate for insufficiencies in the estimated shading. We show how to account for these advanced lighting effects by utilizing precomputed radiance transfer to estimate reflectance and lighting. Given the geometry of an object and one or multiple images, our method reconstructs the object's surface reflectance properties-such as its albedo and glossiness-as well as a colored lighting environment map. Evaluation on synthetic and real data shows that incorporation of indirect light leads to qualitatively and quantitatively improved results.
Time-stamping accuracy in virtualized environments (2011)

The swift acceptance and the widespread use of virtual environments has substantially increased the stress on networks as each of the operating systems running in parallel sends out packets over the same network. As an increased number of packets traverse a network, the importance to continuously monitor whether the network is providing satisfactory service has increased. The metrics for such analyses includes delay, jitter, packet loss and available path capacity. The basic parameter required to quantify these metrics is the time-stamping values of the packets. The purpose of this research work is to characterize the impact of virtualization on a PC's time-stamping process. Operating system virtualization is employed where the time-stamping is done by the operating system kernel. CPU load and packet generating parameters are varied in order to study about the effect of virtualization on the time-stamping process under different operating conditions.
New, functionalised ionic liquids from Michael-type reactions—a chance for combinatorial ionic liquid development (2003)

We describe for the first time an alternative and far more efficient method to synthesise functionalised ionic liquids in a simple, straightforward, two-step synthesis.
Digoxigenin-Labeled <i>In Situ</i> Hybridization for the Detection of <i>Streptococcus suis</i> DNA in Polyserositis and a Comparison with Biotinylated <i>In Situ</i> Hybridization (2013)

The objective of this study was to develop digoxigenin-labeled in situ hybridization (ISH) for the detection of Streptococcus suis in naturally infected pigs with polyserositis and to compare it with biotinylated ISH. Digoxigenin-labeled hybridization signals for S. suis were observed in cells that had infiltrated the fibrous polyserositis and microcolonies in the blood vessels. Mock hybridization showed no hybridization signals for endogenous digoxigenin. Biotinylated hybridization signals for S. suis were observed in cells that had infiltrated the fibrous polyserositis. However, similar hybridization signals were also observed in the fibrous inflammatory area using mock hybridization for endogenous biotin. The present study demonstrated that digoxigenin-labeled ISH is a valuable diagnostic tool for specific detection of S. suis in polyserositic tissues without nonspecific reactions compared with biotinylated ISH.
A fundamental measure of treatment effect heterogeneity (2021)

Abstract The stratum-specific treatment effect function is a random variable giving the average treatment effect (ATE) for a randomly drawn stratum of potential confounders a clinician may use to assign treatment. In addition to the ATE, the variance of the stratum-specific treatment effect function is fundamental in determining the heterogeneity of treatment effect values. We offer a non-parametric plug-in estimator, the targeted maximum likelihood estimator (TMLE) and the cross-validated TMLE (CV-TMLE), to simultaneously estimate both the average and variance of the stratum-specific treatment effect function. The CV-TMLE is preferable because it guarantees asymptotic efficiency under two conditions without needing entropy conditions on the initial fits of the outcome model and treatment mechanism, as required by TMLE. Particularly, in circumstances where data adaptive fitting methods are very important to eliminate bias but hold no guarantee of satisfying the entropy condition, we show that the CV-TMLE sampling distributions maintain normality with a lower mean squared error than TMLE. In addition to verifying the theoretical properties of TMLE and CV-TMLE through simulations, we highlight some of the challenges in estimating the variance of the treatment effect, which lack double robustness and might be biased if the true variance is small and sample size insufficient.