gebhart/patrepeval huggingface dataset:
Anti-herbivore factors of grass endophytes: new prospects from metabolomics (2007)

A defensive role for several of the major alkaloids of Neotyphodium spp. endophytes in forage grasses has been confirmed in genetic experiments. However, many aspects of the activity of endophyte-infected grasses towards herbivores remain unaccounted for, suggesting there are further anti-herbivore factors yet to be uncovered. The development of metabolomics has provided new tools for the discovery of novel metabolites without preconceptions of the likely chemical structural class. Prospects for the application of new methods from metabolomics to further elucidate the defensive chemistry of associations of Neotyphodium spp. endophytes with their grass hosts are reviewed. Keywords: Neotyphodium, EpichloÃ«, defensive chemistry, invertebrate, vertebrate, gene deletion
A Comparison of <scp>B</scp>ayesian and Frequentist Approaches to Incorporating External Information for the Prediction of Prostate Cancer Risk (2012)

We present the most comprehensive comparison to date of the predictive benefit of genetics in addition to currently used clinical variables, using genotype data for 33 single-nucleotide polymorphisms (SNPs) in 1,547 Caucasian men from the placebo arm of the REduction by DUtasteride of prostate Cancer Events (REDUCE®) trial. Moreover, we conducted a detailed comparison of three techniques for incorporating genetics into clinical risk prediction. The first method was a standard logistic regression model, which included separate terms for the clinical covariates and for each of the genetic markers. This approach ignores a substantial amount of external information concerning effect sizes for these Genome Wide Association Study (GWAS)-replicated SNPs. The second and third methods investigated two possible approaches to incorporating meta-analysed external SNP effect estimates - one via a weighted PCa 'risk' score based solely on the meta analysis estimates, and the other incorporating both the current and prior data via informative priors in a Bayesian logistic regression model. All methods demonstrated a slight improvement in predictive performance upon incorporation of genetics. The two methods that incorporated external information showed the greatest receiver-operating-characteristic AUCs increase from 0.61 to 0.64. The value of our methods comparison is likely to lie in observations of performance similarities, rather than difference, between three approaches of very different resource requirements. The two methods that included external information performed best, but only marginally despite substantial differences in complexity.
One-bit recording and fluorescent confocal readout utilizing aluminum oxide single crystals (2003)

Two-photon absorption in new aluminum oxide single crystals is used for recording single bits in multiple layers while one-photon absorption and a confocal fluorescence detection scheme is applied for data readout.
Slice profile and B<sub>1</sub> corrections in 2D magnetic resonance fingerprinting (2017)

This study demonstrates that MRF is sensitive to both SP and B<sub>1</sub> effects, and that corrections can be made to improve the accuracy of MRF with only a 2-s increase in acquisition time. Magn Reson Med 78:1781-1789, 2017. © 2017 International Society for Magnetic Resonance in Medicine.
Microbial-induced Redox Imbalance in the Neonatal Lung Is Ameliorated by Live Biotherapeutics (2022)

Bronchopulmonary dysplasia (BPD) is a common lung disease of premature infants. Hyperoxia exposure and microbial dysbiosis are contributors to BPD development. However, the mechanisms linking pulmonary microbial dysbiosis to worsening lung injury are unknown. Nrf2 (nuclear factor erythroid 2-related factor 2) is a transcription factor that regulates oxidative stress responses and modulates hyperoxia-induced lung injury. We hypothesized that airway dysbiosis would attenuate Nrf2-dependent antioxidant function, resulting in a more severe phenotype of BPD. Here, we show that preterm infants with a Gammaproteobacteria-predominant dysbiosis have increased endotoxin in tracheal aspirates, and mice monocolonized with the representative Gammaproteobacteria <i>Escherichia coli</i> show increased tissue damage compared with germ-free (GF) control mice. Furthermore, we show Nrf2-deficient mice have worse lung structure and function after exposure to hyperoxia when the airway microbiome is augmented with <i>E. coli</i>. To confirm the disease-initiating potential of airway dysbiosis, we developed a novel humanized mouse model by colonizing GF mice with tracheal aspirates from human infants with or without severe BPD, producing gnotobiotic mice with BPD-associated and non-BPD-associated lung microbiomes. After hyperoxia exposure, BPD-associated mice demonstrated a more severe BPD phenotype and increased expression of <i>Nrf2</i>-regulated genes, compared with GF and non-BPD-associated mice. Furthermore, augmenting <i>Nrf2</i>-mediated antioxidant activity by supporting colonization with <i>Lactobacillus</i> species improved dysbiotic-augmented lung injury. Our results demonstrate that a lack of protective pulmonary microbiome signature attenuates an <i>Nrf2</i>-mediated antioxidant response, which is augmented by a respiratory probiotic blend. We anticipate antioxidant pathways will be major targets of future microbiome-based therapeutics for respiratory disease.
Continuum source atomic absorption spectrometry with a pulsed source and a photodiode array detector (1989)

G. P. Moulton, T. C. O'Haver and J. M. Harnly, J. Anal. At. Spectrom., 1989, 4, 673 DOI: 10.1039/JA9890400673
P‐40: A Visual Model of Color Break‐Up for Design Field‐Sequential LCDs (2007)

Abstract A model to evaluate the color break‐up (CBU) of field‐sequential color liquid crystal display (FSC‐LCD) had been successfully established. In order to quantify the CBU, “Color Break‐Up Angle (CBUA)” was proposed as the evaluation index. From the psychophysical experiments, the CBUA=0.22° was reported as the averaged threshold value for indistinguished color break‐up. Consequently, the minimum frame rate could be derived from the model to suppress CBU in the various FSC‐LCDs.
Dielectric isolated FinFETs on bulk substrate (2014)

Dielectric Isolated (DI) FinFETs exhibit superior electrostatic control compared to bulk FinFET without needing heavy sub-fin punchthrough stop doping, which increases device variability. Bottom oxidation through STI (BOTS) [1] and silicon-on-nothing (SON) are viable techniques to fabricate DI FinFETs on inexpensive bulk substates, as alternative to SOI substrate. In this paper we analyze DI FinFETs in terms of mechanical stress, transport, electrostatics and parasitic capacitances.
Intra-Frame Dyadic Spatial Scalable Coding Based on a Subband/Wavelet Framework for MPEG-4 AVC/H.264 Scalable Video Coding (2007)

This paper develops a new intra-frame dyadic spatial scalable coding framework based on a subband/wavelet coding approach for MPEG-4 AVC/H.264 scalable video coding (SVC). It is the first attempt in the literature to join the subband filter banks with the traditional macroblock and DCT based video coding system. We demonstrate that the current H.264 coding tools and syntax set can efficiently work together with the traditional subband filter banks for providing the improved efficiency for intra-frame dyadic spatial scalable coding. More importantly, unlike the classical wavelet coding, the proposed framework still allows the down-sampling filter to be flexibly designed to generate the ideal low resolution video for target applications. The proposed wavelet tool has been adopted by the JSVM for the next-phase SVC standard.
A hybrid approach on generating correlated sea clutter for maritime radar test (2016)

Test, measurement and verification of radar are necessary to ensure function according to specification and meet customer requirements. Extensive field tests are often required to test an entire radar system. This is not only expensive, but also requires a great deal of time. To reduce test complexity and cost, simulation techniques are used to recreate real-world conditions in a laboratory environment. Many subsystems can be tested by radar target generators simulating radar echo signals. They usually consider Swerling models, but struggle to simulate clutter, or in particular sea clutter. This paper introduces an approach to generate sea clutter with a state of the art vector signal generator. It shows common approaches modeling sea clutter and introduces a novel approach to combine the statistical models with a physical ocean surface model. This way, time and spatially correlated data that reproduces real-world sea clutter is generated, thus a cheaper, more time efficient way to conduct sea trials is presented.
Relationship between reliability and effect of solid solution hardening at solder joints at the high temperature (2012)

The Sn-3Ag-0.5Cu alloy has been already put to practical use in the world. However the crack easily propagate in the solder fillet at the big chip resister (6.4 × 3.2mm) after thermal fatigue of 2000 cycles between −55 and +125 degree centigrade at 30 minutes holding. It is the reason why the fine-needled Ag3Sn intermetallic compounds become coarse under the high stress and high temperature. The coarse Ag3Sn cannot play the role of hardening Sn matrix. Therefore some elements of solid solution in Sn matrix such as Sb, Bi and In are needed in order to restrict to propagate cracks in the solder joints after Ag3Sn became coarse. In this research, the relationship between the reliability and the effect of solid solution hardening at Sn-Ag-Cu-Sb and Sn-Ag-Cu-Bi alloys is investigated. Sn-3.9Ag-0.6Cu-3Sb and Sn-3Ag-0.8Cu-3Bi-Ni alloys have about twice life time as Sn-3Ag-0.5Cu alloys at the solder joints with big chip resister on FR4 substrate with six Cu layers at thermal fatigue test between −55 and 125C. Furthermore Sn-3.9Ag-0.6Cu-3Sb and Sn-3Ag-0.8Cu-3Bi-Ni alloys have longer life time than Sn-3Ag-0.5Cu alloys at the solder joints with LED on Al substrate at thermal fatigue tests between −55 and 125C, 150C.
Exploring neutron scatter camera performance using MCNP-PoliMi (2009)

A Monte Carlo model has been developed for the Sandia Neutron Scatter Camera. We have used this model to optimize cell geometry and detector efficiency. The simulations have been used to improve and understand detector response and calibrations.
Faecalibacterium prausnitzii prevents physiological damages in a chronic low-grade inflammation murine model (2015)

Our results show that F. prausnitzii and its SN had beneficial effects on intestinal epithelial barrier impairment in a chronic low-grade inflammation model. These observations confirm the potential of this bacterium as a novel probiotic treatment in the management of gut dysfunction and low-grade inflammation.
Structural and functional characterization of a specific antidote for ticagrelor (2015)

Ticagrelor is a direct-acting reversibly binding P2Y12 antagonist and is widely used as an antiplatelet therapy for the prevention of cardiovascular events in acute coronary syndrome patients. However, antiplatelet therapy can be associated with an increased risk of bleeding. Here, we present data on the identification and the in vitro and in vivo pharmacology of an antigen-binding fragment (Fab) antidote for ticagrelor. The Fab has a 20 pM affinity for ticagrelor, which is 100 times stronger than ticagrelor's affinity for its target, P2Y12. Despite ticagrelor's structural similarities to adenosine, the Fab is highly specific and does not bind to adenosine, adenosine triphosphate, adenosine 5'-diphosphate, or structurally related drugs. The antidote concentration-dependently neutralized the free fraction of ticagrelor and reversed its antiplatelet activity both in vitro in human platelet-rich plasma and in vivo in mice. Lastly, the antidote proved effective in normalizing ticagrelor-dependent bleeding in a mouse model of acute surgery. This specific antidote for ticagrelor may prove valuable as an agent for patients who require emergency procedures.
Optical parametric generation in CdSiP_2 (2010)

We report efficient generation of picosecond pulses in the near- and mid-IR in the new nonlinear material CdSiP(2) pumped at 1.064 μm by an amplified mode-locked Nd:YVO(4) laser at a 100 kHz repetition rate. By using single-pass optical parametric generation in 8-mm-long crystal cut for type I(e→oo) noncritical phase matching, an average idler power of 154 mW at 6.204 μm together with 1.16 W of signal at 1.282 μm has been obtained for 6.1 W of pump at photon conversion efficiencies of 15% and 23%, respectively. Signal pulse durations of 6.36 ps are measured for 9 ps pump pulses.
Hybrids of amino acids and acetylenic DNA-photocleavers: optimising efficiency and selectivity for cancer phototherapy (2012)

Hybrid agents which combine potent DNA-photocleavers with tunable amino acids or small peptides were designed to improve selectivity of Nature's most potent class of antibiotics towards cancer cells. The ability of these compounds to photocleave DNA is controlled by their incorporation into hybrid architectures with functional elements derived from natural amino acids. These conjugates are highly effective at inducing double-strand DNA cleavage and, in some cases, rival or even surpass both naturally occurring DNA cleavers and anticancer agents that are currently in clinical use. The possibility of triggering their activity in a photochemical and pH-sensitive fashion allows for a high degree of selectivity over activation. The conjugates were shown to penetrate cell membranes and induce efficient intracellular DNA cleavage. Initial in vitro tests against a variety of cancer cell lines confirm the potential of these compounds as anticancer agents at low nanomolar concentrations.
Molten salt destruction of energetic material wastes as an alternative to open burning (1994)

The Lawrence Livermore National Laboratory in conjunction with the Energetic Materials Center (a partnership of Lawrence Livermore and Sandia National Laboratories), is developing methods for the safe and environmentally sound destruction of explosives and propellants as a part of the Laboratory`s ancillary demilitarization mission. As a result of the end of the Cold War and the shift in emphasis to a smaller stockpile, many munitions, both conventional and nuclear, are scheduled for retirement and rapid dismantlement and demilitarization. major components of these munitions are the explosives and propellants, or energetic materials. The Department of Energy has thousands of pounds of energetic materials which result from dismantlement operations at the Pantex Plant. The Department of Defense has several hundred million pounds of energetic materials in its demilitarization inventory, with millions more added each year.
SQUID-Detected Liquid State NMR in Microtesla Fields (2004)

Nuclear magnetic resonance (NMR) experiments performed in magnetic fields on the order of microtesla yield line widths comparable to the lifetime limit even in grossly inhomogeneous magnets. The potential loss in sensitivity is overcome by combining prepolarization in fields on the order of millitesla and signal detection with a Superconducting Quantum Interference Device (SQUID). The enhanced spectral resolution attainable in microtesla fields enables NMR studies of pure liquids and solutions without the need for strong magnets. We have investigated a variety of heteronuclear systems in both the weak and strong J-coupling regimes. Six different nuclear species have been detected with the same experimental apparatus. NMR signals of thermally polarized protons were obtained in fields as low as 554 nT.
Multi-feature snore sound analysis in obstructive sleep apnea–hypopnea syndrome (2010)

Snoring is the most common symptom of obstructive sleep apnea hypopnea syndrome (OSAHS), which is a serious disease with high community prevalence. The standard method of OSAHS diagnosis, known as polysomnography (PSG), is expensive and time consuming. There is evidence suggesting that snore-related sounds (SRS) carry sufficient information to diagnose OSAHS. In this paper we present a technique for diagnosing OSAHS based solely on snore sound analysis. The method comprises a logistic regression model fed with snore parameters derived from its features such as the pitch and total airway response (TAR) estimated using a higher order statistics (HOS)-based algorithm. Pitch represents a time domain characteristic of the airway vibrations and the TAR represents the acoustical changes brought about by the collapsing upper airways. The performance of the proposed method was evaluated using the technique of K-fold cross validation, on a clinical database consisting of overnight snoring sounds of 41 subjects. The method achieved 89.3% sensitivity with 92.3% specificity (the area under the ROC curve was 0.96). These results establish the feasibility of developing a snore-based OSAHS community-screening device, which does not require any contact measurements.
A 4096-bit high-speed emitter-coupled-logic (ECL) compatible random-access memory (1975)

A 4096-bit pseudostatic MOS random-access memory with emitter-coupled (ECL) compatibility on all inputs including clocks is described. This device exhibits access times of under 80 ns and cycle times of under 150 ns with a standby dissipation of 300 mW. The fully decoded memory is fabricated on a 204/spl times/237 mil silicon chip and is assembled in a 22-lead ceramic dual-in-line package.
Bone Regeneration in Load-Bearing Segmental Defects, Guided by Biomorphic, Hierarchically Structured Apatitic Scaffold (2021)

The regeneration of load-bearing segmental bone defects remains a significant clinical problem in orthopedics, mainly due to the lack of scaffolds with composition and 3D porous structure effective in guiding and sustaining new bone formation and vascularization in large bone defects. In the present study, biomorphic calcium phosphate bone scaffolds (GreenBone™) featuring osteon-mimicking, hierarchically organized, 3D porous structure and lamellar nano-architecture were implanted in a critical cortical defect in sheep and compared with allograft. Two different types of scaffolds were tested: one made of ion-doped hydroxyapatite/β-tricalcium-phosphate (GB-1) and other made of undoped hydroxyapatite only (GB-2). X-ray diffraction patterns of GB-1 and GB-2 confirmed that both scaffolds were made of hydroxyapatite, with a minor amount of β-TCP in GB-1. The chemical composition analysis, obtained by ICP-OES spectrometer, highlighted the carbonation extent and the presence of small amounts of Mg and Sr as doping ions in GB-1. SEM micrographs showed the channel-like wide open porosity of the biomorphic scaffolds and the typical architecture of internal channel walls, characterized by a cell structure mimicking the natural parenchyma of the rattan wood used as a template for the scaffold fabrication. Both GB-1 and GB-2 scaffolds show very similar porosity extent and 3D organization, as also revealed by mercury intrusion porosimetry. Comparing the two scaffolds, GB-1 showed slightly higher fracture strength, as well as improved stability at the stress plateau. In comparison to allograft, at the follow-up time of 6 months, both GB-1 and GB-2 scaffolds showed higher new bone formation and quality of regenerated bone (trabecular thickness, number, and separation). In addition, higher osteoid surface (OS/BS), osteoid thickness (OS.Th), osteoblast surface (Ob.S/BS), vessels/microvessels numbers, as well as substantial osteoclast-mediated implant resorption were observed. The highest values in OS.Th and Ob. S/BS parameters were found in GB-1 scaffold. Finally, Bone Mineralization Index of new bone within scaffolds, as determined by micro-indentation, showed a significantly higher microhardness for GB-1 scaffold in comparison to GB-2. These findings suggested that the biomorphic calcium phosphate scaffolds were able to promote regeneration of load-bearing segmental bone defects in a clinically relevant scenario, which still represents one of the greatest challenges in orthopedics nowadays.
A new approach for automatic analysis of 3D low dose CT images for accurate monitoring the detected lung nodules (2008)

Our long term research goal is to develop a fully automated, image-based diagnostic system for early diagnosis of pulmonary nodules that may lead to lung cancer. This paper focuses on monitoring the development of lung nodules detected in successive chest low dose (LD) CT scans of a patient. We propose a new methodology for 3D LDCT data registration which is non-rigid and involves two steps: (i) global alignment of one scan (target) to another scan (reference or prototype) using the learned prior appearance model followed by (ii) local alignment in order to correct for intricate deformations. After equalizing signals for two subsequent chest scans, visual appearance of these chest images is modeled with a Markov-Gibbs random field with pairwise interaction. We estimate the affine transformation that globally register the target to the prototype by gradient descent maximization of a special Gibbs energy function. To handle local deformations, we deform each voxel of the target over evolving closed equi-spaced surfaces (iso-surfaces) to closely match the prototype. The evolution of the iso-surfaces is guided by an exponential speed function in the directions that minimize distances between the corresponding voxel pairs on the iso-surfaces in both the data sets. Preliminary results on the 135 LDCT data sets from 27 patients show that our proper registration could lead to precise diagnosis and identification of the development of the detected pulmonary nodules.
Novel and High Affinity 2-[(Diphenylmethyl)sulfinyl]acetamide (Modafinil) Analogues as Atypical Dopamine Transporter Inhibitors (2016)

The development of pharmacotherapeutic treatments of psychostimulant abuse has remained a challenge, despite significant efforts made toward relevant mechanistic targets, such as the dopamine transporter (DAT). The atypical DAT inhibitors have received attention due to their promising pharmacological profiles in animal models of cocaine and methamphetamine abuse. Herein, we report a series of modafinil analogues that have an atypical DAT inhibitor profile. We extended SAR by chemically manipulating the oxidation states of the sulfoxide and the amide functional groups, halogenating the phenyl rings, and/or functionalizing the terminal nitrogen with substituted piperazines, resulting in several novel leads such as 11b, which demonstrated high DAT affinity (K<sub>i</sub> = 2.5 nM) and selectivity without producing concomitant locomotor stimulation in mice, as compared to cocaine. These results are consistent with an atypical DAT inhibitor profile and suggest that 11b may be a potential lead for development as a psychostimulant abuse medication.
Some Recent Developments in the Synthesis and Structure-Activity Relationship of Novel Taxanes (2001)

The 7-methyl thioether 15 (BMS-184476) and the C-4 methylcarbonate 6 (BMS-188797) analogs of paclitaxel 1 were found to be more active than the parent in several preclinical in-vivo anticancer models. Both compounds are currently undergoing Phase I and II clinical trials. Chemistry for synthesizing C-7 sulfur analog of 15 and 6-alpha fluoro paclitaxel 27, a compound which should be resistant to metabolic hydroxylation at C-6 is described. The synthesis of 7-deoxy-6-beta hydroxy paclitaxel 36 and 7-deoxy-6-thiomethyl paclitaxel 37 is also summarized.