gebhart/patrepeval huggingface dataset:
Identification of Motile Sperm Domain–Containing Protein 2 as Regulator of Human Monocyte Migration (2017)

Binding of chemokines to their cognate receptors on monocytes instigates a cascade of events that directs these cells to migrate to sites of inflammation and cancerous tissues. Although targeting of selected chemokine receptors on monocytes exhibited preclinical efficacy, attempts to translate these studies to the clinic have failed thus far, possibly due to redundancy of the target receptor. We reveal that motile sperm domain-containing protein 2 (MOSPD2), a protein with a previously unknown function, regulates monocyte migration in vitro. This protein was found to be expressed on the cytoplasmic membrane of human monocytes. Silencing or neutralizing MOSPD2 in monocytes restricted their migration when induced by different chemokines. Mechanistically, silencing MOSPD2 inhibited signaling events following chemokine receptor ligation. When tested for expression in other immune cell subsets, MOSPD2 was apparent also, though less abundantly, in neutrophils, but not in lymphocytes. Thus, in the presence of neutralizing Abs, neutrophil migration was inhibited to some extent whereas lymphocyte migration remained intact. In view of these results, we suggest MOSPD2 as a potential target protein for treating diseases in which monocyte and neutrophil accumulation is correlated with pathogenesis.
Noncovalent Functionalization of DNA-Wrapped Single-Walled Carbon Nanotubes with Platinum-Based DNA Cross-Linkers (2008)

A method for noncovalent functionalization of DNA-wrapped single-walled carbon nanotubes (SWNTs) using platinum-based DNA cross-linkers is investigated. In particular, cisplatin and potassium tetrachloroplatinate are shown to bind to DNA that encapsulates SWNTs in aqueous solution. The bound platinum salt can then be reduced to decorate the DNA-encapsulated SWNTs with platinum nanoparticles. The resulting SWNT/DNA/Pt hybrids are investigated by optical absorption spectroscopy, circular dichroism spectroscopy, Raman spectroscopy, X-ray diffraction, transmission electron microscopy, and atomic force microscopy. The unique combination of catalytic activity of nanoscale platinum, biological functionality of DNA, and optoelectronic properties of SWNTs suggests a myriad of applications including fuel cells, catalysts, biosensors, and electrochemical devices.
Approximately Optimal Radar Resource Management for Multi-Sensor Multi-Target Tracking (2021)

Radar Resource Management in a multi-sensor multi-target scenario is considered. A dynamic resource balancing algorithm is proposed which optimizes target task parameters assuming an underlying partially observable Markov decision process (POMDP). By applying stochastic optimization methods, such as policy rollout, the POMDP is solved non-myopically. The approximately optimal approach is formulated assuming a central processor. Subsequently, a distributed implementation is introduced that converges to the same results as given by the centralized implementation and requires less computational resources. The performance of the proposed approach for both centralized and distributed implementation is demonstrated through dynamic tracking scenarios.
Characterization of the Joining Chain (J‐Chain) Promoter (1993)

A 300 b.p. promoter from the mouse joining chain (J-chain) gene was studied with regard to functional activity and protein/DNA interactions. The promoter only stimulated expression of a chloramphenicol-acetyl-transferase (CAT) reporter gene when an enhancer was present in the construct, regardless of whether the construct was transfected into cell lines that did or did not express an endogenous J-chain. Furthermore, deletion mutants lacking the 5' portion of the promoter were transcribed at a higher rate than the intact promoter in both J-chain positive and J-chain negative B-cell lines but not in untransformed B lymphocytes stimulated by lipopolysaccharide, indicating the presence of a negative control element in the 5' portion of the J-chain promoter active in tumour cells only. The octamer element in the J-chain promoter was found to bind Oct proteins, albeit with a low affinity. The penta-deca (p.d.) element in the J-chain promoter bound proteins in extracts from untransformed B cells but not in the tested cell lines. The protein binding to the J-chain p.d. element did not compete efficiently with a p.d. element from the SP6 kappa promoter. A protein binding to the 5' portion of the J-chain was expressed in some cell lines but not in others; neither a negative nor a positive correlation to J-chain expression could be seen. It was concluded that the J-chain promoter is equivalent to a kappa promoter and that differentiation-specific J-chain expression is governed by distal, positive control elements located outside the analysed region.
Small molecule inhibition of NOX-1 reduces diabetes conversion in NOD mice (2019)

Inflammation is a major contributor to beta cell destruction leading to diabetes. Generation of reactive oxygen species (ROS) by inflammatory signals facilitates beta cell dysfunction. Disruption of the ROS-generating enzyme NADPH oxidase-1 (NOX-1) confers protection to beta cells. Selective small molecule inhibitors of NOX-1 that confer protection to mouse or human beta cells (ML171 or GKT137831) have been systemically administered to NOD mice. A brief (4 week) administration of the NOX-1 inhibitors reduced the conversion of NOD mice to diabetes, relative to vehicle control. Histologic analysis of islet morphology showed mice administered the NOX-1 inhibitors had a predominant organization of leukocytes that was restricted to the peri-islet region, in contrast to leukocyte invasion of the islet that was predominantly seen in vehicle control mice. The data support the therapeutic potential of NOX-1 inhibition in diabetes and suggest a role for NOX-1 in the cross talk between inflammatory cells, beta cells and the integrity of the islet extracellular matrix.
Hard to Park? (2019)

In this paper we consider the problem of estimating the difficulty of parking at a particular time and place; this problem is a critical sub-component for any system providing parking assistance to users. We describe an approach to this problem that is currently in production in Google Maps, providing inferences in cities across the world. We present a wide range of features intended to capture different aspects of parking difficulty and study their effectiveness both alone and in combination. We also evaluate various model architectures for the prediction problem. Finally, we present challenges faced in estimating parking difficulty in different regions of the world, and the approaches we have taken to address them.
Better beat tracking through robust onset aggregation (2014)

Onset detection forms the critical first stage of most beat tracking algorithms. While common spectral-difference onset detectors can work well in genres with clear rhythmic structure, they can be sensitive to loud, asynchronous events (e.g., off-beat notes in a jazz solo), which limits their general efficacy. In this paper, we investigate methods to improve the robustness of onset detection for beat tracking. Experimental results indicate that simple modifications to onset detection can produce large improvements in beat tracking accuracy.
Comparison of Fractional Micro‐Plasma Radiofrequency and Fractional Microneedle Radiofrequency for the Treatment of Atrophic Acne Scars: A Pilot Randomized Split‐Face Clinical Study in China (2020)

Both fractional micro-plasma RF and fractional microneedle RF are effective and safe methods for improving atrophic acne scars. Fractional micro-plasma RF is significantly more effective for atrophic acne scars, especially for rolling scars. However, fractional microneedle RF has fewer side effects plus shorter downtime, and patients are more comfortable after the treatment. Lasers Surg. Med. © 2020 Wiley Periodicals LLC.
Asymmetric Synthesis of Cis-Fused Bicyclic Pyrrolidines and Pyrrolidinones via Chiral Polycyclic Lactams (1996)

Condensation of racemic keto-ester 2 and 1.1 equiv of (R)-(−)-phenylglycinol in toluene with azeotropic removal of water and methanol gave rise to a tetracyclic lactam in greater than 90% yield. Examination of the crude reaction product by 1H and 13C NMR, capillary GC, and HPLC revealed this product to be a single isomer, the absolute configuration of which was determined to be that illustrated by structure 3. The tetracyclic lactam 3 was stereospecifically reduced to either the cis-fused bicyclic pyrrolidine 4 or the cis-fused bicyclic pyrrolidinone 9. The chiral auxiliaries in both 4 and 9 were removed using different, novel methodologies. This highly stereoselective reaction establishes two contiguous chiral centers via the deracemization of an achiral keto-ester. This methodology has been applied to the synthesis of (1R,5R)-2-azabicyclo[3.3.0]octane 15. This important amine is now readily available from commercial materials in only three steps.
Inkless Microcontact Printing on SAMs of Boc- and TBS-Protected Thiols (2009)

We report a new inkless catalytic muCP technique that achieves accurate, fast, and complete pattern reproduction on SAMs of Boc- and TBS-protected thiols immobilized on gold using a polyurethane-acrylate stamp functionalized with covalently bound sulfonic acids. Pattern transfer is complete at room temperature just after one minute of contact and renders sub-200 nm size structures of chemically differentiated SAMs.
High-temperature molecular beam epitaxial growth of AlGaN/GaN on GaN templates with reduced interface impurity levels (2010)

We present combined in situ thermal cleaning and intentional doping strategies near the substrate regrowth interface to produce high-quality AlGaN/GaN high electron mobility transistors on semi-insulating (0001) GaN templates with low interfacial impurity concentrations and low buffer leakage. By exposing the GaN templates to an optimized thermal dissociation step in the plasma-assisted molecular beam epitaxy environment, oxygen, carbon, and, to lesser extent, Si impurities were effectively removed from the regrowth interface under preservation of good interface quality. Residual Si was further compensated by C-doped GaN via CBr4 to yield highly resistive GaN buffer layers. Improved N-rich growth conditions at high growth temperatures were then utilized for subsequent growth of the AlGaN/GaN device structure, yielding smooth surface morphologies and low residual oxygen concentration with large insensitivity to the (Al+Ga)N flux ratio. Room temperature electron mobilities of the two-dimensional electron gas at the AlGaN/GaN interface exceeded &amp;gt;1750 cm2/V s and the dc drain current reached ∼1.1 A/mm at a +1 V bias, demonstrating the effectiveness of the applied methods.
Hydrogen Optical Fiber Sensors (2008)

Optically-based hydrogen sensors promise to deliver an added level of safety as hydrogen and fuel cell technologies enter the mainstream. More importantly, they offer reduced power consumption and lower cost, which are desirable for mass production applications such as automobiles and consumer appliances. This program addressed two of the major challenges previously identified in porous optrode-based optical hydrogen sensors: sensitivity to moisture (ambient humidity), and interference from the oxygen in air. Polymer coatings to inhibit moisture and oxygen were developed in conjunction with newer and novel hydrogen sensing chemistries. The results showed that it is possible to achieve sensitive hydrogen detection and rapid response with minimal interference from oxygen and humidity. As a result of this work, a new and more exciting avenue of investigation was developed: the elimination of the porous optrode and deposition of the sensor chemistry directly into the polymer film. Initial results have been promising, and open up a wider range of potential applications from extended optical fiber sensing networks, to simple plastic "stickers" for use around the home and office.
Piezoelectric Programmable Optical Mode Conversion in a Photonic Integrated Circuit (2023)

Waveguide-based optical mode conversion requires wavelength-scale patterning of the waveguide's optical properties. We implement a programmable version of this patterning with piezoelectrically actuated photonics.
Collective Proton Dynamics at Highly Charged Interfaces Studied by Ab Initio Metadynamics (2012)

Surface proton conduction is of utmost importance in biology, materials science, and electrochemistry; yet experimental findings of ultrafast proton transport at densely packed arrays of anionic surface groups have remained controversial and unexplained. We present an ab initio molecular dynamics study of proton dynamics at sulfonic-acid terminated surface groups. Results furnish a highly efficient collective mechanism of hydronium ion translocations at a critical surface group separation of ~6.5 Å. Orientational fluctuations of SG trigger hydrogen bond breaking that sets off the hydronium ion motion. The activation free energy of this process is 0.3 eV (±0.1 eV). The soliton-like nature of this mechanism is owed to the trigonal symmetry of sulfonate anions and exceptionally strong interfacial hydrogen bonding. These insights should stimulate surface conductance studies at SG monolayers with sulfonic acid groups, and they bolster efforts in designing proton conducting polymers conducive to fuel cell operation above ~100 °C.
ChemInform Abstract: Conformationally Complex π‐Conjugated Molecular and Polymeric Materials: New Challenges for Organic Synthesis. (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.
Optimization method to reduce blocking artifacts in JPEG images (2014)

This paper presents an optimization method to reduce blocking artifacts in JPEG images by utilizing the image gradient information. A closed-form solution is derived for the optimization method. To address the computational feasibility aspect of the large matrices involved in the closed-form solution, a sliding window approach is devised. The performance of the developed method is compared with several blocking artifacts reduction methods in the literature and also with the deblocking filter deployed in high efficiency video coding by examining the three measures of peak signal-to-noise ratio, generalized block-edge impairment metric (MGBIM), and structural similarity. The comparison results indicate the effectiveness of the introduced method in particular for low bit-rate JPEG images.
Bandwidth shaping of microresonator-based frequency combs via dispersion engineering (2014)

We investigate experimentally and theoretically the role of group-velocity dispersion and higher-order dispersion on the bandwidth of microresonator-based parametric frequency combs. We show that the comb bandwidth and the power contained in the comb can be tailored for a particular application. Additionally, our results demonstrate that fourth-order dispersion plays a critical role in determining the spectral bandwidth for comb bandwidths on the order of an octave.
CloneSifter: enrichment of rare clones from heterogeneous cell populations (2020)

CloneSifter provides a means to track and access specific and rare clones of interest across dynamic changes in population structure to comprehensively explore the basis of these changes.
Doping-induced phase transitions in ferroelectric BaTiO3from first-principles calculations (2012)

Carrier-electron-induced phase transition from tetragonal to cubic phases in BaTiO${}_{3}$ is studied using first-principles calculation. Our results show that the disappearance of the ferroelectric phase is an intrinsic effect resulting from carrier electron doping in BaTiO${}_{3}$. We further clarify that the lattice disorder induced by donor dopants such as oxygen vacancies and substitutionally doped Nb${}^{5+}$ at Ti${}^{4+}$ sites accelerates the disappearance of the tetragonal phase in BaTiO${}_{3}$.
Imaging targeted-agent binding in vivo with two probes (2010)

An approach to quantitatively image targeted-agent binding rate in vivo is demonstrated with dual-probe injection of both targeted and nontargeted fluorescent dyes. Images of a binding rate constant are created that reveal lower than expected uptake of epidermal growth factor in an orthotopic xenograft pancreas tumor (2.3 x 10(-5) s(-1)), as compared to the normal pancreas (3.4 x 10(-5) s(-1)). This approach allows noninvasive assessment of tumor receptor targeting in vivo to determine the expected contrast, spatial localization, and efficacy in therapeutic agent delivery.
ChemInform Abstract: A Practical Process for the Preparation of Tetrahydro‐1‐methyl‐3,3‐ diphenyl‐1H,3H‐pyrrolo(1,2‐c)(1,3,2)oxazaborole‐Bor ane. A Highly Enantioselective Stoichiometric and Catalytic Reducing Agent. (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.
The role of oxyanion holes in the structure and function of type III polyketide synthases (768.18) (2014)

The objective of this study was to combine the tools of protein crystallography and enzyme kinetics to explore the structural mechanisms of type III polyketide synthases (PKSs). Type III PKSs are proteins involved in diverse metabolic processes including cell signaling, pathogen defense and the development of reproductive cells. Mechanistically, these enzymes generate metabolites through the repetitive addition of acetate units onto a starter molecule; a process that produces reactive intermediates that are ultimately cyclized into the final product. How these enzymes control their reactive intermediates and terminal cyclizations is not fully understood and is a major hindrance to protein engineering efforts. We present here our results describing the role of oxyanion holes in the mechanism of type III PKSs. Crystallographic studies of reaction analogs trapped in the active site revealed that remnants of an ancient oxyanion hole are involved in stabilizing reactive intermediates. Unexpectedly, we observed that a small molecule, metazachlor, has different conformations in the active site of functionally distinct PKSs. Enzyme kinetic studies supported our structural findings by establishing that metazachlor differentially inhibits type III PKSs based on their terminal cyclization steps. These structure‐function studies are being used as a guide for altering the terminal cyclization preferences of type III PKSs to build novel compounds. Grant Funding Source : Supported by Howard Hughes Medical Institute and National Science Foundation
Michael Addition of Chiral Fischer Aminocarbene Complexes to Nitroolefins:  Study on the Effect of the Michael Acceptor Structure on Diastereoselectivity (2001)

The anions of the pentacarbonyl(chromium) trans-2,6-dimethylmorpholinyl(methyl)carbene and pentacarbonyl(chromium) trans-3,5-dimethylpiperidinyl(methyl)carbene complexes added to E- and Z-nitrostyrenes through a diastereoselective Michael-type reaction to give precursors of β-aryl-γ-butyric acid derivatives. The diastereoselectivity observed with the former carbene was dependent on the nature of the substituent present in the 4-position of nitrostyrenes and was higher when it was an electron-withdrawing group. The presence of 12-crown-4 ether in the reaction medium increased both reaction times and diastereoselectivity. Theoretical calculations were performed to rationalize the stereochemical outcomes of the reactions and to support the proposed transition state models.
Fano Resonance between Mie and Bragg Scattering in Photonic Crystals (2009)

We report the observation of a Fano resonance between continuum Mie scattering and a narrow Bragg band in synthetic opal photonic crystals. The resonance leads to a transmission spectrum exhibiting a Bragg dip with an asymmetric profile, which can be tunably reversed to a Bragg rise. The Fano asymmetry parameter is linked with the dielectric contrast between the permittivity of the filler and the specific value determined by the opal matrix. The existence of the Fano resonance is directly related to disorder due to nonuniformity of a-SiO2 opal spheres. The theoretical "quasi-3D" model produces results in excellent agreement with the experimental data.
Data from Selective Targeting of Antitumor Immune Responses with Engineered Live-Attenuated <i>Listeria monocytogenes</i> (2023)

&lt;div&gt;Abstract&lt;p&gt;Improved immunization and &lt;i&gt;ex vivo&lt;/i&gt; T-cell culture strategies can generate larger numbers and more potent tumor-specific effector cells than previously possible. Nonetheless, the capacity of these cells to eliminate established tumors is limited by their ability to efficiently enter tumor-bearing organs and mediate their effector function. In the current study, we show that the administration of an engineered organ-homing microbe selectively targets tumor-specific immune responses to metastases within that organ. Specifically, an attenuated &lt;i&gt;Listeria monocytogenes&lt;/i&gt; strain, which preferentially infects the liver following systemic administration, dramatically enhances the activity of a cancer vaccine against liver metastases but not metastases in the lung. This enhanced activity results from both local recruitment of innate immune effectors as well as concentration and increased activation of vaccine-induced antitumor T cells within the liver. These findings show a general approach to focus systemic cancer immunotherapies to specific organs bearing tumor metastases by taking advantage of differential tropisms and the proinflammatory nature of microbes. (Cancer Res 2006; 66(2): 1096-104)&lt;/p&gt;&lt;/div&gt;
An exploration of design opportunities for &#x201C;gardening&#x201D; end-user programmers' ideas (2011)

Despite recent advances in supporting end-user programmers, empirical studies continue to report barriers that end users experience in problem solving with programming environments. We hypothesize that an important barrier that still needs to be overcome is the lack of support for nurturing end-user programmers' ideas on how a program should be written or on how to solve programming difficulties. Therefore, in this paper, we present a qualitative empirical investigation and triangulate the results with theories from problem solving and creativity. Moreover, we explore design opportunities and a design space for “idea gardening”, a new approach to nurturing end-user programmers' ideas and to helping them gradually gain expertise as they overcome barriers. Our results suggest that nurturing end-user programmers' ideas is a fertile area for research with an interesting, multidimensional design space.
MS and bone marrow transplant (2017)

In the article “Autologous hematopoietic stem cell transplantation in multiple sclerosis: A meta-analysis,” Sormani et al.1 found studies that had already been published about autologous hematopoietic stem cell transplantation (aHSCT) for treatment of multiple sclerosis (MS) (see the next page for an introduction to aHSCT in the treatment of MS).