gebhart/patrepeval huggingface dataset:
Bio-Inspired Heterogeneous Catalytic Cascades (2020)

Bio-electrochemistry research in our group has been focused on building suitable materials and design of interfaces to accommodate biocatalysts, both enzymatic and microbial for most advantageous utilization in sensing, energy harvesting and water treatment technologies. Over the years we have demonstrated several enabling materials design approaches to address critical challenges in bio-electrocatalysis: facilitating charge transfer through tethering immobilization, enzyme orientation, hierarchically structured nano-materials integrated into device design, immobilization by encapsulation in polymer and silica matrixes and development of hybrid microbial/enzymatic and microbial/platinum group metal-free bio-electrochemical devices. A critical challenge in building complex bio-nano-devices is the ability to combine several catalytic reactions into a “cascade” with channeling as underlying principle for effective multi-step catalysis. 1 One particularly complex area of our research over the last yeas has been in development of materials solutions for catalytic cascades, which would integrate bio-catalysis with molecular and heterogeneous catalytic steps. 2-4 We are currently engaged in a large program directed towards bringing together functional catalysts from the most distinctly different types: enzymes, molecular catalyst and metallic nanoparticles into a singular functional interface for realization of cascade reactions catalyzed by all these different species/moieties. We will illustrate the approach by discussing the synthesis of a hybrid enzyme/metal nano-particle/atomically-dispersed nano-material functional catalyst cascade. This bio-inspired catalytic cascade aims to demonstrate the possibility of assembling heterogeneous catalytic reactions in sequence while the catalysts of three dissimilar classes are all immobilized on a 2D nanomaterial (graphene). The paper aims to bring a vision of building bio-electrochemical devices, where enzymatic catalysis will be enhanced by the heterogeneous and molecular one, with all catalytic moieties co-present at a single “designer interface” based on graphene-like carbonaceous material. This material allows ease of integration by printing into a paper-based microfluidic analytical platform designed for a confocal Raman microscope with in situ spectro-electrochemical detection. 5,6 1. Wheeldon, I., et al., Nature Chemistry, 8 (2016) 299–309 2. Abdellaoui,S., et al., Chemical Communications , 53(2017) 5368-5371 3. Xia, L., et al., ACS Energy Letters. , 2 (2017) 1435-1438 4. Perry, A., et al., ChemElectroChem , 4 (2017) 2336-2344 5. Andersen, N., et al., ChemElectroChem , 6 (2019) 246-251 6. Andersen, N., et al., ChemElectroChem , 6 (2019) 2448–2455 Figure 1
<title>Multiscale object representation using surface patches</title> (1994)

We introduce an approach to the representation of curved or polyhedral 3-D objects and apply this representation to pose estimation. The representation is based on surface patches with uniform curvature properties extracted at multiple scales. These patches are computed using multiple alternative decompositions of the surface based on the signs of the mean and Gaussian curvatures. Initial coarse decompositions are subsequently refined using a curvature compatibility scheme to rectify the effect of noise and quantization errors. The extraction of simple uniform curvature features is limited by the fact that the optimal scale of processing for a single object is very difficult to determine. As a solution we propose the segmentation of range data into patches at multiple scales. A hierarchical ranking of these patches is then used to describe individual objects based on geometric information. These geometric descriptors are ranked according to several criteria expressing their estimated stability and utility. The applicability of the resulting multi-scale description is demonstrated by estimating the pose of a 3-D object. Pose estimation is cast as an optimal matching problem. The geometric pose transformation is computed by matching two representations, which amounts to finding the three-patch correspondence that produces the best global consistency. Examples of the multi- scale representation applied to both real and simulated range data are presented. Effective pose estimation is demonstrated and the algorithm's behavior in the presence of noise is validated.
Nanoengineered CIGS thin films for low cost photovoltaics (2008)

Low cost manufacturing of Cu(In,Ga)Se<sub>2</sub> (CIGS) films for high efficiency photovoltaic devices by the innovative Field-Assisted Simultaneous Synthesis and Transfer (FASST®) process is reported. The FASST® process is a two-stage reactive transfer printing method relying on chemical reaction between two separate precursor films to form CIGS, one deposited on the substrate and the other on a printing plate in the first stage. In the second stage these precursors are brought into intimate contact and rapidly reacted under pressure in the presence of an applied electrostatic field. The method utilizes physical mechanisms characteristic of anodic wafer bonding and rapid thermal annealing, effectively creating a sealed micro-reactor that ensures high material utilization efficiency, direct control of reaction pressure, and low thermal budget. The use of two independent ink-based or PVD-based nanoengineered precursor thin films provides the benefits of independent composition and flexible deposition technique optimization, and eliminates pre-reaction prior to the second stage FASST® synthesis of CIGS. High quality CIGS with large grains on the order of several microns are formed in just several minutes based on compositional and structural analysis by XRF, SIMS, SEM and XRD. Cell efficiencies of 12.2% have been achieved using this method.
PERFORMANCE ANALYSIS OF VARIABLE-PERIOD HELICAL UNDULATOR WITH PERMANENT MAGNET FOR A KAERI THz FEL (2014)

We could realize a variable-period (V-P) permanentmagnet helical undulator, which shows strong (~ 1 T) and constant field for the whole range of undulator periodlength from 23 to 26 mm. This new compact and strong undulator will be used for developing a table-top highpower terahertz (THz) free-electron laser (FEL).
Low-Temperature Chemical Vapor Deposition Growth of Graphene from Toluene on Electropolished Copper Foils (2012)

A two-step CVD route with toluene as the carbon precursor was used to grow continuous large-area monolayer graphene films on a very flat, electropolished Cu foil surface at 600 °C, lower than any temperature reported to date for growing continuous monolayer graphene. Graphene coverage is higher on the surface of electropolished Cu foil than that on the unelectropolished one under the same growth conditions. The measured hole and electron mobilities of the monolayer graphene grown at 600 °C were 811 and 190 cm(2)/(V·s), respectively, and the shift of the Dirac point was 18 V. The asymmetry in carrier mobilities can be attributed to extrinsic doping during the growth or transfer. The optical transmittance of graphene at 550 nm was 97.33%, confirming it was a monolayer, and the sheet resistance was ~8.02 × 10(3) Ω/□.
Growth temperature dependence of optical modal gain and loss in GaN:Eu active medium on Si (2006)

The dependence of optical modal gain and loss on GaN:Eu growth temperature is reported. GaN:Eu thin films were grown on Si substrates with AlGaN transition and cladding layers at temperatures ranging from 600 degrees C to 850 degrees C. The modal gain and loss in the GaN:Eu layer were a strong function of the optically active Eu atomic concentration and of the interface quality between the active layer and the top cladding layer, which in turn depended on the growth temperature. Optimum optical properties of maximum modal gain of ~ 100 cm(-1) and minimum loss of ~ 46 cm(-1) were obtained for growth at 800 degrees C.
Geographic-style maps for 2-dimensional lattices (2021)

This paper develops geographic-style maps containing 2D lattices in all known crystals parameterised by recent complete invariants. Motivated by rigid crystal structures, lattices are considered up to rigid motion and uniform scaling. The resulting space of 2D lattices is a square with identified edges or a sphere without one point. The new continuous maps show all Bravais classes as low-dimensional subspaces, visualise hundreds of thousands of real crystal lattices from the Cambridge Structural Database, and motivate the development of continuous and invariant-based crystallography.
An iterative unsupervised learning method for information distillation (2008)

Information distillation techniques are used to analyze and interpret large volumes of speech and text archives in multiple languages and produce structured information of interest to the user. In this work, we propose an iterative unsupervised sentence extraction method to answer open-ended natural language queries about an event. The approach consists of finding the subset of sentences that are very likely to be relevant or irrelevant for the query from candidate documents, and iteratively training a classification model using these examples. Our results indicate that performance of the system may be improved by around 30% relative in terms of F-measure, by using the proposed method.
Parametric Study of the Power Absorption for a Linear Generator Wave Energy Converter (2015)

Ocean wave energy is considered to be one of the important potential renewable energy resources for sustainable development. Various wave energy converter technologies have been proposed to harvest the energy from ocean waves. This thesis is based on the linear generator wave energy converter developed at Uppsala University. The research in this thesis focuses on the foundation optimization and the power absorption optimization of the wave energy converters and on the wave climate modelling at the Lysekil wave converter test site.The foundation optimization study of the gravity-based foundation of the linear wave energy converter is based on statistical analysis of wave climate data measured at the Lysekil test site. The 25 years return extreme significant wave height and its associated mean zero-crossing period are chosen as the maximum wave for the maximum heave and surge forces evaluation.The power absorption optimization study on the linear generator wave energy converter is based on the wave climate at the Lysekil test site. A frequency-domain simplified numerical model is used with the power take-off damping coefficient chosen as the control parameter for optimizing the power absorption. The results show a large improvement with an optimized power take-off damping coefficient adjusted to the characteristics of the wave climate at the test site.The wave climate modelling studies are based on the wave climate data measured at the Lysekil test site. A new mixed distribution method is proposed for modelling the significant wave height. This method gives impressive goodness of fit with the measured wave data. A copula method is applied to the bivariate joint distribution of the significant wave height and the wave period. The results show an excellent goodness of fit for the Gumbel model. The general applicability of the proposed mixed-distribution method and the copula method are illustrated with wave climate data from four other sites. The results confirm the good performance of the mixed-distribution and the Gumbel copula model for the modelling of significant wave height and bivariate wave climate.
A metal thermal shunt design for hybrid silicon microring laser (2012)

In order to overcome the bottlenecks of limited bandwidth and increasing power consumption in CMOS chips due to conventional metal interconnects, photonic data links are an increasingly important research topic for both academia and industry. Recently demonstrated hybrid silicon(Si) microring lasers[1] can be good candidates for Si-based light sources for photonic data links.
Kinetic analysis of curing of tetraepoxides and diamines in the presence of etherification side reactions (1988)

Abstract The theory of branching processes is used to describe the polymer network formation resulting from the reaction of tetraepoxides with diamines using various initial compositions. Differences in reactivities of primary and secondary amine groups and the reaction between the epoxide groups and reaction‐generated hydroxyl groups are taken into account; however, intramolecular reactions in the pregel stage are neglected. Expressions are derived for the critical epoxide conversion at the gel point, molecular weight in the pregel stage, changes in sol and gel fraction in the post‐gel stage, and the concentration of elastically active network chains as a function of reaction conditions. The analysis of the simulation results shows that etherification reactions significantly raise the concentration of elastically active network chains of the mixture under stoichiometric excess of epoxide groups.
Using accelerometer as a diagnostic tool to detect drug-induced parkinsonism (DIP) secondary to first-generation anti-psychotic medications (2020)

Accelerometers were able to accurately detect patients with DIP better than some clinical rating scale including the SAS. Further larger-scale studies must be conducted to further demonstrate the accuracy of accelerometers in detecting DIP.
A human recombinant Fab identifies a human immunodeficiency virus type 1-induced conformational change in cell surface-expressed CD4 (1995)

To explore the role of the CD4 molecule in human immunodeficiency virus (HIV) infection following initial virus-CD4 binding, we have characterized CD4-specific antibodies raised by immunizing an HIV-1-infected human with human recombinant soluble CD4 (rsCD4). Fabs were selected from a human recombinant Fab library constructed from the bone marrow of this immunized individual. Here, we describe a human rsCD4-specific recombinant Fab clone selected by panning the library over complexes of human rsCD4 and recombinant HIV-1 envelope protein. While this Fab does not bind to CD4-positive T-cell lines or to human T lymphocytes, it recognizes cell surface-expressed CD4 following the incubation of these cells with a recombinant form of HIV-1 gp120 or with HIV-1 virions. The Fab is not HIV-1 envelope specific, since it does not bind to recombinant gp120 or to native cell surface-expressed HIV-1 envelope proteins. As confirmation of its CD4 specificity, we show that this Fab immunoprecipitates a 55-kDa protein, corresponding to the molecular mass of cellular CD4, from an H9 cell lysate. The specificity of this human Fab provides evidence for a virus-induced conformational change in cell surface-expressed on CD4. The characterization of this altered CD4 conformation and its effects on the host cell will be important in defining postbinding events in HIV infection.
Transcriptomic Impact of IMA-08401, a Novel AHR Agonist Resembling Laquinimod, on Rat Liver (2019)

IMA-08401 (C2) is a novel aryl hydrocarbon receptor (AHR) agonist and selective AHR modulator (SAHRM) that is structurally similar to laquinimod (LAQ). Both compounds are converted to the AHR-active metabolite DELAQ (IMA-06201) in vivo. SAHRMs have been proposed as therapeutic options for various autoimmune disorders. Clinical trials on LAQ have not reported any significant toxic outcomes and C2 has shown low toxicity in rats; however, their functional resemblance to the highly toxic AHR agonist 2,3,7,8-tetrachlorodibenzo-<i>p</i>-dioxin (TCDD) raises questions. Here, we characterize the hepatic transcriptomic changes induced by acute (single-dose) and subacute exposure (repeated dosing for 5 days followed by a 5-day recovery period) to C2 in Sprague-Dawley rats. Exposure to C2 leads to activation of the AHR, as shown by altered transcription of <i>Cyp1a1</i>. We identify a heightened response early after exposure that drops off by day 10. Acute exposure to C2 leads to changes to transcription of genes involved in antiviral and antibacterial responses, which highlights the immunomodulator effects of this AHR agonist. Subacute exposure causes an oxidative stress response in the liver, the consequences of which require further study on target tissues such as the CNS and immune system, both of which may be compromised in this patient population.
How Relevant is the Turing Test in the Age of Sophisbots? (2019)

Popular culture has contemplated societies of thinking machines for generations, envisioning futures from utopian to dystopian. These futures are, arguably, here now-we find ourselves at the doorstep of technology that can at least simulate the appearance of thinking, acting, and feeling. The real question is: now what?
Theoretical Prediction from Classical Equations and Rational Synthesis of Ultrafine LTL Zeolite Nanocrystals (2020)

Much more attention has been paid to zeolite nanocrystals due to their use as catalysts and zeolite membranes as well as composites and hierarchical structures. Recently, zeolite nanocrystals of several structures have been successfully obtained, but rational synthesis of these zeolite nanocrystals is still challenging. Here, we report a theoretical prediction to synthesize zeolite nanocrystals from classical equations. According to the new equation, we finally obtained ultrafine zeolite L nanocrystals in accordance with the theoretical prediction. The smallest zeolite L we synthesized exhibits the crystals with a [100] length of 18 ± 5 nm and a [001] width of 8 ± 2 nm. After loading Pt species (0.5 wt %), this zeolite L supported Pt catalyst is very active and selective for the formation of isomers and cracking products in the region of 260–280 and 320–340 °C in n-dodecane hydroisomerization, showing adjustable catalytic properties by temperature control over one catalyst in the same bed reactor. The new equation in this work might offer a good opportunity for rational synthesis of expanded zeolite nanocrystals in the near future.
A Concurrent CSMA MAC protocol for Mobile Ad Hoc Networks using beamnulling (2015)

Traditional algorithms for Media Access Control (MAC) in Mobile Ad Hoc Networks (MANET) such as CSMA-CA allow only a single user to transmit at a given time. This means that the sum throughput in a MANET cannot increase to service additional users. Such MAC protocols disregard the possibility that by utilizing multiple antenna processing to handle interference intelligently at the Physical layer (PHY), many concurrent user transmissions can co-exist. Previous works have proposed altered versions of CSMA-CA that allow multi user operation but may not necessarily be able to coexist with an existing IEEE 802:11 based network. This paper proposes a Concurrent CSMA MAC protocol that is completely compatible with traditional CSMA based MAC and follows the same timing structure allowing co-existence of both protocols. Specifically, in Concurrent CSMA after a primary user has captured the channel, secondary users listen to the RTS/CTS handshake and form a beamnull towards the primary receiver. Hence secondary users can communicate concurrently with minimal increase in interference to the primary receiver. Simulations show that the proposed PHY and MAC scheme is able to achieve 2 to 3 times the network spectral efficiency of CSMA with a single antenna and this improvement factor is sustained as the network scales in size. Further the proposed scheme allows the network spectral efficiency (sum throughput per unit bandwidth) to scale with users and improves upon a previous promising approach which uses Interference Alignment.
Cache Allocations for Consecutive Requests of Categorized Contents: Service Provider’s Perspective (2020)

In wireless caching networks, a user generally has a concrete purpose of consuming contents in a certain preferred category, and requests multiple contents in sequence. While most existing research on wireless caching and delivery has focused only on one-shot requests, the popularity distribution of contents requested consecutively is definitely different from the one-shot request and has been not considered. Also, especially from the perspective of the service provider, it is advantageous for users to consume as many contents as possible. Thus, this paper proposes two cache allocation policies for categorized contents and consecutive user demands, which maximize 1) the cache hit rate and 2) the number of consecutive content consumption, respectively. Numerical results show how categorized contents and consecutive content requests have impacts on the cache allocation.
Combinatorial Latency Reactivation for HIV-1 Subtypes and Variants (2010)

The eradication of HIV-1 will likely require novel clinical approaches to purge the reservoir of latently infected cells from a patient. We hypothesize that this therapy should target a wide range of latent integration sites, act effectively against viral variants that have acquired mutations in their promoter regions, and function across multiple HIV-1 subtypes. By using primary CD4(+) and Jurkat cell-based in vitro HIV-1 latency models, we observe that single-agent latency reactivation therapy is ineffective against most HIV-1 subtypes. However, we demonstrate that the combination of two clinically promising drugs-namely, prostratin and suberoylanilide hydroxamic acid (SAHA)-overcomes the limitations of single-agent approaches and can act synergistically for many HIV-1 subtypes, including A, B, C, D, and F. Finally, by identifying the proviral integration position of latent Jurkat cell clones, we demonstrate that this drug combination does not significantly enhance the expression of endogenous genes nearest to the proviral integration site, indicating that its effects may be selective.
Risk of Kaposi's sarcoma-associated herpes virus transmission from donor allografts among Italian posttransplant Kaposi's sarcoma patients. (1997)

Kaposi's sarcoma-associated herpesvirus (KSHV) is a newly discovered herpes virus found in all forms of Kaposi's sarcoma (KS) including KS among immunosuppressed transplant patients. It is unknown whether this virus is transmitted by organ transplantation or is reactivated during immunosuppression among those patients infected before transplantation. To investigate the risk of KSHV transmission during organ transplantation, we conducted a case-control study of transplant recipients with and without KS matched to their respective donors. Sera were collected at time of transplantation and tested in a randomized and blinded fashion using four KSHV serologic assays testing for antibodies to both latent and lytic phase antigens. Ten (91%) of 11 organ recipients who developed KS were seropositive prior to transplantation by one or more of the assays compared with two (12%) of 17 control organ recipients (OR = 75, 95% CI = 4.7, 3500). KS cases were more likely to have been born in southern Italy where KS is endemic than the recipient controls or either donor group. Only four (36%) of 11 donors to case patients and three (18%) of 17 donors to control patients were seropositive (P = .38, two-tailed Fisher's exact test). KSHV transmission could not be ruled out for the single KS patient seronegative at transplantation and clear evidence for organ-related transmission was found for another KS patient outside of the case-control study. Antibodies to KSHV are detectable in the sera from most transplant recipients before initiation of immunosuppressive treatment suggesting that KS among immunosuppressed transplant patients is primarily due to virus reactivation. KSHV transmission, however, from an infected allograft can occur, and our study reports the first documented case of person-to-person transmission of KSHV.