gebhart/patrepeval huggingface dataset:
Inhibition of the synthesis of polyamines and DNA in activated lymphocytes by a combination of alpha-methylornithine and methylglyoxal bis(guanylhydrazone). (1977)

&lt;p&gt;Advanced energy minimization techniques (i.e. DVFS, Thermal Management, etc) and their high-level HW/SW requirements are well established in high-throughput multi-core systems. These techniques would have an intolerable overhead in low-cost, performance-constrained microcontroller units (MCU's). These devices can further reduce power by operating at a lower voltage, at the cost of increased sensitivity to PVT variation and increased design margins. In this paper, we propose an runtime environment for next-generation dual-core MCU platforms. These platforms complement a single-core with a low area overhead, reduced design margin shadow-processor. The runtime decreases the overall energy consumption by exploiting design corner heterogeneity between the two cores, rather than increasing the throughput. This allows the platform's power envelope to be dynamically adjusted to application-specific requirements. Our simulations show that, depending on the ratio of core to platform energy, total energy savings can be up to 20%.&lt;/p&gt;
synDNA—a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing (2022)

Microbiome studies have the common goal of determining which microbial taxa are present, respond to specific conditions, or promote phenotypic changes in the host. Most of these studies rely on relative abundance measurements to drive conclusions. Inherent limitations of relative values are the inability to determine whether an individual taxon is more or less abundant and the magnitude of this change between the two samples. These limitations can be overcome by using absolute abundance quantifications, which can allow for a more complete understanding of community dynamics by measuring variations in total microbial loads. Obtaining absolute abundance measurements is still technically challenging. Here, we developed synthetic DNA (synDNA) spike-ins that enable precise and cost-effective absolute quantification of microbiome data by adding defined amounts of synDNAs to the samples. We designed 10 synDNAs with the following features: 2,000-bp length, variable GC content (26, 36, 46, 56, or 66% GC), and negligible identity to sequences found in the NCBI database. Dilution pools were generated by mixing the 10 synDNAs at different concentrations. Shotgun metagenomic sequencing showed that the pools of synDNAs with different percentages of GC efficiently reproduced the serial dilution, showing high correlation (<i>r</i> = 0.96; <i>R</i><sup>2</sup> ≥ 0.94) and significance (<i>P</i> <<i> </i>0.01). Furthermore, we demonstrated that the synDNAs can be used as DNA spike-ins to generate linear models and predict with high accuracy the absolute number of bacterial cells in complex microbial communities. <b>IMPORTANCE</b> The synDNAs designed in this study enable accurate and reproducible measurements of absolute amount and fold changes of bacterial species in complex microbial communities. The method proposed here is versatile and promising as it can be applied to bacterial communities or genomic features like genes and operons, in addition to being easily adaptable by other research groups at a low cost. We also made the synDNAs' sequences and the plasmids available to encourage future application of the proposed method in the study of microbial communities.
10-Gb/s direct modulation of polymer-based tunable external cavity lasers (2014)

We demonstrate a directly-modulated 10-Gb/s tunable external cavity laser (ECL) fabricated by using a polymer Bragg reflector and a high-speed superluminescent diode (SLD). The tuning range and output power of this ECL are measured to be >11 nm and 2.6 mW (@ 100 mA), respectively. We directly modulate this laser at 10 Gb/s and transmit the modulated signal over 20 km of standard single-mode fiber. The power penalty is measured to be <2.8 dB at the bit-error rate (BER) of 10(-10).
Biophysical aspects of lipid interaction with mineral: Liposome model studies (1989)

The present paper reviews the use of liposomes as synthetic models for studying various biophysical aspects of matrix vesicle calcification, especially the involvement of acidic phospholipids in the nucleation and growth processes which occur during the initial stages of mineral formation in and around these membrane-bound structures. Recent results showed that acidic phospholipids incorporated into phosphatidylcholine-rich anionic liposome membranes were ineffective in initiating extraliposomal calcium phosphate precipitation from metastable solutions at physiological pH. On the contrary, certain acidic phospholipids such as phosphatidic acid and phosphatidylserine retarded the development of such precipitation when the latter was endogenously induced. The extent of inhibition correlated with the strength of the electrostatic interaction between the polar head group of the acidic phospholipid and the surface of the mineral phase. The results suggest that acidic phospholipids may play an important role in controlling the rate of early mineral development in matrix vesicle calcification.
Revealing conserved mechanisms of neurodegeneration in a colonial chordate (2021)

ABSTRACT Loss of the brain’s functional ability is a common symptom of aging and neurodegenerative diseases 1,2 . While the genetic and molecular mechanisms underlying human neurodegeneration are studied in-depth 3–6 , very little is known about the evolutionary origin of these traits and their involvement in loss of nervous system function in aged invertebrate species. Here we study evolutionarily conserved elements of brain degeneration using the colonial chordate model species Botryllus schlosseri. B. schlosseri reproduces both sexually and asexually 7 , with adult brains regenerating and degenerating multiple times throughout its adult life. Combining microscopy, transcriptomics and behavioral assays, we characterized adult brains from diverse stages and ages. We found that the number of neurons fluctuates each week, reaching a maximum of ∼1000 cells, and thereafter decreasing while the number of immunocytes increases. Comparing the number of neurons in the adult brains of young and old colonies, we found that older brains are smaller and contain fewer cells. Both during weekly degeneration cycles and overall with age, the decrease in neuron number correlates with reduced response to stimuli and with significant changes in the expression of genes with mammalian homologs associated with neural stem cells and neurodegenerative pathways. These results suggest persistent neural stem cell activity across ages and that cellular and molecular mechanisms of neurodegeneration are evolutionary conserved between tunicates and humans.
Phenanthroline Complexation Enhances the Cytotoxic Activity of the VO-Chrysin System (2021)

Metal complexation in general improves the biological properties of ligands. We have previously measured the anticancer effects of the oxidovanadium(IV) cation with chrysin complex, VO(chrys)2. In the present study, we synthesized and characterized a new complex generated by the replacement of one chrysin ligand by phenanthroline (phen), VO(chrys)phenCl, to confer high planarity for DNA chain intercalation and more lipophilicity, giving rise to a better cellular uptake. In effect, the uptake of vanadium has been increased in the complex with phen and the cytotoxic effect of this complex proved higher in the human lung cancer A549 cell line, being involved in its mechanisms of action, the production of cellular reactive oxygen species (ROS), the decrease of the natural antioxidant compound glutathione (GSH) and the ratio GSH/GSSG (GSSG, oxidized GSH), and mitochondrial membrane damage. Cytotoxic activity studies using the non-tumorigenic HEK293 cell line showed that [VO(chrys)phenCl] exhibits selectivity action towards A549 cells after 24 h incubation. The interaction with bovine serum albumin (BSA) by fluorometric determinations showed that the complex could be carried by the protein and that the binding of the complex to BSA occurs through H-bond and van der Waals interactions.
TIP (2019)

While digital tools are more and more used in classrooms, teachers' common practice remains to use photocopied paper documents to share and collect learning exercises from their students. With the Tangible e-Ink Paper (TIP) system, we aim to explore the use of tangible manipulatives interacting with paper sheets as a bridge between digital and paper traces of learning. Featuring an e-Ink display, a paper-based localisation system and a wireless connection, TIPs are envisioned to be used as a versatile tool across various curriculum activities. In this paper, we present the design principles of TIPs and a first functional prototype. We conclude by presenting future works in the evaluation of TIPs as a distributed sensor for teachers in their classroom, including learning scenario examples to illustrate our statements.
Of Topo and Maxwell's Dream (1997)

[ David E. Pulleyblank ][1] Topoisomerases are remarkable enzymes that remove knots and kinks from DNA. In this issue [ Rybenkov et al .][2] report that topoisomerase II (topo II) and the closely related topoisomerase IV (topo IV) actually drive a population of catenated, supercoiled, and knotted DNA molecules to an untangled state far from equilibrium. Pulleyblank explains these results in his Perspective and discusses how these topoisomerases may use ATP hydrolysis to generate this dysequilibrated state.

 [1]: http://www.sciencemag.org#affiliation
 [2]: http://www.sciencemag.org/cgi/content/short/277/5326/690
Mechanical Properties and Biocompatibility of Porous Titanium Prepared by Powder Sintering (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Feedforward control strategy for the state-decoupling Stand-alone UPS with LC output filter (2017)

In this paper, the disturbance rejection performance of the cascaded control strategy for UPS system is investigated. The comparison of closed loop system performance between conventional cascaded control (CCC) strategy and state-decoupling cascaded control (SDCC) strategy are further explored. In order to further increase the load current disturbance rejection capability of the state-decoupling in UPS system, a feedforward control strategy is proposed. In addition, the design principle for the current and voltage regulators are discussed. Simulation and experimental results are provided to verify the theoretical analysis.
Monitoring the Recovery after 2016 Hurricane Matthew in Haiti via Markovian Multitemporal Region-Based Modeling (2021)

The aim of this paper is to address the monitoring of the recovery phase in the aftermath of Hurricane Matthew (28 September–10 October 2016) in the town of Jérémie, southwestern Haiti. This is accomplished via a novel change detection method that has been formulated, in a data fusion perspective, in terms of multitemporal supervised classification. The availability of very high resolution images provided by last-generation satellite synthetic aperture radar (SAR) and optical sensors makes this analysis promising from an application perspective and simultaneously challenging from a processing viewpoint. Indeed, pursuing such a goal requires the development of novel methodologies able to exploit the large amount of detailed information provided by this type of data. To take advantage of the temporal and spatial information associated with such images, the proposed method integrates multisensor, multisource, and contextual information. Markov random field modeling is adopted here to integrate the spatial context and the temporal correlation associated with images acquired at different dates. Moreover, the adoption of a region-based approach allows for the characterization of the geometrical structures in the images through multiple segmentation maps at different scales and times. The performances of the proposed approach are evaluated on multisensor pairs of COSMO-SkyMed SAR and Pléiades optical images acquired over Jérémie, in the aftermath of and during the three years after Hurricane Matthew. The effectiveness of the change detection results is analyzed both quantitatively, through the computation of accuracy measures on a test set, and qualitatively, by visual inspection of the classification maps. The robustness of the proposed method with respect to different algorithmic choices is also assessed, and the detected changes are discussed in relation to the recovery endeavors in the area and ground-truth data collected in the field in April 2019.
Dataset of COVID-19 outbreak and potential predictive features in the USA (2021)

This dataset provides information related to the outbreak of COVID-19 disease in the United States, including data from each of 3142 US counties from the beginning of the outbreak (January 2020) until June 2021. This data is collected from many public online databases and includes the daily number of COVID-19 confirmed cases and deaths, as well as 46 features that may be relevant to the pandemic dynamics: demographic, geographic, climatic, traffic, public-health, social-distancing-policy adherence, and political characteristics of each county. We anticipate many researchers will use this dataset to train models that can predict the spread of COVID-19 and to identify the key driving factors.
Inferring the dynamic range of electrode current by using an information theoretic model of cochlear implant stimulation (2014)

Information theory has been used in estimating the performance of cochlear implants, which restore partial hearing to people by replacing the function of missing inner hair cells with an electrode array. Previous work has already developed a channel model of the electrode-neural interface in which the channel input is defined as the choice of electrodes and the channel output is defined as the normalized location of all active auditory nerve fibers. This model enables prediction of the optimal number of electrodes for cochlear implants by calculating the mutual information between channel input and channel output. In this paper, we calculate the mutual information with a varied model parameter, in particular, the electrode current. First, we investigate to what extent the different electrode current levels impact on the performance of the modeling framework. Then we estimate the dynamic range of electrode current based on the mutual information calculation. The results in this paper may provide a theoretical guide for optimizing stimulation strategies for future users of cochlear implants.
Development of Small-Diameter Vascular Grafts Based on Silk Fibroin Fibers from Bombyx mori for Vascular Regeneration (2010)

In the field of surgical revascularization, the need for functional small-diameter (1.5-4.0 mm in diameter) vascular grafts is increasing. Several synthetic biomaterials have been tested for this purpose, but in many cases they cause thrombosis. In this study, we report the development of small-diameter vascular grafts made from silk fibroin fibers from the domestic silkworm Bombyx mori or recombinant silk fibroin fibers from a transgenic silkworm. The vascular grafts were prepared by braiding, flattening and winding the silk fibers twice onto a cylindrical polymer tube followed by coating with an aqueous silk fibroin solution. The grafts, which are 1.5 mm in inner diameter and 10 mm in length, were implanted into rat abdominal aorta. An excellent patency (ca. 85%, n= 27) at 12 months after grafting with wild-type silk fibers was obtained. Endothelial cells and smooth muscle cells migrated into the silk fibroin graft early after implantation, and became organized into an endothelium and a media-like smooth muscle layer.
Effects of Chlorpyrifos Oxon on M2 Muscarinic Receptor Internalization in Different Cell Types (2008)

The muscarinic M2 receptor is a member of the G protein-coupled receptor (GPCR) superfamily. Agonist activation of GPCR leads to their phosphorylation, desensitization, internalization, and subsequent endocytic recycling or lysosomal degradation. Agonist-induced phosphorylation of M2 receptors is mediated by G-protein receptor kinase 2 (GRK2). The active metabolite of the organophosphorus insecticide chlorpyrifos, i.e., chlorpyrifos oxon (CPO), inhibited agonist-induced phosphorylation of human recombinant M2 receptors by GRK2 in vitro in a concentration-dependent manner. In both intact HEL 299 cells (human embryonic lung fibroblasts expressing M2 receptors) and CHO-M2 cells (stably expressing M2 receptors), the muscarinic agonist carbachol (100 microM) led to receptor internalization as determined by reduced specific binding to the membrane-impermeable radioligand [(3)H]-N-methylscopolamine (NMS). CPO alone (100 microM) exerted no significant effect on NMS binding in either HEL 299 or CHO-M2 cells. In HEL 299 cells, CPO did not influence carbachol-induced internalization, whereas in CHO-M2 cells CPO blocked internalization. In primary striatal neurons, M2 receptors appeared widely and diffusely distributed. Exposure to either carbachol or CPO led to apparent receptor internalization with an increased percent of cells exhibiting punctate domains of immunostaining, while combined exposure to both carbachol and CPO led to a significantly higher percent of cells exhibiting this appearance. The data suggest that CPO may differentially influence agonist-stimulated M2 receptor internalization in a cell-dependent manner.
Bidirectional Joint Representation Learning with Symmetrical Deep Neural Networks for Multimodal and Crossmodal Applications (2016)

Common approaches to problems involving multiple modalities (classification, retrieval, hyperlinking, etc.) are early fusion of the initial modalities and crossmodal translation from one modality to the other. Recently, deep neural networks, especially deep autoencoders, have proven promising both for crossmodal translation and for early fusion via multimodal embedding. In this work, we propose a flexible crossmodal deep neural network architecture for multimodal and crossmodal representation. By tying the weights of two deep neural networks, symmetry is enforced in central hidden layers thus yielding a multimodal representation space common to the two original representation spaces. The proposed architecture is evaluated in multimodal query expansion and multimodal retrieval tasks within the context of video hyperlinking. Our method demonstrates improved crossmodal translation capabilities and produces a multimodal embedding that significantly outperforms multimodal embeddings obtained by deep autoencoders, resulting in an absolute increase of 14.14 in precision at 10 on a video hyperlinking task.
Reconstruction of fetal brain MRI with intensity matching and complete outlier removal (2012)

We propose a method for the reconstruction of volumetric fetal MRI from 2D slices, comprising super-resolution reconstruction of the volume interleaved with slice-to-volume registration to correct for the motion. The method incorporates novel intensity matching of acquired 2D slices and robust statistics which completely excludes identified misregistered or corrupted voxels and slices. The reconstruction method is applied to motion-corrupted data simulated from MRI of a preterm neonate, as well as 10 clinically acquired thick-slice fetal MRI scans and three scan-sequence optimized thin-slice fetal datasets. The proposed method produced high quality reconstruction results from all the datasets to which it was applied. Quantitative analysis performed on simulated and clinical data shows that both intensity matching and robust statistics result in statistically significant improvement of super-resolution reconstruction. The proposed novel EM-based robust statistics also improves the reconstruction when compared to previously proposed Huber robust statistics. The best results are obtained when thin-slice data and the correct approximation of the point spread function is used. This paper addresses the need for a comprehensive reconstruction algorithm of 3D fetal MRI, so far lacking in the scientific literature.
Antibiotics from Gliding Bacteria, LXX Chondramides A–D, New Cytostatic and Antifungal Cyclodepsipeptides from Chondromyces crocatus (Myxobacteria): Isolation and Structure Elucidation (1996)

Abstract As a result of the extension of our screening to strains of Chondromyces four new antifungal and highly cytostatic depsipeptides were isolated, the chondramides A ( 1 ) – D ( 4 ). Their macrocyclic structures comprise three amino acids and a polyketide, viz. alanine, N ‐methyltryptophan, α‐methoxyl‐β‐tyrosine, and a 7 ‐hydroxytrimethyloctenoic acid. Thus, they were found to be closely related to a small class of cyclodepsipeptides including jaspamide, the geodiamolides, and neosiphoniamolide which all have been isolated from marine sponges.
A High Stable Television Synchronizing System With a Ceramic Resonator (1973)

Normally, television receivers require manual adjustment for the horizontal and the vertical synchronization. In this paper, a highly-stable synchronizing circuit is described. It requires no manual adjustment.
<title>Compact neutron source development at LBNL</title> (2001)

A compact neutron generator based on D-D or D-T fusion reactions is being developed at the Lawrence Berkeley National laboratory. The deuterium or tritium ions are produced in a radio-frequency (RF) driven multicusp plasma source. Seven beamlets are extracted and are accelerated to energy of 100 keV by means of a three-electrode electrostatic accelerator column. The ion beam then impinges on a titanium coated copper target where either the 2.4 MeV D-D or 13 MeV D-T neutrons are generated by fusion reaction. The development of the neutron tube is divided into three phases. First, the accelerator column is operated at hydrogen beam intensity of 15 mA. Second phase consists of deuterium beam runs at pulsed, low duty cycle 150 mA operation. The third phase consists of deuterium or tritium operation at 1.5 A beam current. Phase one is completed and the results of hydrogen beam testing are discussed. Low duty cycle 150 mA deuterium operation is being investigated. Neutron flux will be measured. Finally the phase three operation and the advance neutron generator designs are described.
Augmented State Feedback for Improving Observability of Linear Systems\n with Nonlinear Measurements (2019)

This paper is concerned with the design of an augmented state feedback\ncontroller for finite-dimensional linear systems with nonlinear observation\ndynamics. Most of the theoretical results in the area of (optimal) feedback\ndesign are based on the assumption that the state is available for measurement.\nIn this paper, we focus on finding a feedback control that avoids state\ntrajectories with undesirable observability properties. In particular, we\nintroduce an optimal control problem that specifically considers an index of\nobservability in the control synthesis. The resulting cost functional is a\ncombination of LQR-like quadratic terms and an index of observability. The main\ncontribution of the paper is presenting a control synthesis procedure that on\none hand, provides closed loop asymptotic stability, and addresses the\nobservability of the system--as a transient performance criteria--on the other.\n