gebhart/patrepeval huggingface dataset:
Organocatalyzed Asymmetric Allylic Alkylation Enables Synthesis of Chiral γ-Lactones Bearing Vicinal Tertiary and Quaternary Stereocenters (2022)

The synthesis of enantioenriched α-aryl-α'-allyl-γ-butyrolactones bearing vicinal tertiary and quaternary stereocenters through organocatalyzed asymmetric allylic alkylation is reported. The process demonstrated that weakly stabilized enolates derived from α-aryl-γ-butyrolactones can undergo regio-, diastereo-, and enantioselective allylation using the proper activation of Morita-Baylis-Hillman (MBH) carbonates.
Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy (2023)

Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as 'lost caps'. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting 'cap angle' (ϕ), a size-independent measure of a particle's distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density.
Exploring the Effects of a Social Robot's Speech Entrainment and Backstory on Young Children's Emotion, Rapport, Relationship, and Learning (2019)

In positive human-human relationships, people frequently mirror or mimic each other's behavior. This mimicry, also called entrainment, is associated with rapport and smoother social interaction. Because rapport in learning scenarios has been shown to lead to improved learning outcomes, we examined whether enabling a social robotic learning companion to perform rapport-building behaviors could improve children's learning and engagement during a storytelling activity. We enabled the social robot to perform two specific rapport and relationship-building behaviors: speech entrainment and self-disclosure (shared personal information in the form of a backstory about the robot's poor speech and hearing abilities). We recruited 86 children aged 3-8 years to interact with the robot in a 2 × 2 between-subjects experimental study testing the effects of robot entrainment <i>Entrainment</i> vs. <i>No entrainment</i> and backstory about abilities <i>Backstory</i> vs. <i>No Backstory</i>. The robot engaged the children one-on-one in conversation, told a story embedded with key vocabulary words, and asked children to retell the story. We measured children's recall of the key words and their emotions during the interaction, examined their story retellings, and asked children questions about their relationship with the robot. We found that the robot's entrainment led children to show more positive emotions and fewer negative emotions. Children who heard the robot's backstory were more likely to accept the robot's poor hearing abilities. Entrainment paired with backstory led children to use more of the key words and match more of the robot's phrases in their story retells. Furthermore, these children were more likely to consider the robot more human-like and were more likely to comply with one of the robot's requests. These results suggest that the robot's speech entrainment and backstory increased children's engagement and enjoyment in the interaction, improved their perception of the relationship, and contributed to children's success at retelling the story.
Control of analog ferroelectric states by small dc-bias in conjunction with fluctuating waveforms (2009)

In this paper we demonstrate several possibilities to create and control partially switched analog states of ferroelectric materials, from measurements on PZT capacitors. By employing various types of fluctuating waveforms and controlling the domain dynamics with dc bias of small intensities, we have shown that it is possible to generate sequences of analog ferroelectric states that may appear identical from macroscopic measurements, yet they are unique at the local level. The experimental results have been analyzed theoretically by a simple microscopic model of switching. According to the model simulations, each analog state can be associated with a domain structure that captures subtle variations of the previously applied electric field as well as structural information about the inhomogeneities at the local level. The generation and control of such partially switched analog states may be important for new applications of ferroelectric materials to multi-value memories or in the field of artificial intelligence.
Abstract 9793: Pcsk9 Loss-of-function Variants, Low-density Lipoprotein Cholesterol, and Risk of Coronary Heart Disease and Stroke: Data From the REGARDS Study and CHARGE Consortium (2015)

Introduction: PCSK9 loss-of-function variants are associated with reduced low-density lipoprotein cholesterol (LDL-C) concentrations. Genetic association studies of PCSK9 loss-of-function variants allow for the examination of the effects of lifetime low LDL-C on cardiovascular outcomes. Hypothesis: PCSK9 loss-of-function variants are associated with lower concentrations of LDL-C and reduced risk of coronary heart disease (CHD) and stroke. Methods: We studied the association of PCSK9 loss-of-function Y142X and C679X nonsense variants (n=366; 2.1%) in 17,459 African Americans (AAs) and R46L missense variants (n=962; 3.1%) in 31,469 whites with LDL-C, CHD and stroke in the US-based REasons for Geographic And Racial Difference in Stroke (REGARDS) study and 8 cohorts in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. We combined multivariable adjusted differences in LDL-C between participants with and without PCSK9 variants across studies using inverse-variance weighted fixed-effects models. We calculated unadjusted odds ratios (ORs) for associations between PCSK9 variants and incident CHD (851 events in AAs and 2,662 events in whites) and stroke (523 events in AAs and 1,660 events in whites) using pooled Mantel-Haenszel estimates with continuity correction factors. Results: In the pooled cohorts, PCSK9 variants were associated with 36 mg/dL (95% confidence interval [CI]: 31, 40) lower LDL-C in AAs and 13 mg/dL (95% CI: 11, 16) lower LDL-C in whites. PCSK9 variants were associated with a pooled OR for CHD of 0.51 (95% CI: 0.28, 0.92) in AAs and 0.82 (95% CI: 0.63, 1.06) in whites. PCSK9 variants were not associated with incident stroke (OR=0.84 [95% CI: 0.48, 1.47] in AAs and OR=1.06 [95% CI: 0.80, 1.41] in whites). Conclusions: These results provide evidence that PCSK9 variants are associated with lifelong reduction in LDL-C and may lead to lower CHD risk, but no effect on stroke risk.
Data from Endocytosis of PEGylated Agents Enhances Cancer Imaging and Anticancer Efficacy (2023)

&lt;div&gt;Abstract&lt;p&gt;PEGylated nanoparticles and macromolecules are increasingly used in cancer imaging and anticancer treatment. The role of receptor-mediated endocytosis in the efficacy of these agents, however, has not been clearly defined. Here, we developed a matched pair of endocytic and nonendocytic receptors to directly and unambiguously assess this issue. The ligand-binding domains of the low-density lipoprotein receptor (LDLR) or a truncated LDLR lacking the NPXY endocytosis motif (ΔLDLR) were replaced with an anti–polyethylene glycol antibody (αPEG) to form endocytic αPEG-LDLR and nonendocytic αPEG-ΔLDLR receptors. The receptors were stably expressed at similar levels on the surface of HCC36 cells. HCC36/αPEG-LDLR cells, but not HCC36/αPEG-ΔLDLR cells, rapidly endocytosed PEG-quantum dots and PEG-liposomal doxorubicin (Lipo-Dox) &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;. Lipo-Dox was significantly more cytotoxic to HCC36/αPEG-LDLR cells than to HCC36/αPEG-ΔLDLR cells. HCC36/αPEG-LDLR tumors also accumulated significantly more PEGylated near-IR probes (PEG-NIR797) and PEG-liposomal-&lt;sup&gt;111&lt;/sup&gt;In than HCC36/αPEG-ΔLDLR tumors &lt;i&gt;in vivo&lt;/i&gt;. Furthermore, Lipo-Dox more significantly suppressed the growth of established HCC36/αPEG-LDLR tumors as compared with HCC36/αPEG-ΔLDLR tumors. Our data show that endocytosis of PEGylated probes and drugs enhances both cancer imaging and anticancer efficacy, indicating that endocytic receptors are superior targets for the design of cancer imaging probes and immunoliposomal drugs. Mol Cancer Ther; 9(6); 1903–12. ©2010 AACR.&lt;/p&gt;&lt;/div&gt;
Fullerene‐Mediated Activation of Dihydrogen: A New Method of Metal‐Free Catalytic Hydrogenation (2010)

A new type of metal-free catalytic hydrogenation has been developed, which allows for the reduction of various nitroarenes to the corresponding anilines with excellent yields and chemoselectivities. The hydrogenation takes place under very mild conditions using dihydrogen in combination with fullerene catalysts.
Trl-6 Qualification of Jwst Mirror Segments (2013)

Since 1996, all key mirror technology for a JWST Primary Mirror Segment Assembly (PMSA), as defined directly from the JWST Level 1 Science Requirements, have been developed and matured from a Technology Readiness Level (TRL) of 3 to 6. This has occurred as the result of a highly successful technology development program including sub-scale Beryllium Mirror Demonstrator (SBMD), Advanced Mirror System Demonstrator (AMSD), and JWST flight mirror fabrication. Directly traceable prototypes (and in some cases the flight hardware itself) has been built, tested and operated in a relevant environment.
The effect of trehalose, antioxidants, and acetate buffer concentration on oxytocin stability (2021)

Oxytocin is a cyclic nonapeptide used to induce labor and prevent bleeding after childbirth. Due to its instability, storage and transport of oxytocin formulations can be problematic in hot/tropical climates. The aim of this study was to investigate the effect of trehalose and select antioxidants (uric acid, butylated hydroxytoluene, and l-ascorbic acid) on oxytocin stability in solution. The effect of buffer composition and acetate buffer concentration was also studied. Acetate buffer was found to work better than citrate/phosphate buffer for the oxytocin stability. Lower acetate buffer concentrations (0.025 M or less) were also found to yield improved oxytocin stability compared to higher concentrations. Although known degradation pathways of oxytocin include oxidation, the antioxidants uric acid and butylated hydroxytoluene had negligible effect on the oxytocin stability while l-ascorbic acid led to significantly faster degradation. Despite trehalose's reputation as a great stabilizer for biomolecules, it also had small to negligible effect on oxytocin stability at concentrations up to 1 M in acetate buffer. These results were surprising given the present literature on trehalose as a stabilizer for various biomolecules, including proteins and lipids.
Genetic deficiency of Wnt5a diminishes disease severity in a murine model of rheumatoid arthritis (2017)

These data suggest that Wnt5a modulates the development of arthritis by promoting inflammation and osteoclast fusion, and provide the first mouse genetic evidence of a role for endogenous Wnt5a in autoimmune disease.
Learning from satisfying assignments under continuous distributions (2019)

What kinds of functions are learnable from their satisfying assignments? Motivated by this simple question, we extend the framework of [DDS15], which studied the learnability of probability distributions over {0, 1}n defined by the set of satisfying assignments to “low-complexity” Boolean functions, to Boolean-valued functions defined over continuous domains. In our learning scenario there is a known “background distribution” over ℝn (such as a known normal distribution or a known log-concave distribution) and the learner is given i.i.d. samples drawn from a target distribution f, where f is restricted to the satisfying assignments of an unknown low-complexity Boolean-valued function f. The problem is to learn an approximation ′ of the target distribution f which has small error as measured in total variation distance. We give a range of efficient algorithms and hardness results for this problem, focusing on the case when f is a low-degree polynomial threshold function (PTF). When the background distribution is log-concave, we show that this learning problem is efficiently solvable for degree-1 PTFs (i.e., linear threshold functions) but not for degree-2 PTFs. In contrast, when is a normal distribution, we show that this learning problem is efficiently solvable for degree-2 PTFs but not for degree-4 PTFs. Our hardness results rely on standard assumptions about secure signature schemes.
Approximating Gradients for Differentiable Quality Diversity in Reinforcement Learning (2022)

Consider the problem of training robustly capable agents. One approach is to generate a diverse collection of agent polices. Training can then be viewed as a quality diversity (QD) optimization problem, where we search for a collection of performant policies that are diverse with respect to quantified behavior. Recent work shows that differentiable quality diversity (DQD) algorithms greatly accelerate QD optimization when exact gradients are available. However, agent policies typically assume that the environment is not differentiable. To apply DQD algorithms to training agent policies, we must approximate gradients for performance and behavior. We propose two variants of the current state-of-the-art DQD algorithm that compute gradients via approximation methods common in reinforcement learning (RL). We evaluate our approach on four simulated locomotion tasks. One variant achieves results comparable to the current state-of-the-art in combining QD and RL, while the other performs comparably in two locomotion tasks. These results provide insight into the limitations of current DQD algorithms in domains where gradients must be approximated. Source code is available at https://github.com/icaros-usc/dqd-rl
ChemInform Abstract: Enantioselective Allylation, Crotylation, and Reverse Prenylation of Substituted Isatins: Iridium‐Catalyzed C—C Bond‐Forming Transfer Hydrogenation. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Mechanism and influencing factors of enhanced oil recovery for active SiDots nanofluid assisted fracturing-drainage in low permeability reservoirs: An experimental and numerical simulation study (2023)

Fracturing-drainage in low permeability reservoirs is a special method to facilitate oil production, however, conventional chemical oil displacement agents cannot adequately take advantage of this technology. Active SiDots nanofluid has special surface/interface properties and excellent stability that can contribute to improving the effect of fracturing-drainage. This paper investigates the influencing factors and mechanisms of active SiDots nanofluid assisted fracturing-drainage to enhance oil recovery (EOR) through experiments and reservoir numerical simulation. The results on the performance of the active SiDots nanofluid show that 0.10 wt% concentration was sufficient to reduce the oil-water interfacial tension from 20 mN/m to 0.32 mN/m and modify the oil-wet core to water-wet. Experimental and reservoir numerical simulation results indicate that the incremental oil recovery after the active SiDots nanofluid fracturing-drainage was more than 10%, which was more effective than surfactant alone. The optimum injection concentration and volume of active SiDots nanofluid were 0.10 wt% and 0.6 PV, respectively. To improve the utilization of active SiDots nanofluid, the well shut-in time should be at least 24 h. One-cycle active SiDots nanofluid injection was more conducive to replenishing the formation energy and expanding the swept volume. The field injection rate of the SiDots nanofluid should not be too high to prevent breakthroughs. The EOR experimental results indicate that the fracturing-drainage could increase the injection volume to replenish energy and reduce the active SiDots nanofluid adsorption loss thereby effectively peeling the oil film. This paper addresses the supply shortage of conventional chemicals used for fracturing-drainage in low-permeability reservoirs and expands the study of the influencing factors and mechanisms of fracturing-drainage.
Vascular Devices (1999)

Our group at the Beth Israel Deaconess Medical Center (formerly Deaconess Hospital) and a team at Circe Biomedical, Inc. (formerly Grace Biomedcal, WR Grace and Co.-Conn) have studied the use of a vascularized bioartificial pancreas (VB AP) for treatment of diabetes for the past 6 years.1–4 We were the first to demonstrate the long-term use of a bioartificial pancreas in large animals, and our data represented the longest survival of discordant xenogeneic islets. In this report we will briefly describe the VBAP device, a large animal diabetes model, experimental results with the use of allogeneic and xenogeneic islets in the device, and plans to initiate a clinical trial of the VBAP containing porcine islets for treatment of patients with earlystage IDDM.KeywordsExogenous InsulinBeth Israel Deaconess MedicalPorcine IsletClinical Phase IIII TrialBioartificial PancreasThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Custom CMOS Reed Solomon coder for the Hubble Space Telescope (2002)

A VLSI coder is presented that can function either as an encoder or decoder for Reed-Solomon codes. Full-custom VLSI is used to achieve both circuit density and speed, and allows control of the amount of interconnect. Speed, which is a function of capacitance, which is a function of interconnect, is an important parameter in high-performance VLSI. A single 8.2 mm*8.4 mm, 200000 transistor CMOS chip implementation of the Reed-Solomon code required by the Hubble Space Telescope is reported. The chip features a 10-MHz sustained byte rate independent of error pattern. The 1.6- mu m CMOS integrated circuit has complete decoder and encoder functions and uses a single data/system clock. Block lengths up to 255 bytes and shortened codes are supported with no external buffering. Erasure corrections and random error corrections are supported with programmable correction of up to 10 symbol errors. Correction time is independent of error pattern and the number of errors in the incoming message.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Engineering mesoporous silica nanoparticles towards oral delivery of vancomycin (2021)

Vancomycin (Van) is a key antibiotic of choice for the treatment of systemic methicillin resistant <i>Staphylococcus aureus</i> (MRSA) infections. However, due to its poor membrane permeability, it is administered parenterally, adding to the cost and effort of treatment. The poor oral bioavailability of Van is mainly due to its physico-chemical properties that limit its paracellular and transcellular transport across gastrointestinal (GI) epithelium. Herein we report the development of silica nanoparticles (SNPs)-based formulations that are able to enhance the epithelial permeability of Van. We synthesized SNPs of different pore sizes (2 nm and 9 nm) and modified their surface charge and polarity by attaching different functional groups (-NH<sub>2</sub>, -PO<sub>3</sub>, and -CH<sub>3</sub>). Van was loaded within these SNPs at a loading capacity in the range of <i>ca.</i> 18-29 wt%. The Van-loaded SNPs exhibited a controlled release behaviour when compared to un-encapsulated Van which showed rapid release due to its hydrophilic nature. Among Van-loaded SNPs, SNPs with large pores showed a prolonged release compared to SNPs with small pores while SNPs functionalised with -CH<sub>3</sub> groups exhibited a slowest release among the functionalised SNPs. Importantly, Van-loaded SNPs, especially the large pore SNPs with negative charge, enhanced the permeability of Van across an epithelial cell monolayer (Caco-2 cell model) by up to 6-fold, with <i>P</i><sub>app</sub> values up to 1.716 × 10<sup>-5</sup> cm s<sup>-1</sup> (<i>vs.</i> 0.304 × 10<sup>-5</sup> cm s<sup>-1</sup> for un-encapsulated Van) after 3 h. The enhancement was dependent on both the type of SNPs and their surface functionalisation. The permeation enhancing effect of SNPs was due to its ability to transiently open the tight junctions measured by decrease in transepithelial resistance (TEER) which was reversible after 3 h. All in all, our data highlights the potential of SNPs (especially SNPs with large pores) for oral delivery of Van or other antimicrobial peptides.
Novel functions for chromatin dynamics in mRNA biogenesis beyond transcription (2017)

The first step of gene expression results in the production of mRNA ribonucleoparticles (mRNPs) that are exported to the cytoplasm via the NPC for translation into the cytoplasm. During this process, the mRNA molecule synthesized by RNA polymerase II (Pol II) undergoes extensive maturation, folding and packaging events that are intimately coupled to its synthesis. All these events take place in a chromatin context and it is therefore not surprising that a growing number of studies recently reported specific contributions of chromatin dynamics to various steps of mRNP biogenesis. In this extra view, we replace our recent findings highlighting the contribution of the yeast chromatin remodeling complex ISW1 to nuclear mRNA quality control in the context of the recent literature.
Çerkezlerin 1864 yılındaki zorunlu göçten sonra Türkiye'ye uyum sağlama süreci (2014)

Ankara : İhsan Doğramacı Bilkent Üniversitesi İktisadi, İdari ve Sosyal Bilimler Fakültesi, Tarih Bölümü, 2014.