gebhart/patrepeval huggingface dataset:
Stairway to the Conical Intersection:  A Computational Study of the Retinal Isomerization (2007)

The potential-energy surface of the first excited state of the 11-cis-retinal protonated Schiff base (PSB11) chromophore has been studied at the density functional theory (DFT) level using the time-dependent perturbation theory approach (TDDFT) in combination with Becke's three-parameter hybrid functional (B3LYP). The potential-energy curves for torsion motions around single and double bonds of the first excited state have also been studied at the coupled-cluster approximate singles and doubles (CC2) level. The corresponding potential-energy curves for the ground state have been calculated at the B3LYP DFT and second-order Møller-Plesset (MP2) levels. The TDDFT study suggests that the electronic excitation initiates a turn of the beta-ionone ring around the C6-C7 bond. The torsion is propagating along the retinyl chain toward the cis to trans isomerization center at the C11=C12 double bond. The torsion twist of the C10-C11 single bond leads to a significant reduction in the deexcitation energy indicating that a conical intersection is being reached by an almost barrierless rotation around the C10-C11 single bond. The energy released when passing the conical intersection can assist the subsequent cis to trans isomerization of the C11=C12 double bond. The CC2 calculations also show that the torsion barrier for the twist of the retinyl C10-C11 single bond adjacent to the isomerization center almost vanishes for the excited state. Because of the reduced torsion barriers of the single bonds, the retinyl chain can easily deform in the excited state. Thus, the CC2 and TDDFT calculations suggest similar reaction pathways on the potential-energy surface of the excited state leading toward the conical intersection and resulting in a cis to trans isomerization of the retinal chromophore. According to the CC2 calculations the cis to trans isomerization mechanism does not involve any significant torsion motion of the beta-ionone ring.
Cell-Free Biosynthesis of Fluoroacetate and 4-Fluorothreonine in Streptomyces cattleya (2002)

Die Biosynthese von Organofluorverbindungen, z. B. Fluoracetat, gelingt ausgehend von (S)-Adenosyl-L-methionin (SAM) mit Fluoridionen in einem zellfreien Extrakt von Streptomyces cattleya. Durch Inkubieren von 5′-Fluor-5′-desoxyadenosin (5′-FDA), dem ersten Organofluorprodukt auf dem Weg zum Fluoracetat, mit dem zellfreien Extrakt wird Fluoracetaldehyd angereichert, was dessen Bedeutung als Intermediat in der Synthese von Fluormetaboliten bestätigt (siehe Schema). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2002/z19887_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Probing Specificities of Alcohol Acyltransferases for Designer Ester Biosynthesis with a High-Throughput Microbial Screening Platform (2021)

ABSTRACT Alcohol acyltransferases (AATs) enables microbial biosynthesis of a large space of esters by condensing an alcohol and an acyl CoA. However, substrate promiscuity of AATs prevents microbial biosynthesis of designer esters with high selectivity. Here, we developed a high-throughput microbial screening platform that facilitates rapid identification of AATs for designer ester biosynthesis. First, we established a microplate-based culturing technique with in situ fermentation and extraction of esters. We validated its capability in rapid profiling of the alcohol substrate specificity of 20 chloramphenicol acetyltransferase variants derived from Staphylococcus aureus (CAT Sa ) for microbial biosynthesis of acetate esters with various exogeneous alcohol supply. By coupling the microplate-based culturing technique with a previously established colorimetric assay, we developed a high-throughput microbial screening platform for AATs. We demonstrated that this platform could not only confirm CAT Sa F97W with enhanced isobutyl acetate synthesis but also identify three ATF1 Sc (P348M, P348A, and P348S) variants, derived from Saccharomyces cerevisiae ’s AAT and engineered by model-guided protein design, for enhanced butyl acetate production. We anticipate the high-throughput microbial screening platform is a useful tool to identify novel AATs that have important roles in nature and industrial biocatalysis for designer bioester production.
Deep Unrolled Recovery in Sparse Biological Imaging (2021)

Deep algorithm unrolling has emerged as a powerful model-based approach to develop deep architectures that combine the interpretability of iterative algorithms with the performance gains of supervised deep learning, especially in cases of sparse optimization. This framework is well-suited to applications in biological imaging, where physics-based models exist to describe the measurement process and the information to be recovered is often highly structured. Here, we review the method of deep unrolling, and show how it improves source localization in several biological imaging settings.
Functional Separation of mRNA Domains Coordinates Pluripotent Cell Behavior (2022)

Differential expression of mRNA coding sequences (CDSs) and 3-prime untranslated regions (UTRs) is widespread, yet whether these domains contribute independently to cellular function remains unclear. Here, using Nanog as a model, we find that Nanog mRNA domain usage is spatially organized in mouse and human pluripotent cells and in the blastocyst, with cells enriched in 3-prime UTR transcripts marking colony borders and cells enriched for the Nanog CDS located interior. Functional perturbation reveals a marked asymmetry between mRNA domains. Loss of the Nanog 3-prime UTR leads to defects in colony architecture, cell spreading and morphogenetic behavior, accompanied by decreased extracellular matrix modeling gene expression and ROCK dependent cytoskeletal organization. In contrast, deletion of the Nanog CDS primarily disrupts epithelial polarity-associated transcriptional programs and the expression of chromatin regulators, consistent with a dominant role for the Nanog protein in transcriptional and epigenetic control. These domain specific effects are not redundant but instead reflect separable regulatory activities encoded within a single transcript. Together, these findings demonstrate that distinct regions of a single mRNA can encode separable and asymmetric biological functions, revealing mRNA domain usage as a distinct regulatory layer through which genes can encode multiple biological outputs beyond protein coding capacity.
Ubiquitous Advertising: The Killer Application for the 21st Century (2010)

This article discusses the trend toward ad-supported ubiquitous computing as well as the problems advertisers face and how ubiquitous computing can solve them. It mentions that advertising will be the next major application for ubiquitous computing. Ads will support ubiquitous computing, and ubiquitous computing will support advertisers with ad targeting, ad feedback, customer awareness, and privacy.
EU FP7 INFSO-ICT-317669 METIS, D3.1 Positioning of multi-node/multi-antenna technologies (2013)

This document describes the research activity in multi-node/multi-antenna technologies within METIS and positions it with respect to the state-of-the-art in the academic literature and in the standardization bodies. Based on the state-of-the-art and as well as on the METIS objectives,
we set the research objectives and we group the different activities (or technology components) into research clusters with similar research objectives. The technology
components and the research objectives have been set to achieve an ambidextrous purpose. On one side we aim at providing the METIS system with those technological components that are a natural but non-trivial evolution of 4G. On the other side, we aim at seeking for disruptive
technologies that could radically change 5G with respect to 4G. Moreover, we mapped the different technology components to METIS’ other activities and to the overall goals of the
project.
White matter volume in the brainstem and inferior parietal lobule is related to motor performance in children with autism spectrum disorder: A voxel‐based morphometry study (2016)

Many studies have reported poor motor performance in autism spectrum disorder (ASD); however, the underlying brain mechanisms remain unclear. Recent neuroimaging studies have suggested that abnormalities of the white matter (WM) are related to the features of ASD. In this study, we used voxel-based morphometry (VBM) to investigate which WM regions correlate with motor performance in children with ASD, and whether the WM volume in those brain regions differed between children with ASD and typically developing (TD) children. The subjects included 19 children with ASD and 20 TD controls. Motor performance was assessed using the Movement Assessment Battery for Children 2 (M-ABC 2). Children with ASD showed poorer motor performance than did the controls. There was a significant positive correlation between the total test score on the M-ABC 2 and the volume of WM in the brainstem and WM adjacent to the left supramarginal gyrus (SMG). In addition, compared with the TD controls, children with ASD had a decreased volume of WM in the brainstem and adjacent to the left intraparietal sulcus, which is close to the SMG. These findings suggest that structural changes in the WM in the brainstem and left inferior parietal lobule may contribute to poor motor performance in children with ASD. Autism Res 2016, 9: 981-992. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.
Supplementary Figures from Rebalancing Protein Homeostasis Enhances Tumor Antigen Presentation (2023)

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Kernel Based Reconstruction for Generalized Graph Signal Processing (2023)

In generalized graph signal processing (GGSP), the signal associated with each vertex in a graph is an element from a Hilbert space. In this paper, we study GGSP signal reconstruction as a kernel ridge regression (KRR) problem. By devising an appropriate kernel, we show that this problem has a solution that can be evaluated in a distributed way. We interpret the problem and solution using both deterministic and Bayesian perspectives and link them to existing graph signal processing and GGSP frameworks. We then provide an online implementation via random Fourier features. Under the Bayesian framework, we investigate the statistical performance under the asymptotic sampling scheme. Finally, we validate our theory and methods on real-world datasets.
Group-based Object Alignment in Virtual Reality Environments (2022)

Group-based object alignment is an essential manipulation task, particularly for complex scenes. In conventional 2D user interfaces, such alignment tasks are generally achieved via a command/menu-based interface. Virtual reality (VR) head-mounted displays (HMDs) provide a rich immersive interaction experience, which opens more design options for group-based object alignment interaction techniques. However, object alignment techniques in immersive environments are underexplored. In this paper, we present four interaction techniques for 3 degrees-of-freedom translational alignments: AlignPanel, AlignWidget, AlignPin, and AlignGesture. We evaluated their performance, workload, and usability in a user study with 20 participants. Our results indicate different benefits and drawbacks of these techniques for group-based alignment in immersive systems. Based on the findings, we distill a set of design choices and recommendations for these techniques in various application scenarios.
Large-field dielectric loss in relaxor ferroelectric PLZT (2014)

Lead zirconate titanate ceramics are often used at unipolar drive field levels approaching or exceeding the coercive field, yet dielectric losses are characterized by a loss tangent measured at a significantly lower drive field. As the magnitude of the drive field is increased the energy dissipation can increase significantly over that predicted by the low-field loss tangent. This experimental study addresses the effects of temperature and bias stress on large-field dielectric loss in lanthanum-doped lead zirconate titanate, Pb0.92La0.08(Zr0.65Ti0.35)0.98O3 (PLZT 8/65/35). Large-field dielectric loss was experimentally determined by measuring the area within a unipolar electric displacement–electric field hysteresis loop. The results show the effects of saturation on the effective loss tangent.
Potential use of microbubbles (MBs) as contrast material in x-ray dark field (DF) imaging: How does the DF signal change with the characteristic parameters of the MBs? (2016)

One of the most exciting aspects of the grating based x-ray differential phase contrast (DPC) acquisition method is the concurrent generation of the so-called dark field (DF) signal, along with the classical absorption signal and the novel DPC signal. The DF signal is associated with local distribution of small angle scatterers in an image object, while the absorption signal and DPC signal are often used to characterize the relatively uniform structure of the image object. Besides the endogenous image contrast, exogenous contrast media are often used in x-ray imaging to locally enhance the image signal. This paper proposes a potential contrast medium for DF signal enhancement: microbubbles (MBs). MBs have already been developed for clinical use in ultrasound imaging, and recent experimental studies have shown that MBs may also enhance the DF signal, although it remained unclear how the physical characteristics of the MBs quantitatively impact the DF signal. In this paper, a systematic study was performed to investigate the quantitative relationships between the DF signal and the following properties of MBs: size, concentration, shell thickness, size uniformity, and whether gold nanoparticles were attached. The experimental results demonstrated that, an increased MB size (about 4 microns) may generate a stronger DF signal for our DPC imaging system; additionally, a moderately increased shell thickness and the use of gold nanoparticles on the shell surface also resulted in further enhancement of the DF signal. These findings may provide critical information needed for using MBs as the contrast agent of x-ray DF imaging.
Sugar Sulfamates for Seizure Control: Discovery and Development of Topiramate, a Structurally Unique Antiepileptic Drug (2009)

TOPAMAX((R)) (topiramate) 1, is a broad-spectrum anticonvulsant that has been marketed worldwide for the treatment of epilepsy and migraine. We discovered this blockbuster drug serendipitously in a project that originally sought a new antidiabetic agent. Topiramate has useful neurological effects that derive from multiple CNS mechanisms of action, but it is basically a "neurostabilizer" by virtue of attenuating the excitability of brain neuronal pathways. During its extensive clinical use, topiramate was also found to possess antimetabolic dysfunction activity, which could be applicable in the treatment of diabetes and obesity. This article discusses research results and events surrounding the discovery and development of topiramate.
Mechanisms of Bacteriophage Inactivation via Singlet Oxygen Generation in UV Illuminated Fullerol Suspensions (2009)

Nonenveloped viruses are shown to be inactivated by singlet oxygen ((1)O2) produced in UVA photosensitized aqueous suspensions of a polyhydroxylated fullerene (C60(OH)22-24; fullerol, 40 microM). Experiments were performed with MS2, a ssRNA bacteriophage, as well as two dsDNA phages: PRD1, which has an internal lipid membrane, and T7, which entirely lacks lipids. MS2 was highly susceptible to inactivation, having a rate constant of 0.034 min(-1) with UVA alone, which increased to 0.102 min(-1) with photoactivated fullerol. PRD1 and T7 were not susceptible to UVA alone but were photoinactivated by fullerol with rate constants of 0.026 and 0.035 min(-1), respectively. The role of 1(O)2 was demonstrated by three independent observations: (i) viruses that were insensitive to UVA alone were photoinactivated by rose bengal in the absence of fullerol, (ii) beta-carotene reduced (but did not eliminate) photoinactivation rates, and (iii) singlet oxygen sensor green fluorescence spectroscopy directly detected (1)O2 in UVA illuminated fullerol suspensions. Qualitative evidence is also presented that fullerol aggregates were closely associated with viruses allowing efficient transfer of 1(O)2 to their capsids. Fourier transform infrared spectroscopy revealed significant oxidative modifications to capsid proteins but comparatively minor changes to the DNA and (phospho)lipids. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) suggested (1)O2 induced crosslinking of proteins. Hence, phage inactivation by photoactivated fullerol nanoparticles appears to be caused by cross-linking of capsid protein secondary structures by exogenous (1)O2 and consequentimpairmentof their ability to bind to surface receptors of their bacterial hosts (loss of infectivity) rather than by direct reactions with fullerol.
Milliwatt midinfrared from intrapulse difference frequency with a single erbium fiber laser (2020)

We generate about 2 mW of midinfrared in orientation-patterned gallium phosphide pumped by an erbium fiber laser. The midinfrared spectrum has a strong component around 8 to 10 &mu;m wavelength, with a broad background from about 7 to 12 &mu;m. The pump laser has 5 W, single mode output at 96 MHz compressed to 65 fs, with a peak power of up to about 0.6 MW. Before midinfrared generation, we further broaden and recompress the pulses in a small length of fiber, obtaining 3 W of 17 fs pulses with peak power near 1 MW but broader bandwidth to generate midinfrared.
Astrocyte‐derived adenosine excites sleep‐promoting neurons in the ventrolateral preoptic nucleus: Astrocyte‐neuron interactions in the regulation of sleep (2022)

Although ATP and/or adenosine derived from astrocytes are known to regulate sleep, the precise mechanisms underlying the somnogenic effects of ATP and adenosine remain unclear. We selectively expressed channelrhodopsin-2 (ChR2), a light-sensitive ion channel, in astrocytes within the ventrolateral preoptic nucleus (VLPO), which is an essential brain nucleus involved in sleep promotion. We then examined the effects of photostimulation of astrocytic ChR2 on neuronal excitability using whole-cell patch-clamp recordings in two functionally distinct types of VLPO neurons: sleep-promoting GABAergic projection neurons and non-sleep-promoting local GABAergic neurons. Optogenetic stimulation of VLPO astrocytes demonstrated opposite outcomes in the two types of VLPO neurons. It led to the inhibition of non-sleep-promoting neurons and excitation of sleep-promoting neurons. These responses were attenuated by blocking of either adenosine A<sub>1</sub> receptors or tissue-nonspecific alkaline phosphatase (TNAP). In contrast, exogenous adenosine decreased the excitability of both VLPO neuron populations. Moreover, TNAP was expressed in galanin-negative VLPO neurons, but not in galanin-positive sleep-promoting projection neurons. Taken together, these results suggest that astrocyte-derived ATP is converted into adenosine by TNAP in non-sleep-promoting neurons. In turn, adenosine decreases the excitability of local GABAergic neurons, thereby increasing the excitability of sleep-promoting GABAergic projection neurons. We propose a novel mechanism involving astrocyte-neuron interactions in sleep regulation, wherein endogenous adenosine derived from astrocytes excites sleep-promoting VLPO neurons, and thus decreases neuronal excitability in arousal-related areas of the brain.
Catalytic activity of Co–Nx/C electrocatalysts for oxygen reduction reaction: a density functional theory study (2012)

First-principles DFT computations are performed to explain the origin and the mechanism of oxygen reduction reaction (ORR) on Co-N(x) (x = 2, 4) based self-assembled carbon supported electrocatalysts in alkaline and acidic media. The results show that the formation of graphitic Co-N(4) defect is energetically more favorable than the formation of graphitic Co-N(2) defect. Furthermore graphitic Co-N(4) defects are predicted to be stable at all potentials (U = 0-1.23 V) in the present study while Co-N(2) defects are predicted to be unstable at high potentials. Therefore the Co-N(4) defect is predicted to be the dominant in-plane graphitic defect in Co-N(x)/C electrocatalysts. O(2) chemisorbs to Co-N(4) and Co-N(2) defects indicating that both defect motifs are active for the reduction of O(2) to peroxide. However, the weak interaction between peroxide and Co-N(4) defect shows that this defect does not promote complete ORR and a second site for the reduction of peroxide is required, supporting a 2 × 2e(-) dual site ORR mechanism independent of pH of the electrolyte. In contrast, the much stronger interaction between peroxide and Co-N(2) defect supports a 2 × 2e(-) single site ORR mechanism in alkaline and acidic media.
Useful computations need useful numbers (2007)

Most of us have taken the exact rational and approximate numbers in our computer algebra systems for granted for a long time, not thinking to ask if they could be significantly better. With exact rational arithmetic and adjustable-precision floating-point arithmetic to precision limited only by the total computer memory or our patience, what more could we want for such numbers? It turns out that there is much more that can be done that permits us to obtain exact results more often, more intelligible results, approximate results guaranteed to have requested error bounds, and recovery of exact results from approximate ones.
Morphology development for three‐component emulsion polymers: Theory and experiments (1993)

Abstract Three‐component emulsion polymer systems constitute an overall four‐component system from a morphological viewpoint. The aqueous phase is always the continuous phase within which 22 distinct and thermodynamically stable particle morphologies may exist. Six uniquely different categories of particles compose this morphological menu and may be identified as core–shell–shell, hemicore, hemishell, trisectional, “snowman,” and cored hemisphere. Extension of previously published free‐energy thermodynamic analyses of two component emulsion polymers has resulted in the ability to predict the most likely equilibrium morphology to be found for three‐component particles. Predictions have been carried out for each possible three‐component combination of poly(methyl methacrylate), polystyrene, poly(dimethyl siloxane), and polycarbonate. The results show that in nearly every instance two or three different morphologies are computed to possess nearly equivalent free energies, whereas all other possibilities would result in much higher free energies. This indicates that more precise knowledge of all interfacial tensions is required when considering three‐component systems than was found to be generally needed for two‐component systems. Experiments were carried out for each polymer combination using a very surface‐active emulsifier (sodium lauryl sulfate) and, separately, a weakly surface‐active emulsifier (natural pectin). For this choice of polymers and emulsifiers, only three of the six unique morphological categories were found experimentally. In all cases, the thermodynamic analysis predicted the experimentally determined morphology to possess the lowest or next to lowest free energy. © 1993 John Wiley &amp; Sons, Inc.