gebhart/patrepeval huggingface dataset:
Machine learning–assisted molecular design and efficiency prediction for high-performance organic photovoltaic materials (2019)

In the process of finding high-performance materials for organic photovoltaics (OPVs), it is meaningful if one can establish the relationship between chemical structures and photovoltaic properties even before synthesizing them. Here, we first establish a database containing over 1700 donor materials reported in the literature. Through supervised learning, our machine learning (ML) models can build up the structure-property relationship and, thus, implement fast screening of OPV materials. We explore several expressions for molecule structures, i.e., images, ASCII strings, descriptors, and fingerprints, as inputs for various ML algorithms. It is found that fingerprints with length over 1000 bits can obtain high prediction accuracy. The reliability of our approach is further verified by screening 10 newly designed donor materials. Good consistency between model predictions and experimental outcomes is obtained. The result indicates that ML is a powerful tool to prescreen new OPV materials, thus accelerating the development of the OPV field.
Spinoculation Triggers Dynamic Actin and Cofilin Activity That Facilitates HIV-1 Infection of Transformed and Resting CD4 T Cells (2011)

Centrifugal inoculation, or spinoculation, is widely used in virology research to enhance viral infection. However, the mechanism remained obscure. Using HIV-1 infection of human T cells as a model, we demonstrate that spinoculation triggers dynamic actin and cofilin activity, probably resulting from cellular responses to centrifugal stress. This actin activity also leads to the upregulation of the HIV-1 receptor and coreceptor, CD4 and CXCR4, enhancing viral binding and entry. We also demonstrate that an actin inhibitor, jasplakinolide, diminishes spin-mediated enhancement. In addition, small interfering RNA (siRNA) knockdown of LIMK1, a cofilin kinase, decreases the enhancement. These results suggest that spin-mediated enhancement cannot be explained simply by a virus-concentrating effect; rather, it is coupled with spin-induced cytoskeletal dynamics that promote receptor mobilization, viral entry, and postentry processes. Our results highlight the importance of cofilin and a dynamic cytoskeleton for the initiation of viral infection. Our results also indicate that caution needs to be taken in data interpretation when cells are spinoculated; some of the spin-induced cellular permissiveness may be beyond the natural capacity of an infecting virus.
One-step electrochemical approach to the synthesis of Graphene/MnO2 nanowall hybrids (2011)

We have demonstrated a one-step and effective electrochemical method to synthesize graphene/MnO2 nanowall hybrids (GMHs). Graphene oxide (GO) was electrochemically reduced to graphene (GN), accompanied by the simultaneous formation of MnO2 with a nanowall morphology via cathodic electrochemical deposition. The morphology and structure of the GMHs were systematically characterized by scanning electron microscope (SEM), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and Raman spectroscopy. The resulting GMHs combine the advantages of GN and the nanowall array morphology of MnO2 in providing a conductive network of amorphous nanocomposite, which shows good electrochemical capacitive behavior. This simple approach should find practical applications in the large-scale production of GMHs.
Low-emittance electron-beam generation with laser pulse shaping in photocathode radio-frequency gun (2002)

A technique of laser-pulse shaping was developed for low-emittance electron-beam generation in a photocathode radio-frequency (rf) gun. The emittance growth due to space charge and rf effects in the rf gun was experimentally investigated with square and gaussian temporal pulse shapes. It was found that the square pulse shaping was a useful tool for both the reduction of nonlinear space-charge force and the correction of linear space charge. The normalized transverse rms emittance at 1 nC was obtained to be 1.20 πmm-mrad for the square pulse shape with pulse length of 9 ps full width at half maximum. The emittance was measured as a function of the electron bunch charge and the laser-pulse length.
Original Mitsunobu-Triggered Sequence Involved in a One-Pot Domino Process toward Tetracyclic Systems Bearing a Bis-<i>N</i>,<i>O</i>-acetal Junction (2016)

Herein is reported an efficient, one-pot domino process through a 1,6-aza-Michael addition-triggered sequence and an original Mitsunobu-type concerted sequence for the synthesis of tetracyclic systems containing a bis-N,O-acetal junction. This methodology led to the construction of four new bonds, the cleavage of three C-O bonds, and the generation of an asymmetric center. Mitsunobu activation afforded final ring closure involving the creation of two bonds, which remains unprecedented among reported Mitsunobu-type sequences. The latter occurred in a regioselective fashion at the challenging C<sub>6</sub>-position of 2-pyridone intermediates. In the case of adequately substituted enantiopure amino alcohols, up to 95:5 of diastereoisomeric excess was achieved. Computational studies allowed the discrimination of a favored pathway for Mitsunobu sequence and supported the regioselectivity as well as the diastereoselectivity observed for this step.
D<scp>OCKGROUND</scp> system of databases for protein recognition studies: Unbound structures for docking (2007)

Computational docking approaches are important as a source of protein-protein complexes structures and as a means to understand the principles of protein association. A key element in designing better docking approaches, including search procedures, potentials, and scoring functions is their validation on experimentally determined structures. Thus, the databases of such structures (benchmark sets) are important. The previous, first release of the DOCKGROUND resource (Douguet et al., Bioinformatics 2006; 22:2612-2618) implemented a comprehensive database of cocrystallized (bound) protein-protein complexes in a relational database of annotated structures. The current release adds important features to the set of bound structures, such as regularly updated downloadable datasets: automatically generated nonredundant set, built according to most common criteria, and a manually curated set that includes only biological nonobligate complexes along with a number of additional useful characteristics. The main focus of the current release is unbound (experimental and simulated) protein-protein complexes. Complexes from the bound dataset are used to identify crystallized unbound analogs. If such analogs do not exist, the unbound structures are simulated by rotamer library optimization. Thus, the database contains comprehensive sets of complexes suitable for large scale benchmarking of docking algorithms. Advanced methodologies for simulating unbound conformations are being explored for the next release. The future releases will include datasets of modeled protein-protein complexes, and systematic sets of docking decoys obtained by different docking algorithms. The growing DOCKGROUND resource is designed to become a comprehensive public environment for developing and validating new docking methodologies.
Distributed Kalman filtering (2012)

In this chapter, the theory and analytical development of distributed Kalman filtering based on various methods are provided. In one method, the weighted averages, based on the Bayesian point of view, yield the best possible estimate of the state at a particular time instant that can be computed from the conditional probability distribution of state x given all past measurements up to the particular time.
VideoBrush/sup TM/: experiences with consumer video mosaicing (2002)

We present technical advances that were made in creating consumer level video mosaicing applications with inputs from hand held inexpensive cameras, and with near-real time response. In developing the VideoBrush/sup TM/ technologies, the goal was to give easily usable but robust video mosaicing capabilities in the hands of lay users. We highlight a number of problems that needed to be solved to enable this: 2D & 1D modes of scene scanning and alignment, progressive complexity of alignment models to provide real-time response to the user and multi-resolution blending for high quality mosaic output. The solution to these key technical challenges has led us to video mosaic technologies that can "scan" scenes as diverse as natural panoramic scenes to white boards and documents.
ROLE OF AMINOTRANSFERASE AND INDOLE-3-PYRUVIC ACID IN THE SYNTHESIS OF INDOLE-3-ACETIC ACID IN PSEUDOMONAS SAVASTANOI (1970)

An aminotransferase with broad specificity was partially purified from Pseudomonas savastanoi. The enzyme catalyzes the conversion of L-tryptophan to indole-3-pyruvic acid (IPYA) but transaminates more readily with other amino acids. Optimal activity occurs at pH 8.8. The aminotransferase shows broad specificity for both amino donors and acceptors. Indole- 3-acetic acid (IAA) and indole-3-acetamide (IAM) at 3×10-3M inhibit minotransferase activity 30% and 26%, respectively. Specific activity of aminotransferase from cells grown in a medium with L-tryptophan or IAA does not appear to affect production of the enzyme. Whole cells of Pseudomonas savastanoi convert IPYA to IAA but the overall conversion is slower than the rate of conversion of IAM to IAA. The role of aminotransferase in the synthesis of IAA from tryptophan is considered to be minor to that of the oxidative decarboxylase-hydrolase system in this bacterium.
Structure of synthetic high polymers (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure of synthetic high polymersFrank C. McGrew Cite this: J. Chem. Educ. 1958, 35, 4, 178Publication Date (Print):April 1, 1958Publication History Received3 August 2009Published online1 April 1958Published inissue 1 April 1958https://doi.org/10.1021/ed035p178RIGHTS & PERMISSIONSArticle Views222Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (7 MB) Get e-Alerts Get e-Alerts
An on-line fault location technique for DC microgrid using transient measurements (2017)

Locating faults in meshed dc microgrids poses challenges due to low impedance offered by the dc network. In this paper, an on-line fault location scheme which can be implemented as an additional feature in a relay is proposed. The algorithm is developed to determine fault location based on voltage and current transients. Both line to line and monopole ground faults are analysed separately and algorithms are developed based on the rate of change of current. Direct short circuit faults are located using transient measurements captured locally, while communication based technique is utilized to locate the impedance faults. The developed fault location technique is also capable of estimating the fault resistance accurately. The algorithm is validated on a ±600 V meshed dc grid, for both the types of faults under wide range of fault impedance at different fault locations.
Reconfigurable FEC codes for software-defined optical transceivers (2014)

Flexible Optical Networks can optimize the network resources by offering increased spectral utilization. However, these networks require the use of novel software-defined Optical Transceivers that can adapt their features to the channel's requirements. This paper presents a novel optical transceiver architecture using a reconfigurable FEC coding scheme for flexible optical networks. The proposed approach can dynamically support different versions of FEC codes (with different overheads, code lengths, and LLR-widths) based on the network's Quality-of-Service requirements, whereas it can also be applied for the dynamic reconfiguration of the DSP units and the realization of dynamic coded-modulation schemes. The proposed approach has been implemented into an FPGA platform. The performance evaluation shows that the reconfiguration time is always less than 12 ms, which means that the proposed scheme could be utilized in many optical networks, where the reconfiguration time (e.g. for the optical switches or the WSS) is in the order of a few ms.
New Evidence of Similarity between Human and Plant Steroid Metabolism: 5α-Reductase Activity in Solanum malacoxylon (2002)

The physiological role of steroid hormones in humans is well known, and the metabolic pathway and mechanisms of action are almost completely elucidated. The role of plant steroid hormones, brassinosteroids, is less known, but an increasing amount of data on brassinosteroid biosynthesis is showing unexpected similarities between human and plant steroid metabolic pathways. Here we focus our attention on the enzyme 5alpha-reductase (5alphaR) for which a plant ortholog of the mammalian system, DET2, was recently described in Arabidopsis thaliana. We demonstrate that campestenone, the natural substrate of DET2, is reduced to 5alpha-campestanone by both human 5alphaR isozymes but with different affinities. Solanum malacoxylon, which is a calcinogenic plant very active in the biosynthesis of vitamin D-like molecules and sterols, was used to study 5alphaR activity. Leaves and calli were chosen as examples of differentiated and undifferentiated tissues, respectively. Two separate 5alphaR activities were found in calli and leaves of Solanum using campestenone as substrate. The use of progesterone allowed the detection of both activities in calli. Support for the existence of two 5alphaR isozymes in S. malacoxylon was provided by the differential actions of inhibitors of the human 5alphaR in calli and leaves. The evidence for the presence of two isozymes in different plant tissues extends the analogies between plant and mammalian steroid metabolic pathways.
Embryonic stem cell-derived neural stem cells improve spinal muscular atrophy phenotype in mice (2009)

Spinal muscular atrophy, characterized by selective loss of lower motor neurons, is an incurable genetic neurological disease leading to infant mortality. We previously showed that primary neural stem cells derived from spinal cord can ameliorate the spinal muscular atrophy phenotype in mice, but this primary source has limited translational value. Here, we illustrate that pluripotent stem cells from embryonic stem cells show the same potential therapeutic effects as those derived from spinal cord and offer great promise as an unlimited source of neural stem cells for transplantation. We found that embryonic stem cell-derived neural stem cells can differentiate into motor neurons in vitro and in vivo. In addition, following their intrathecal transplantation into spinal muscular atrophy mice, the neural stem cells, like those derived from spinal cord, survived and migrated to appropriate areas, ameliorated behavioural endpoints and lifespan, and exhibited neuroprotective capability. Neural stem cells obtained using a drug-selectable embryonic stem cell line yielded the greatest improvements. As with cells originating from primary tissue, the embryonic stem cell-derived neural stem cells integrated appropriately into the parenchyma, expressing neuron- and motor neuron-specific markers. Our results suggest translational potential for the use of pluripotent cells in neural stem cell-mediated therapies and highlight potential safety improvements and benefits of drug selection for neuroepithelial cells.
TM6SF2 rs58542926 impacts lipid processing in liver and small intestine (2016)

These data strongly support a role of TM6SF2 in the regulation of postprandial lipemia, potentially through a similar function for TM6SF2 in the lipidation and/or export of both hepatically and intestinally derived triglyceride-rich lipoproteins. (Hepatology 2017;65:1526-1542).
NTrace: Function Boundary Tracing for Windows on IA-32 (2009)

For a long time, dynamic tracing has been an enabling technique for reverse engineering tools. Tracing can not only be used to record the control flow of a particular component such as a piece of malware itself, it is also a way to analyze the interactions of a component and their impact on the rest of the system. Unlike Unix-based systems, for which several dynamic tracing tools are available, Windows has been lacking appropriate tools. From a reverse engineering perspective, however, Windows may be considered the most relevant OS, particularly with respect to malware analysis. In this paper, we present NTrace, a dynamic tracing tool for the Windows kernel, drivers, system libraries, and applications that supports function boundary tracing. NTrace incorporates 2 novel approaches: (1) a way to integrate with Windows Structured Exception Handling and (2) a technique to instrument binary code on IA-32 architectures that is both safe and more efficient than DTrace.
A fully integrated CMOS sensor system for chronocoulometry (2004)

In this paper, a monolithically integrated electrochemical sensor system based on a CMOS chip is presented, which allows to per-form microminiaturized chronocoulometric analyses on chip with high sensitivity and large bandwidth. The chip is based on a standard 0.5 /spl mu/m CMOS technology extended by gold electrodes on the chip's surface. A possible exploration of this approach is the realization of electrochemical sensors, e.g. electronic DNA arrays, for the analysis of liquids.
Manufacturing and mechanical characterization of perforated hybrid composites based on flexible polyurethane foam (2015)

ABSTRACT This study focused on the fabrication and mechanical evaluation of nonwoven reinforced flexible polyurethane foam composites. Effects of perforation ratio, aperture size, and perforation depth on bursting and low‐velocity impact responses of perforated composite panels were investigated. The nonwoven fabric used for cover sheet was composed of flame retardant polyester, low‐melting point polyester, and recycled Kevlar staple fibers. Blending ratio of Kevlar fiber was confirmed to have relation to mechanical mechanism of cushioning layer. The highest mechanical strength value was obtained at 5 wt % of Kevlar ratio because of the highest cohesive force among recycled Kevlar, flame retardant polyester, and low‐melting point polyester fibers was provided at the blending ratio. The perforated high‐density flexible polyurethane foam composites panel was adhered with intra‐ply hybrid laminates with various areal densities on each face to form sandwich structural composites. The results revealed that perforation ratio and aperture significantly influenced the bursting and low‐velocity impact resistance behaviors of the perforated composites panel. Perforated composites with 10% perforation ratio and 4 mm aperture lead to maximum bursting strength of 437 N. Additional hybrid laminates significantly promoted the maximum bursting strength of the semiperforated hybrid composites by 212%. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132 , 42288.
Pathogenesis and Management of COVID-19 (2021)

COVID-19, occurring due to SARS-COV-2 infection, is the most recent pandemic disease that has led to three million deaths at the time of writing. A great deal of effort has been directed towards altering the virus trajectory and/or managing the interactions of the virus with its subsequent targets in the human body; these interactions can lead to a chain reaction-like state manifested by a cytokine storm and progress to multiple organ failure. During cytokine storms the ratio of pro-inflammatory to anti-inflammatory mediators is generally increased, which contributes to the instigation of hyper-inflammation and confers advantages to the virus. Because cytokine expression patterns fluctuate from one person to another and even within the same person from one time to another, we suggest a road map of COVID-19 management using an individual approach instead of focusing on the blockbuster process (one treatment for most people, if not all). Here, we highlight the biology of the virus, study the interaction between the virus and humans, and present potential pharmacological and non-pharmacological modulators that might contribute to the global war against SARS-COV-2. We suggest an algorithmic roadmap to manage COVID-19.
A static memory cell based on the negative resistance of the gate terminal of p-n-p-n devices (1994)

We propose a new static memory cell that is based on bistable operation of a three-terminal p-n-p-n device working in the blocking state. The bistable operation is verified by the measurements of Si/amorphous Si prototypes. The experimental prototypes achieve delay times in the nanosecond range when operating with external gate and anode resistors. In order to decrease the power consumption of the memory cell, we propose to operate it with MOS transistor switches instead of the gate resistors. The memory cell can be integrated into VLSI processes, and is of a size suitable for VLSI applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Epidermal Electronics: Cephalopod‐Inspired Miniaturized Suction Cups for Smart Medical Skin (Adv. Healthcare Mater. 1/2016) (2016)

On page 80, D.-H. Kim and co-workers exploit bio-inspired designs and geometries to create cephalopod-inspired dry adhesives in combination with ultrathin stretchable electronics. The ultra-low modulus (∼108 kPa) miniaturized suction cups support stretchable electronics and drug-loaded therapeutic nanoparticles, enabling tight skin coupling without irritations. The integrated system allows continuous vital sign monitoring, controllable drug release, and wireless communication to external devices for remote data transmission and drug delivery actuation.
Conquering the Divide: Continuous Clustering of Distributed Data Streams (2007)

Data is often collected over a distributed network, but in many cases, is so voluminous that it is impractical and undesirable to collect it in a central location. Instead, we must perform distributed computations over the data, guaranteeing high quality answers even as new data arrives. In this paper, we formalize and study the problem of maintaining a clustering of such distributed data that is continuously evolving. In particular, our goal is to minimize the communication and computational cost, still providing guaranteed accuracy of the clustering. We focus on the k-center clustering, and provide a suite of algorithms that vary based on which centralized algorithm they derive from, and whether they maintain a single global clustering or many local clusterings that can be merged together. We show that these algorithms can be designed to give accuracy guarantees that are close to the best possible even in the centralized case. In our experiments, we see clear trends among these algorithms, showing that the choice of algorithm is crucial, and that we can achieve a clustering that is as good as the best centralized clustering, with only a small fraction of the communication required to collect all the data in a single location.