gebhart/patrepeval huggingface dataset:
Building Stable Radical Cations for Non-Aqueous Redox Flow Batteries (2016)

E-mail: luzhang@anl.gov, shkrob@anl.gov Abstract: In advanced electrical grids of the future, electrochemically rechargeable fluids of high energy density could capture the power generated from intermittent sources like solar and wind. To meet this outstanding technological demand there is a need to understand the fundamental limits and interplay of electrochemical potential, stability, and solubility in low-weight redox-active molecules, among which, stability is the crucial factor for determining the real cycling performance. 1 , 2 The derivatives of 1,4-dimethoxybenzene are thus far the best performing catholyte molecules and have been intensively studied for non-aqueous redox flow batteries (NRFBs). However, most of these molecules have been found by trial and error, and the structural factors that determine durability of their radical cations (and even the nature of reactions controlling the life times of these radical cations) are insufficiently understood. In this report, an exploratory study focusing on the correlation between molecular symmetry and electrochemical stability was conducted. As shown in Fig 1, we examined a large selection of previously reported stable redox molecules 3-5 seeking for the root causes of the radical cation stability. By comparing their cycling performance, we observed that symmetric molecules are more likely to be stable than asymmetric ones. We rationalize this connection through the effect of symmetry on fragmentation (e.g., deprotonation) of a conformationally frozen radical cation. In asymmetric radical cations, the extra positive charge residing on the functional groups is unevenly distributed between them, causing more rapid fragmentation in the more positively charged groups. Following this observation, we have designed and synthesized several novel structures that are expected to be exceptionally stable redox molecules. Figure 1. Molecular Structures for Redox Active compounds. The Symmetry Group and Estimated Dipole Moments (in Debye) are indicated in the Parentheses. (1) Wei, X.; Xu, W.; Huang, J.; Zhang, L.; Walter, E.; Lawrence , C.; Vijayakumar, M.; Henderson, W. A.; Liu, T.; Cosimbescu, L.; Li, B.; Sprenkle, V.; Wang, W. Angewandte Chemie International Edition 2015 , 54 , 8684. (2) Wei, X.; Cosimbescu, L.; Xu, W.; Hu, J. Z.; Vijayakumar, M.; Feng, J.; Hu, M. Y.; Deng, X.; Xiao, J.; Liu, J.; Sprenkle, V.; Wang, W. Adv. Energy Mater. 2015 , 5 , 10.1002/aenm.201570002. (3) Huang, J.; Cheng, L.; Assary, R. S.; Wang, P.; Xue, Z.; Burrell, A. K.; Curtiss, L. A.; Zhang, L. Adv. Energy Mater. 2015 , 5 , 1401782. (4) Zhang, L.; Zhang, Z.; Redfern, P. C.; Curtiss, L. A.; Amine, K. Energy &amp; Environ. Sci. 2012 , 5 , 8204. (5) Zhang, Z.; Zhang, L.; Schlueter, J. A.; Redfern, P. C.; Curtiss, L.; Amine, K. J. Power Sources 2010 , 195 , 4957. Figure 1
Interfacial plasticity facilitates high reaction rate of E. coli FAS malonyl-CoA:ACP transacylase, FabD (2020)

Fatty acid synthases (FASs) and polyketide synthases (PKSs) iteratively elongate and often reduce two-carbon ketide units in de novo fatty acid and polyketide biosynthesis. Cycles of chain extensions in FAS and PKS are initiated by an acyltransferase (AT), which loads monomer units onto acyl carrier proteins (ACPs), small, flexible proteins that shuttle covalently linked intermediates between catalytic partners. Formation of productive ACP-AT interactions is required for catalysis and specificity within primary and secondary FAS and PKS pathways. Here, we use the <i>Escherichia coli</i> FAS AT, FabD, and its cognate ACP, AcpP, to interrogate type II FAS ACP-AT interactions. We utilize a covalent crosslinking probe to trap transient interactions between AcpP and FabD to elucidate the X-ray crystal structure of a type II ACP-AT complex. Our structural data are supported using a combination of mutational, crosslinking, and kinetic analyses, and long-timescale molecular dynamics (MD) simulations. Together, these complementary approaches reveal key catalytic features of FAS ACP-AT interactions. These mechanistic inferences suggest that AcpP adopts multiple, productive conformations at the AT binding interface, allowing the complex to sustain high transacylation rates. Furthermore, MD simulations support rigid body subdomain motions within the FabD structure that may play a key role in AT activity and substrate selectivity.
Optimization of Mixed-ADC Multi-Antenna Systems for Cloud-RAN Deployments (2017)

We propose a mixed analog-to-digital converter ADC (mixed-ADC) structure for a cloud-RAN system, where a single-antenna user terminal communicates with a multi-antenna remote radio head (RRH). In the proposed structure, the RRH is equipped with a mixed-ADC pool that includes multiple ADC units with various resolutions. In this pool, the RRH selects the appropriate ADCs and connects the selected ADCs to each antenna to quantize the received signals; thereby each antenna can have a different resolution ADC. The fronthaul capacity is limited, so that the sum of the bits produced in the selected ADCs is also limited. To maximize the spectral efficiency or the energy efficiency of such a system, we propose algorithms for ADC resolution selection based on an approximation of the generalized mutual information in the low signal-to-noise regime. In the proposed algorithms, we show that for spectral efficiency, using high-resolution ADC on the strong channels is beneficial. The results for energy efficiency maximization are similar, though the largest resolutions are reduced to save power. The simulations show that the proposed method provides significant performance improvement.
Reconstructing the Human Hematopoietic Niche: Opportunities for Studying Normal and Malignant Hematopoiesis, (2011)

Abstract Abstract 3412 Interactions with the hematopoietic niche in the bone marrow (BM) microenvironment are essential for hematopoietic stem cell (HSC) self-renewal. In addition, in hematological malignancies this niche is considered to serve as a sanctuary site for leukemic stem cells during chemotherapy, and to contribute to disease relapse. Although many advances have been made in understanding how the niche regulates HSC self-renewal and confers therapy resistance, most of this knowledge is based on genetic loss- or gain-of-function murine models. Since these models do not recapitulate the human physiology, there is a need for models that more closely resemble the human niche. Here, we describe a unique humanized model, which implements a novel scaffold-based technology for generating a human bone environment in RAG2−/−gc−/−-mice. Inoculation of these mice with normal human CD34+ hematopoietic progenitor cells, isolated from umbilical cord blood, resulted in homing to the human bone environment and the generation of human hematopoietic cells of distinct lineages, but more importantly also the engraftment of CD34+ cells themselves. In a next series of experiments the supportive nature of the humanized niche was further investigated with patient-derived acute myeloid leukemia (pAML) and multiple myeloma (pMM) cells, two hematopoietic malignancies that are highly dependent on the BM microenvironment for survival and growth. Inoculation of the humanized mice with pAML cells, obtained from a poor-risk patient (M1; complex karyotype) or cells from a good risk AML patient (M4; inv(16)) revealed the ability of the reconstructed human bone environment to support outgrowth of the leukemia with the cells having a similar phenotype as those from the patient sample. Interestingly, engraftment of good risk AML samples, including inv(16), has been reported to be very difficult in the NOD/SCID-based AML xenotransplant model. The humanized model that we developed was further substantiated by the ability to support the outgrowth of pMM from 7 out of 7 patients. MM is a hematological malignancy that fails to grow in mouse tissues without extra support, e.g. fetal human bone chips. Moreover, the outgrowth of pMM in our humanized model is accompanied by an increase in osteoclast activity, indicating the presence of bone resorption, one of the most relevant clinical sequelae of MM. In addition, by gene-marking pMM cells with luciferase and using bioluminescent imaging, we were able to follow myeloma outgrowth in time. Treatment of pMM-bearing mice with identical drugs as given to the patients showed that the pMM cells growing in the humanized environment in the mice responded similar as the MM patients. Hence, our model allows, for the first time, to investigate essential interactions within the human BM microenvironment for the development of normal and malignant hematopoiesis and thus for therapy development. Disclosures: de Bruijn: Xpand Biotechnology BV: Employment. Weers:Genmab BV: Employment. Parren:Genmab BV: Employment.
Preclinical metabolism and disposition of an orally bioavailable macrocyclic FXIa inhibitor (2021)

FXIa-6f is a high affinity, orally bioavailable macrocyclic FXIa inhibitor with antithrombotic activity in preclinical species.The objectives of this study were to characterize the in vitro metabolism, determine circulating metabolites in pre-clinical species, and examine the disposition of the compound in a bile duct-cannulated rat study (BDC) study to inform clinical development of the compound and the medicinal chemistry approach to identify molecules with improved properties.Across species, metabolic pathways included several oxidative metabolites, including hydroxylated metabolites on the macrocycle or P1 region, descarbamoylation of the methyl carbamate side chain, and a glutathione conjugate on the 2,6-difluoro-3-chlorophenyl ring.In BDC rat, the absorbed dose of [<sup>3</sup>H]FXIa-6f was cleared mainly by metabolism, with excretion of drug-related material in the bile, mostly as metabolites.In all preclinical species, the parent drug was the primary drug-related component in circulation, but the species differences in the metabolic pathways observed in vitro were reflected in the plasma, where M6, a descarbamoylated metabolite, was more prominent in rat plasma, and M9, a hydroxylated metabolite, was more prominent in monkey plasma. Based on the available data, the human metabolism appears to be most similar to monkey.
Simulation of defect detection schemes for wafer inspection in VLSI manufacturing (2002)

The detection of critical defects on modern VLSI wafers is a challenging and complex problem. Simulation of these critical defects allows for rapid characterization and optimization of in-line detection schemes. In this paper we introduce a 3D electromagnetic field simulator (METRO 3D) that calculates the scattering of light from wafer topographies. An approach that allows highly absorptive materials to be investigated is discussed for the three dimensional topography simulator. With this enhancement to the simulator, several defect studies were performed and the results of these studies illustrate the ability of the simulator to model wafer topographies and defects that occur in modern fab lines.
Thermal conductivity manipulation in lithographically patterned single crystal silicon phononic crystal structures (2011)

The thermal conductivity of single crystal silicon was engineered using lithographically formed phononic crystals. Specifically, sub-micron periodic through-holes were patterned in 500nm-thick silicon membranes to construct phononic crystals, and through phonon scattering enhancement, heat transfer was significantly reduced. The thermal conductivity of silicon phononic crystals was measured as low as 32.6W/mK, which is a ∼75% reduction compared to bulk silicon thermal conductivity [1]. This corresponds to a 37% reduction even after taking into account the contributions of the thin-film and volume reduction effects, while the electrical conductivity was reduced only by as much as the volume reduction effect. The demonstrated method uses conventional lithography-based technologies that are directly applicable to diverse micro/nano-scale devices, leading toward huge performance improvements where heat management is important.
An Acoustic Echo Canceller Using Subband Adaptive Filters (1996)

The use of hands-free communication in cars, computer applications and video-conferencing has created a demand for high-quality acoustic echo cancellation. In these applications have the acoustic channel typically a long impulse response in the order of 100ms. Typical lengths of adaptive FIR-filters can be 500-1500 taps. In order to reduce the complexity and also improve the convergence rate have subband processing schemes been suggested. This paper presents an implementation of a delayless subband adaptive filter. The study shows a possible suppression of about 30 dB and also a more rapid convergence than a fullband LMS-filter.
A Materials Aging Problem in Theory and Practice (2000)

olyesters are widely used in plastic objects, films, and fabrics. A recurring mechanism of polyester aging is attack by humidity (hydrolysis), whereby the long chain molecules are cleaved and the material softens. This article offers an approach for modeling the hardness/aging behavior of commercial polyesters. The model is qualitatively consistent with exposure tests on fresh polyester plastic material made from a commercially available resin and hardening agent. It expresses the rate of polyester hydrolysis in terms of the relative humidity, and then connects the degree of hydrolysis to hardness using a relation that accounts for stabilizers that are present in commercial polymers to counter the hydrolysis. (Keywords: Balance of life, Environmental exposure, Ester hydrolysis, Materials aging, Polyester hydrolysis, Polyesters.)
Generalized Planning With Deep Reinforcement Learning (2020)

A hallmark of intelligence is the ability to deduce general principles from examples, which are correct beyond the range of those observed. Generalized Planning deals with finding such principles for a class of planning problems, so that principles discovered using small instances of a domain can be used to solve much larger instances of the same domain. In this work we study the use of Deep Reinforcement Learning and Graph Neural Networks to learn such generalized policies and demonstrate that they can generalize to instances that are orders of magnitude larger than those they were trained on.
Direction of Arrival Estimation using Eigenanalysis of the Parameterized Spatial Correlation Matrix (2007)

The estimation of the direction-of-arrival (DOA) of one or more acoustic sources is an area that has generated much interest in recent years, with applications like automatic video camera steering and multi-party stereophonic teleconferencing entering the market. Time-difference-of-arrival (TDOA) based methods compute each relative delay using only two microphones, even though additional microphones are usually available, and thus suffer from the effects of background noise and reverberation. This paper deals with DOA estimation based on spatial spectral estimation, and proposes a novel DOA estimator based on the eigenvalues of the parameterized spatial correlation matrix. Simulation results confirm the ability of the proposed method to provide reliable estimates even in heavily reverberant environments.
Biphasic Electrical Stimulation Promotes Insulin Release (2018)

Biphasic (anodal pulse followed immediately by a cathodal pulse) electrical stimulation (10Hz, 5 ms duration) of rat insulinoma (Ins‐1) cells resulted in a 2–3‐fold increase in insulin release over 30 min that was stimulation period‐ and voltage‐dependent. Electrical stimulation of tissue culture medium (in the absence of cells) did not increase insulin release when subsequently added to cells, confirming that the insulin released by electrical stimulation was not due to substances generated by the culture medium. Electrical stimulation‐induced insulin release occurred in the absence or presence of glucose. Calcium channel blockade (using nifedipine or verapamil) inhibited basal insulin secretion and insulin secretion evoked by electrical stimulation, demonstrating that electrical stimulation‐induced insulin release involved activation of voltage‐dependent calcium channels and was not a non‐specific effect of stimulation on the plasma membrane. Basal insulin secretion and the increase in insulin release induced by electrical stimulation were also inhibited by the mitochondrial poisons antimycin A or oligomycin A, suggesting a role for mitochondrial function in insulin secretion. Electrical stimulation of cells also resulted in a more pronounced uptake of MitoTracker Red by mitochondria, indicating a more negative inner mitochondrial membrane potential. The failure of cells to accumulate the fluorogenic dye Cytotox green confirmed that electrical stimulation was not significantly disrupting the plasma membrane or inducing overt toxicity to the cells during the period of stimulation. These results provide further evidence that biphasic electrical stimulation can exert significant biological effects and elicit insulin release in a manner that is dependent upon mitochondrial activity and calcium channel activation but independent of glucose. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
InP–InGaAsP Integrated 1 $\times$ 5 Optical Switch Using Arrayed Phase Shifters (2008)

An integrated semiconductor 1times5 InP-InGaAsP optical phased-array switch is fabricated and characterized. Using the carrier-induced refractive index change of InGaAsP waveguide, we achieve successful switching to five output ports with less than 60-mA current injection. Wide operating bandwidth covering the entire C-band (1520-1580 nm) and nanoseconds dynamic response are demonstrated, making it potentially applicable to large-capacity wavelength-multiplexed optical-packet-switching routers.
Supplementary Figure 1 from XPO1 (CRM1) Inhibition Represses STAT3 Activation to Drive a Survivin-Dependent Oncogenic Switch in Triple-Negative Breast Cancer (2023)

&lt;p&gt;PDF file - 66K, Molecular structures of the KPT-SINES.&lt;/p&gt;
Continuous Power Transfer Control of Triple Active Bridge Converter during Magnetic Saturation (2022)

A multi input, multi output power converter has become more prevalent in recent years due to the proliferation of renewable energy and electric vehicles. Recently, a triple active bridge (TAB) converter that connects plural electric devices has attracted attention. In this study, the overcurrent preventive control during magnetic saturation and the high-speed recovery control are proposed. The effectiveness of these controls is verified using a 2 kW experiment.
Re: Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation (2020)

No AccessJournal of UrologyUrological Survey1 Sep 2020Re: Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation Anthony AtalaMD Anthony AtalaAnthony Atala More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000001179AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation." The Journal of Urology, 204(3), p. 622 Suggested Reading : Long noncoding RNA MALAT-1 is a new potential therapeutic target for castration resistant prostate cancer. J Urol 2013; 190: 2278. Link, Google Scholar © 2020 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 204Issue 3September 2020Page: 622-622 Advertisement Copyright & Permissions© 2020 by American Urological Association Education and Research, Inc.MetricsAuthor Information Anthony Atala More articles by this author Expand All Advertisement Loading ...
Determining plasmonic hot-carrier energy distributions via single-molecule transport measurements (2020)

Hot carriers in plasmonic nanostructures, generated via plasmon decay, play key roles in applications such as photocatalysis and in photodetectors that circumvent bandgap limitations. However, direct experimental quantification of steady-state energy distributions of hot carriers in nanostructures has so far been lacking. We present transport measurements from single-molecule junctions, created by trapping suitably chosen single molecules between an ultrathin gold film supporting surface plasmon polaritons and a scanning probe tip, that can provide quantification of plasmonic hot-carrier distributions. Our results show that Landau damping is the dominant physical mechanism of hot-carrier generation in nanoscale systems with strong confinement. The technique developed in this work will enable quantification of plasmonic hot-carrier distributions in nanophotonic and plasmonic devices.
Novel data processing and image co-registration algorithm for region-specific lipid profiling in colorectal cancer tissue using DESI imaging mass spectrometry. (2013)

e14620 Background: Imaging mass spectrometry (iMS) is a promising technique for cancer biomarker discovery. Clinical translation of iMS requires advanced data treatment methods and efficient co-registration of histology and iMS imaging modalities. In this study desorption electrospray ionisation (DESI) iMS has been used to address four aims: 1. To develop a data processing workflow to address current limitations; 2. To design an interactive software platform for image co-registration; 3. To investigate region-specific lipid biochemistry in colorectal cancer (CRC) tissue using the strategy outlined in aims 1-2; 4.To introduce an automated tissue recognition system based on multivariate molecular ion patterns (MIPs). Methods: Fresh CRC tissue sections (n=49) were subjected to DESI-iMS using a Thermo Exactive mass spectrometer coupled with a DESI ion source. Mass spectra were collected in the range m/z = 200-1000. Sections were then H&amp;E stained and scanned at high resolution. DESI-iMS data pre-processing involved peak detection, removal of noise/solvent related peaks and variance stabilising normalisation. An interactive image co-registration interface was developed using a feature-based image alignment algorithm for precise exploration of tissue region-specific biochemistry. A Recursive Maximum Margin Criterion (RMMC) algorithm was introduced for improved extraction of tissue specific MIPs. Results: CRC DESI-iMS profiles consisted mainly of complex lipids including phosphatidyl-inositols, phosphatidyl-serines, and phosphatidyl-ethanolamine plasmalogens. Different histological tissue regions showed characteristic lipid profiles. An automated tissue recognition system using multivariate MIPs derived by the proposed RMMC approach demonstrated highly accurate (classification accuracy &gt;98%) identification of pixels according to tissue type (cancer, healthy mucosa, smooth muscle, fibrous tissue, stroma). Conclusions: This workflow permits accurate tissue-specific lipidomic characterisation of the CRC tumor microenvironment and permits accurate reconstruction of different tissue types based on MIPs.