gebhart/patrepeval huggingface dataset:
One-Step Targeted Minimum Loss-based Estimation Based on Universal Least Favorable One-Dimensional Submodels (2016)

Consider a study in which one observes n independent and identically distributed random variables whose probability distribution is known to be an element of a particular statistical model, and one is concerned with estimation of a particular real valued pathwise differentiable target parameter of this data probability distribution. The targeted maximum likelihood estimator (TMLE) is an asymptotically efficient substitution estimator obtained by constructing a so called least favorable parametric submodel through an initial estimator with score, at zero fluctuation of the initial estimator, that spans the efficient influence curve, and iteratively maximizing the corresponding parametric likelihood till no more updates occur, at which point the updated initial estimator solves the so called efficient influence curve equation. In this article we construct a one-dimensional universal least favorable submodel for which the TMLE only takes one step, and thereby requires minimal extra data fitting to achieve its goal of solving the efficient influence curve equation. We generalize these to universal least favorable submodels through the relevant part of the data distribution as required for targeted minimum loss-based estimation. Finally, remarkably, given a multidimensional target parameter, we develop a universal canonical one-dimensional submodel such that the one-step TMLE, only maximizing the log-likelihood over a univariate parameter, solves the multivariate efficient influence curve equation. This allows us to construct a one-step TMLE based on a one-dimensional parametric submodel through the initial estimator, that solves any multivariate desired set of estimating equations.
Allosteric inhibitors of HMG-CoA reductase, the key enzyme involved in cholesterol biosynthesis (2013)

The corrole-based catalytic antioxidant reduced the cholesterol biosynthesis ability of macrophages, harvested from mice treated with it. and a non-redox active analogue of it affect the committed step of the biosynthetic pathway--the HMG-CoA reductase catalysed reaction--by acting as allosteric inhibitors of this key enzyme.
Foucault's currents based position sensor (2021)

In this paper the design, implementation and assessment of a position sensor based on Foucault currents is described. The proposed sensor aims to replace traditional Hall effect sensors in the competitive automotive industry. Results, for an angular position sensor, demonstrate high immunity to external magnetic fields, non-linearity of 0.186° up to 3000 rpm. Furthermore, the exciter and sensing coils can be produced using a standard multilayer Printed Circuit Board (PCB) process leading to very low production costs and the analog readout circuitry used requires standard low cost automotive electronic components, relying on the firmware developed in an embedded automotive microcontroller to achieve the automotive angular position sensor's requirements.
ChemInform Abstract: Anti‐Pneumocystis carinii Pneumonia Activity of Dicationic Diaryl Methylpyrimidines. (1998)

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.
Bond Angle Effects on the Migratory Insertion of Ethylene and Carbon Monoxide into Palladium(II)−Methyl Bonds in Complexes Bearing Bidentate Phosphine Ligands (2001)

Labile (P−P)Pd(CH3)(OEt2)+BAr‘4- complexes (2) have been prepared via protonation of (P−P)PdMe2 (1), where P−P = cis-1,2-bis(diphenylphosphino)ethylene (a, dppee), 1,2-bis(diphenylphosphino)benzene (b, dpbz), 1,2-bis(diphenylphosphino)ethane (c, dppe), 1,2-bis(dimethylphosphino)ethane (d, dmpe), 1,3-bis(diphenylphosphino)propane (e, dppp), 1,3-bis(diisopropylphosphino)propane (f, dippp), 1,4-bis(diphenylphosphino)butane (g, dppb) and Ar‘ = 3,5-(CF3)2C6H3. Unstable complex 2d (P−P = dmpe) was generated in situ. X-ray structures are reported for 1e and 2e−g. Treatment of 2a−g with CO in CH2Cl2 at −90 °C yields the (P−P)Pd(CH3)(CO)+ complexes 3a−g. Barriers to migratory insertion in 3a−g were determined with the ordering to be: 3f (dippp) ≈ 3g (dppb) < 3e (dppp) ≪ 3a (dppee) ≈ 3b (dpbz) ≈ 3c (dppe) < 3d (dmpe). Exposure of 2a−g to ethylene at −80 °C yields the ethylene complexes (P−P)Pd(CH3)(C2H4)+ (5a−g). Barriers to migratory insertion in these complexes were determined by NMR spectroscopy to be: 5b (dpbz) ≈ 5e (dppp) ≈ 5f (dippp) ≈ 5g (dppb) < 5a (dppee) ≈ 5c (dppe) < 5d (dmpe). Complexes (P−P)Pd(CH2CH3)(C2H4)+ (6a−e,g) produced from 5a−e,g under C2H4 are catalyst resting states for the dimerization of C2H4 to butenes. In the case of 5f (P−P = dippp), the catalyst resting state produced is the β-agostic ethyl complex (dippp)Pd(CH2CH2-μ-H)+ (8f), which has been isolated. This complex exhibits two dynamic processes studied by VT-NMR: interchange of Cα and Cβ (ΔG⧧ = 10.3(2) kcal/mol) and rotation of the agostic methyl group (ΔG⧧ ca. 6.4 kcal/mol). The β-agostic propyl complex 7f has been generated and identified as the n-propyl isomer (dippp)Pd(CH2CH2-μ-HCH3)+.
<title>Laser synthesis of single-wall carbon nanotubes with time-resolved in situ diagnostics</title> (2002)

Laser vaporization (LV) is a remarkably versatile technique for the catalytically-aided synthesis of nanomaterials, such as single-wall carbon nanotubes (SWNT). SWNT show remarkable promise for future generations of electronics and structural materials, however their application and commercialization has been hampered by a lack of control over the synthesis process, and low production quantities. Time-resolved in situ spectroscopic investigations of the laser-vaporization SWNT-synthesis process are described which are yielding some of the first direction determinations of carbon nanotube growth mechanisms and rates necessary to evaluate strategies for controllable synthesis and large-scale production. Our measurements indicate that SWNT grow over extended annealing times during the LV process by the conversion of condensed phase nanoparticle feedstock. These measurements were extended to grow carbon nanotubes by CO<SUB>2</SUB>- laser-annealing heat treatments of carbon and metal nanoparticle mixtures, offering an alternative synthesis approach to vapor- phase methods. These results present opportunities for scaled-up production of nanomaterials compatible with commercial high- power-laser technology.
Spontaneous optical pattern formation in a large array of optoelectronic feedback circuits (2000)

Strong nonlinear optical effects and optical pattern-forming systems can be designed with the optical system architectures introduced here on the basis of large-scale arrays of optoelectronic feedback circuits. Experiments were performed with a liquid-crystal television panel as a large-scale array of phase modulators and a CCD camera as a photoarray. By synthesizing various nonlinearities and using controllable spatial coupling, we obtained a variety of transversal optical patterns, localized states, waves, and chaotic regimes.
Formation of Type I-IR and Type II-IR gratings with an ultrafast IR laser and a phase mask (2005)

The formation of two grating types in SMF-28 fiber by focusing 125 fs, 0.5-2 mJ pulses through a phase mask onto a fiber sample is studied. The first type, specified as type I-IR, occurs below the damage threshold of the medium. The scaling behavior of the type I-IR gratings with field intensity and annealing properties suggests that their formation is related to nonlinear absorption processes, possibly resulting in color center formation. The second type, denoted as type II-IR, occurs coincidentally with white light generation within the fiber. These type II-IR gratings are stable at temperatures in excess of 1000 masculineC and are most likely a consequence of damage to the medium following ionization.
Dual Cervical Thoracic Coil for Spine Magnetic Resonance Imaging (1989)

The need for repositioning of surface coils and patients in MR examinations of the cervical and thoracic spine prolongs examination time. A new receiver design is proposed which overcomes this problem. The device is composed of two actively decoupled receiver coils mounted on the frame of a Philadelphia collar. These coils may be used separately to image either the thoracic or cervical spine or together to produce larger field-of-view images of the combined region. Signal-to-noise ratios of the separate cervical and thoracic spine images are not degraded as a result of mounting the receivers together. The full cervical and thoracic region is shown to be imaged at a signal-to-noise ratio significantly higher than that afforded by the body coil. A retrospective review of our case load suggests that a time saving could be achieved in approximately 1/3 of spine examinations by using this coil.
Direct radioimmunoassay of rat urinary kallikrein and comparison with other measures of urniary kallikrein activity. [/sup 125/I] (1979)

A highly sensitive radioimmunoassay for rat urinary kalikrein (minimal detectable amount, 40 pg/tube) has been developed. The assay uses a sheep antibody (Keq = 3.25 x 10/sup 10/M/sup -1/) against purified Sprague-Dawley rat urinary kallikrein in a final dilution of 1:1,200,000. The assay incorporates a convenient and inexpensive PEG technique for separation of free from bound antigen. Parallel standard curves with rat urine or kidney homogenates were obtained. No cross-reactivity with human or dog urine samples or purified human urinary kallikrein was seen. Correlations among this assay, an esterolytic method, and a kininogenase radioimmunoassay for kallikrein were highly significant, with only the esterolytic assay demonstrating any significant nonspecificity. The radioimmunoassay can detect changes in urinary kallikrein levels produced by a maneuver known to alter urinary kallikrein excretion.
Comparing a Generic and Individualized Information Decision Support Intervention for Men Newly Diagnosed With Localized Prostate Cancer (2007)

A randomized study was conducted to compare a generic and individualized approach to providing decisional support to men newly diagnosed with localized prostate cancer. Patients (N = 324) were referred by community urologists to a patient education center where they were randomly assigned to receive either an individualized or generic information intervention. Men assigned to the generic group viewed a video on the various treatments available for localized prostate cancer. Men in the individualized information group used a computer program to identify their information preferences. Computer printouts on top information preferences were individualized according to patient's specific disease characteristics, followed by a discussion of the pros and cons of each recommended treatment option. Both groups received a standardized package of written information. Men completed measures of decision control, satisfaction, and decision conflict at baseline and after a definitive treatment decision was made. Results demonstrated that overall both groups reported increased levels of decision control and lower levels of decision conflict after their treatment decision. All men reported being satisfied with their preparation to make a treatment decision. Compared to the generic information group, men who received the individualized information were more satisfied with the type, amount and method of providing information, and role played in treatment decision making with their physician (P < .002). Both information interventions seem to be similar in providing decisional support to this group of men at the time of diagnosis. Further research is required to determine how to identify men who may benefit from a more individualized approach.
Spermidine Protects against Oxidative Stress in Inflammation Models Using Macrophages and Zebrafish (2017)

Spermidine is a naturally occurring polyamine compound that has recently emerged with anti-aging properties and suppresses inflammation and oxidation. However, its mechanisms of action on anti-inflammatory and antioxidant effects have not been fully elucidated. In this study, the potential of spermidine for reducing pro-inflammatory and oxidative effects in lipopolysaccharide (LPS)-stimulated macrophages and zebrafish was explored. Our data indicate that spermidine significantly inhibited the production of pro-inflammatory mediators such as nitric oxide (NO) and prostaglandin E<sub>2</sub> (PGE<sub>2</sub>), and cytokines including tumor necrosis factor-α and interleukin-1β in RAW 264.7 macrophages without any significant cytotoxicity. The protective effects of spermidine accompanied by a marked suppression in their regulatory gene expression at the transcription levels. Spermidine also attenuated the nuclear translocation of NF-κB p65 subunit and reduced LPS-induced intracellular accumulation of reactive oxygen species (ROS) in RAW 264.7 macrophages. Moreover, spermidine prevented the LPS-induced NO production and ROS accumulation in zebrafish larvae and was found to be associated with a diminished recruitment of neutrophils and macrophages. Although more work is needed to fully understand the critical role of spermidine on the inhibition of inflammation-associated migration of immune cells, our findings clearly demonstrate that spermidine may be a potential therapeutic intervention for the treatment of inflammatory and oxidative disorders.
Gaussian processes at the Helm(holtz): A more fluid model for ocean currents (2023)

Given sparse observations of buoy velocities, oceanographers are interested in reconstructing ocean currents away from the buoys and identifying divergences in a current vector field. As a first and modular step, we focus on the time-stationary case - for instance, by restricting to short time periods. Since we expect current velocity to be a continuous but highly non-linear function of spatial location, Gaussian processes (GPs) offer an attractive model. But we show that applying a GP with a standard stationary kernel directly to buoy data can struggle at both current reconstruction and divergence identification, due to some physically unrealistic prior assumptions. To better reflect known physical properties of currents, we propose to instead put a standard stationary kernel on the divergence and curl-free components of a vector field obtained through a Helmholtz decomposition. We show that, because this decomposition relates to the original vector field just via mixed partial derivatives, we can still perform inference given the original data with only a small constant multiple of additional computational expense. We illustrate the benefits of our method with theory and experiments on synthetic and real ocean data.
Members of the Arabidopsis HRT/RPP8 Family of Resistance Genes Confer Resistance to Both Viral and Oomycete Pathogens (2000)

Michael B. Cooley, Sudam Pathirana, Hui-Ju Wu, Pradeep Kachroo, Daniel F. Klessig, Members of the Arabidopsis HRT/RPP8 Family of Resistance Genes Confer Resistance to Both Viral and Oomycete Pathogens, The Plant Cell, Vol. 12, No. 5 (May, 2000), pp. 663-676
Mechanism of Insulin Resistance in Normal Pregnancy (2013)

Normal pregnancy is associated with insulin resistance although the mechanism is not understood. Increased intramyocellular lipid is closely associated with the insulin resistance of type 2 diabetes and obesity, and the aim of this study was to determine whether this was so for the physiological insulin resistance of pregnancy. Eleven primiparous healthy pregnant women (age: 27-39 years, body mass index 24.0±3.1 kg/m2) and no personal or family history of diabetes underwent magnetic resonance studies to quantify intramyocellular lipid, plasma lipid fractions, and insulin sensitivity. The meal-related insulin sensitivity index was considerably lower in pregnancy (45.6±9.9 vs. 193.0±26.1; 10(-4) dl/kg/min per pmol/l, p=0.0002). Fasting plasma triglyceride levels were elevated 3-fold during pregnancy (2.3±0.2 vs. 0.8±0.1 mmol/l, p<0.01) and the low-density density lipoprotein fraction, responsible for fatty acid delivery to muscle and other tissues, was 6-fold elevated (0.75±0.43 vs. 0.12±0.09 mmol/l; p=0.001). However, mean intramyocellular lipid concentrations of the soleus muscle were not different during pregnancy (20.0±2.3 vs. 19.1±3.2 mmol/l, p=0.64). The pregnancy effect on muscle insulin resistance is distinct from that underlying type 2 diabetes.
EV-3, an endogenous human erythropoietin isoform with distinct functional relevance (2017)

Generation of multiple mRNAs by alternative splicing is well known in the group of cytokines and has recently been reported for the human erythropoietin (EPO) gene. Here, we focus on the alternatively spliced EPO transcript characterized by deletion of exon 3 (hEPOΔ3). We show co-regulation of EPO and hEPOΔ3 in human diseased tissue. The expression of hEPOΔ3 in various human samples was low under normal conditions, and distinctly increased in pathological states. Concomitant up-regulation of hEPOΔ3 and EPO in response to hypoxic conditions was also observed in HepG2 cell cultures. Using LC-ESI-MS/MS, we provide first evidence for the existence of hEPOΔ3 derived protein EV-3 in human serum from healthy donors. Contrary to EPO, recombinant EV-3 did not promote early erythroid progenitors in cultures of human CD34+ haematopoietic stem cells. Repeated intraperitoneal administration of EV-3 in mice did not affect the haematocrit. Similar to EPO, EV-3 acted anti-apoptotic in rat hippocampal neurons exposed to oxygen-glucose deprivation. Employing the touch-screen paradigm of long-term visual discrimination learning, we obtained first in vivo evidence of beneficial effects of EV-3 on cognition. This is the first report on the presence of a naturally occurring EPO protein isoform in human serum sharing non-erythropoietic functions with EPO.
Visible–infrared achromatic imaging by wavefront coding with wide-angle automobile camera (2016)

Abstract We perform an experiment of achromatic imaging with wavefront coding (WFC) using a wide-angle automobile lens. Our original annular phase mask for WFC was inserted to the lens, for which the difference between the focal positions at 400 nm and at 950 nm is 0.10 mm. We acquired images of objects using a WFC camera with this lens under the conditions of visible and infrared light. As a result, the effect of the removal of the chromatic aberration of the WFC system was successfully determined. Moreover, we fabricated a demonstration set assuming the use of a night vision camera in an automobile and showed the effect of the WFC system.
Minimization of Gate-Induced Drain Leakage by Controlling Gate Underlap Length for Low-Standby-Power Operation of 20-nm-Level Four-Terminal Silicon-on-Insulator Fin-Shaped Field Effect Transistor (2010)

Recently, gate-induced drain leakage (GIDL) has become a crucial factor of current characteristics as junction doping concentration becomes more abruptly graded owing to device scaling. It should be effectively suppressed for the low-standby-power operation of ultra small metal–oxide–semiconductor field effect transistor (MOSFET) devices. In this work, the appropriate underlap length range for the effective minimization of GIDL in 20-nm-level four-terminal (4-T) fin-shaped FET (FinFET) on silicon-on-insulator (SOI) is established. In order to identify the effect of underlap length on GIDL more precisely, the source and drain (S/D) junction doping profile and the majority/minority carrier lifetimes have been extracted by the measurement of a p–n junction test element group (TEG). The TEG was fabricated under the same process conditions that were used in forming the S/D junctions of 100-nm-level 4-T SOI FinFET in our previous research. The GIDL component in the off-state current is investigated with underlap length variation along with the inspection of basic current characteristics. For low-standby-power operation, an underlap junction is more desirable than an overlap junction, and the underlap length should be at least 10 nm to suppress GIDL effectively.
Downregulation of HER3 by a Novel Antisense Oligonucleotide, EZN-3920, Improves the Antitumor Activity of EGFR and HER2 Tyrosine Kinase Inhibitors in Animal Models (2013)

Among the four human EGF receptor (HER) family members (EGFR, HER2, HER3, HER4), HER3 is of particular interest as it interacts with HER2 and EGFR via heterodimerization and is a key link to the phosphoinositide 3-kinase (PI3K)/AKT signal transduction axis. Recent studies indicate that HER3 plays a critical role in mediating resistance to agents that target EGFR or HER2. As HER3 lacks significant kinase activity and cannot be inhibited by tyrosine kinase inhibitors, neutralizing antibodies and alternative inhibitors of HER3 have been sought as cancer therapeutics. We describe here a locked nucleic acid (LNA)-based HER3 antisense oligonucleotide, EZN-3920, that specifically downmodulated the expression of HER3, which was associated with growth inhibition. EZN-3920 effectively downmodulated HER3 expression, HER3-driven PI3K/AKT signaling pathway, and growth in tumors derived from BT474M1 breast and HCC827 lung carcinoma cell lines, which overexpress HER2 and EGFR, respectively. Furthermore, when EZN-3920 was coadministered with gefitinib or lapatinib in xenograft tumor models, enhanced antitumor activity compared with the effect of monotherapy was found. The effect was associated with a blockade of induced HER3 mRNA expression caused by lapatinib or gefitinib treatment. Finally, EZN-3920 sustained its antiproliferative effect in trastuzumab-resistant cells and three independently derived gefitinib-resistant cells. Our findings show that downmodulation of HER3 by EZN-3920 leads to the suppression of tumor growth in vitro and in vivo, suggesting that HER3 can be an effective target for the treatment of various cancers that have been activated by HER3 alone or where HER3 activation is associated with EGFR or HER2 expression.
A systematic approach for peptide characterization of B-cell receptor in chronic lymphocytic leukemia cells (2017)

A wide variety of immunoglobulins (Ig) is produced by the immune system thanks to different mechanisms (V(D)J recombination, somatic hypermutation, and antigen selection). The profiling of Ig sequences (at both DNA and peptide levels) are of great relevance to developing targeted vaccines or treatments for specific diseases or infections. Thus, genomics and proteomics techniques (such as Next-Generation Sequencing (NGS) and mass spectrometry (MS)) have notably increased the knowledge in Ig sequencing and serum Ig peptide profiling in a high-throughput manner. However, the peptide characterization of membrane-bound Ig (e.g., B-cell receptors, BCR) is still a challenge mainly due to the poor recovery of mentioned Ig.Herein, we have evaluated three different sample processing methods for peptide sequencing of BCR belonging to chronic lymphocytic leukemia (CLL) B cells identifying up to 426 different peptide sequences (MS/MS data are available via ProteomeXchange with identifier PXD004466). Moreover, as a consequence of the results here obtained, recommended guidelines have been described for BCR-sequencing of B-CLL samples by MS approaches.For this purpose, an in-house algorithm has been designed and developed to compare the MS/MS results with those obtained by molecular biology in order to integrate both proteomics and genomics results and establish the steps to follow when sequencing membrane-bound Ig by MS/MS.
ChemInform Abstract: THE ((4 + 2) + (3 + 2)) ROUTE TO MULTIPLY FUSED RING SYSTEMS: A NEW NOTION IN POLYCYCLE CONSTRUCTION (1984)

Abstract Die sukzessive DieIs‐Alder‐Reaktion der ausgehend von (I) dargestellten Nitroverbindung (III) mit geeigneten Dienophilen und die [3 + Zl‐Cycloaddition des aus der Nitrogruppe erhaltenen intermediären Nitriloxids mit der vorhandenen olefinischen Doppelbindung wird als Methode zur Darstellung mehrfach verknüpfter Ringe vorgestellt.