gebhart/patrepeval huggingface dataset:
Genetic Circuits in Salmonella typhimurium (2012)

Synthetic biology has rapidly progressed over the past decade and is now positioned to impact important problems in health and energy. In the clinical arena, the field has thus far focused primarily on the use of bacteria and bacteriophages to overexpress therapeutic gene products. The next generation of multigene circuits will control the triggering, amplitude, and duration of therapeutic activity in vivo. This will require a host organism that is easy to genetically modify, leverages existing successful circuit designs, and has the potential for use in humans. Here, we show that gene circuits that were originally constructed and tested in Escherichia coli translate to Salmonella typhimurium, a therapeutically relevant microbe with attenuated strains that have exhibited safety in several human clinical trials. These strains are essentially nonvirulent, easy to genetically program, and specifically grow in tumor environments. Developing gene circuits on this platform could enhance our ability to bring sophisticated genetic programming to cancer therapy, setting the stage for a new generation of synthetic biology in clinically relevant microbes.
Optical ammonia sensing films based on an immobilized metalloporphyrin (1996)

Optical sensing films for ammonia gas have been developed by immobilizing zinc 5,10,15,20-tetraphenylporphine (ZnTPP) in silicone rubber. The detection of ammonia can be achieved using both absorbance and fluorescence emission measurements. Spectral changes were observed due to the coordination of NH3 molecules to the ZnII ion in the immobilized metalloporphyrin. Effects of other immobilization matrices on sensor properties were investigated. ZnTPP-silicone films were found to show a reasonably high sensitivity to ammonia, with a linear range of 0–6 mg m–3(0–8.5 ppm). The detection limit for ammonia in nitrogen was 0.5 mg m–3(0.7 ppm). The equilibrium response time of the films was approximately 4 min and the reaction with ammonia was reversible. ZnTPP films were also found to be sensitive to triethylamine.
Plasmonic laser antenna (2006)

The authors have demonstrated a surface plasmon device composed of a resonant optical antenna integrated on the facet of a commercial diode laser, termed a plasmonic laser antenna. This device generates enhanced and spatially confined optical near fields. Spot sizes of a few tens of nanometers have been measured at a wavelength ∼0.8μm. This device can be implemented in a wide variety of semiconductor lasers emitting in spectral regions ranging from the visible to the far infrared, including quantum cascade lasers. It is potentially useful in many applications including near-field optical microscopes, optical data storage, and heat-assisted magnetic recording.
Using Key Performance Indicators To Manage Energy Costs (2005)

ABSTRACT Modern management systems rely heavily on information technology to set goals, track performance, and communicate results. Energy management approaches (such as those offered by the US Department of Energy and Natural Resources Canada) and measurement and verifi cation protocols (such as IPMVP 2001) often highlight the importance an information system has in maximizing results. The increasing adoption of energy information systems has led, however, to an interesting paradox: while it is now cost-effective to collect much more data than ever before, many energy managers fi nd themselves drowning in the volume of data generated. Business information systems faced a similar challenge a decade ago, and it is now common practice to use key performance indicators (KPIs) to summarize volumes of data into a few critical “nuggets” of actionable information. These KPIs provide both the metrics that will be used to determine the success of a business plan as well as the timely information managers need to track performance and make adjustments to ensure success. A similar approach can be used in the practice of energy management, where KPIs can be designed to measure the success of key elements in an energy management plan and provide energy managers with the timely “nuggets” of information they need to ensure success. This article describes how to defi ne and use KPIs to track the performance and measure the success of an energy management plan. A framework is provided to assist in selecting measurable goals from an energy management plan and determine the raw data and processing required to generate the associated KPIs.
The dimensionality of Sn anodes in Li-ion batteries (2012)

As a potential anode material, tin (Sn) has attracted great attention due to its low cost and its high theoretical specific capacity. However, its electrochemical performance is strongly related to its structure, including the crystalline nature, particle size, dimensionality, interface, and so on. In this review article, we will outline Sn-based nanomaterials with different dimensionalities from 0D to 3D, covering the synthesis procedures and their structure-related electrochemical performances when applied as anode materials in lithium ion batteries (LIBs). By discussing their structural dimensionalities, we aim to provide some scientific insights into the development of advanced Sn-based anode nanomaterials for next-generation LIBs.
Ribonucleic Acid Modification in Microorganisms (1993)

Ribonucleic acid contains more than 80 modified nucleosides that play multiple functional roles, including regulation of gene expression, adaptation to stress and promotion of fidelity of protein synthesis. Transfer RNA is the most highly modified RNA, and serves as a rich source of modified nucleosides that may be restricted to one or another of the archaeal (formerly archaebacterial (1)), bacterial, or eucaryal phylogenetic domains. The presence (or absence) of certain modified nucleosides can thus serve as phylogenetic markers. Nuclease digests of tRNA (about one nanomole) can be analyzed directly as mixtures using thermospray liquid chromatography/mass spectrometry (LC/MS) to characterize modified nucleosides from both their mass spectra and chromatographic retention times.
Functions of microtubules in the Saccharomyces cerevisiae cell cycle. (1988)

We used the inhibitor nocodazole in conjunction with immunofluorescence and electron microscopy to investigate microtubule function in the yeast cell cycle. Under appropriate conditions, this drug produced a rapid and essentially complete disassembly of cytoplasmic and intranuclear microtubules, accompanied by a rapid and essentially complete block of cellular and nuclear division. These effects were similar to, but more profound than, the effects of the related drug methyl benzimidazole carbamate (MBC). In the nocodazole-treated cells, the selection of nonrandom budding sites, the formation of chitin rings and rings of 10-nm filaments at those sites, bud emergence, differential bud enlargement, and apical bud growth appeared to proceed normally, and the intracellular distribution of actin was not detectably perturbed. Thus, the cytoplasmic microtubules are apparently not essential for the establishment of cell polarity and the localization of cell-surface growth. In contrast, nocodazole profoundly affected the behavior of the nucleus. Although spindle-pole bodies (SPBs) could duplicate in the absence of microtubules, SPB separation was blocked. Moreover, complete spindles present at the beginning of drug treatment appeared to collapse, drawing the opposed SPBs and associated nuclear envelope close together. Nuclei did not migrate to the mother-bud necks in nocodazole-treated cells, although nuclei that had reached the necks before drug treatment remained there. Moreover, the double SPBs in arrested cells were often not oriented toward the budding sites, in contrast to the situation in normal cells. Thus, microtubules (cytoplasmic, intranuclear, or both) appear to be necessary for the migration and proper orientation of the nucleus, as well as for SPB separation, spindle function, and nuclear division.
Design of a Catadioptric VCASS Helmet-Mounted Display (1981)

A new wide-angle, dual-eye, helmet-mounted display has been designed. Two images combine, with a 15 deg. central field overlap, to provide a panoramic display 102 deg. wide by 45 deg. tall, with a resolution to approximately 1000 TV lines per eye. The image-generating device is a miniature 18-mm CRT. The optics, which are symmetrical for both eyes, comprise partially reflective plastic reflectors, five small glass lens elements, and a 2:1 fiber optic magnifier. A 12-mm exit pupil is obtained with enough eye relief to permit the user to wear glasses, with an interpupillary adjustment of 58 to 73 mm. Total weight of the device, not including the Air Force flight helmet type HGU-2A/P upon which it is mounted, is less than 3 pounds. (Author)
A bibliometric analysis of publications on pluripotent stem cell research. (2015)

The comprehensive analysis of highly cited articles in the stem cell field could identify milestones and important contributors, giving a historic perspective on scientific progress.
Improved resolution 3D object sensing and recognition using time multiplexed computational integral imaging (2003)

In this paper we present a high-resolution technique to passively sense, detect and recognize a 3D object using computational integral imaging. We show that the use of a non-stationary microlens array improves the longitudinal distance estimation quantization error. The proposed method overcomes the Nyquist upper limit for the resolution. We use 3D non-linear correlation to recognize the 3D coordinates and shape of the desired object.
Notch Signaling Limits Supporting Cell Plasticity in the Hair Cell-Damaged Early Postnatal Murine Cochlea (2013)

In mammals, auditory hair cells are generated only during embryonic development and loss or damage to hair cells is permanent. However, in non-mammalian vertebrate species, such as birds, neighboring glia-like supporting cells regenerate auditory hair cells by both mitotic and non-mitotic mechanisms. Based on work in intact cochlear tissue, it is thought that Notch signaling might restrict supporting cell plasticity in the mammalian cochlea. However, it is unresolved how Notch signaling functions in the hair cell-damaged cochlea and the molecular and cellular changes induced in supporting cells in response to hair cell trauma are poorly understood. Here we show that gentamicin-induced hair cell loss in early postnatal mouse cochlear tissue induces rapid morphological changes in supporting cells, which facilitate the sealing of gaps left by dying hair cells. Moreover, we provide evidence that Notch signaling is active in the hair cell damaged cochlea and identify Hes1, Hey1, Hey2, HeyL, and Sox2 as targets and potential Notch effectors of this hair cell-independent mechanism of Notch signaling. Using Cre/loxP based labeling system we demonstrate that inhibition of Notch signaling with a γ- secretase inhibitor (GSI) results in the trans-differentiation of supporting cells into hair cell-like cells. Moreover, we show that these hair cell-like cells, generated by supporting cells have molecular, cellular, and basic electrophysiological properties similar to immature hair cells rather than supporting cells. Lastly, we show that the vast majority of these newly generated hair cell-like cells express the outer hair cell specific motor protein prestin.
Improving the moisture stability of perovskite solar cells by using PMMA/P3HT based hole-transport layers (2017)

In recent years, the performance of lead halide perovskite solar cells has increased dramatically, setting a record efficiency of 22.1%; however, their sensitivity towards water limits their utility and still needs to be addressed.
Computing all skyline probabilities for uncertain data (2009)

Skyline computation is widely used in multi-criteria decision making. As research in uncertain databases draws increasing attention, skyline queries with uncertain data have also been studied, e.g. probabilistic skylines. The previous work requires "thresholding" for its efficiency -- the efficiency relies on the assumption that points with skyline probabilities below a certain threshold can be ignored. But there are situations where "thresholding" is not desirable -- low probability events cannot be ignored when their consequences are significant. In such cases it is necessary to compute skyline probabilities of all data items. We provide the first algorithm for this problem whose worst-case time complexity is sub-quadratic. The techniques we use are interesting in their own right, as they rely on a space partitioning technique combined with using the existing dominance counting algorithm. The effectiveness of our algorithm is experimentally verified.
Discovery of (R)-(2-Fluoro-4-((-4-methoxyphenyl)ethynyl)phenyl) (3-Hydroxypiperidin-1-yl)methanone (ML337), An mGlu3 Selective and CNS Penetrant Negative Allosteric Modulator (NAM) (2013)

A multidimensional, iterative parallel synthesis effort identified a series of highly selective mGlu3 NAMs with submicromolar potency and good CNS penetration. Of these, ML337 resulted (mGlu3 IC50 = 593 nM, mGlu2 IC50 >30 μM) with B:P ratios of 0.92 (mouse) to 0.3 (rat). DMPK profiling and shallow SAR led to the incorporation of deuterium atoms to address a metabolic soft spot, which subsequently lowered both in vitro and in vivo clearance by >50%.
Battery-driven dynamic power management of portable systems (2000)

Battery life-time extension is a primary design objective for portable systems. Traditionally, battery life-time has been prolonged mainly by reducing average power consumption of system components. A careful analysis of discharge characteristics and the adoption of accurate high-level battery models in system-level design open new opportunities for life-time extension. In this paper, we introduce dynamic power management (DPM) policies specifically tailored to battery-powered systems. Battery-driven DPM strives to enhance life-time by automatically adapting discharge rate and current profiles to battery state-of-charge. The distinctive feature of these policies is the control of system operation based on the observation of battery output voltage. The effectiveness of the proposed policies and, more in general, of the idea of accounting for battery behavior during system design, is proved by the experiments carried out on a realistic case study, namely, an MP3 audio player.
The Pathogenesis of Insulin-Dependent Diabetes Mellitus (1994)

Insulin-dependent diabetes mellitus (IDDM) is a chronic disorder that results from autoimmune destruction of the insulin-producing pancreatic beta cells. Much has been learned during the past decade about the underlying genetics, natural history, and pathogenesis of IDDM. In this review, we shall describe some of this new information and discuss how it might be used to prevent the disease.EpidemiologyIDDM occurs most frequently in persons of northern European descent. Among other racial groups, such as blacks, Native Americans, and Asians, the disease is less common1. The incidence ranges from a low of 1 to 2 per 100,000 per . . .
In-Fusion BioBrick assembly and re-engineering (2010)

Genetic circuits can be assembled from standardized biological parts called BioBricks. Examples of BioBricks include promoters, ribosome-binding sites, coding sequences and transcriptional terminators. Standard BioBrick assembly normally involves restriction enzyme digestion and ligation of two BioBricks at a time. The method described here is an alternative assembly strategy that allows for two or more PCR-amplified BioBricks to be quickly assembled and re-engineered using the Clontech In-Fusion PCR Cloning Kit. This method allows for a large number of parallel assemblies to be performed and is a flexible way to mix and match BioBricks. In-Fusion assembly can be semi-standardized by the use of simple primer design rules that minimize the time involved in planning assembly reactions. We describe the success rate and mutation rate of In-Fusion assembled genetic circuits using various homology and primer lengths. We also demonstrate the success and flexibility of this method with six specific examples of BioBrick assembly and re-engineering. These examples include assembly of two basic parts, part swapping, a deletion, an insertion, and three-way In-Fusion assemblies.
Drug Design Targeting Protein–Protein Interactions (PPIs) Using Multiple Ligand Simultaneous Docking (MLSD) and Drug Repositioning: Discovery of Raloxifene and Bazedoxifene as Novel Inhibitors of IL-6/GP130 Interface (2014)

The IL-6/GP130/STAT3 pathway is critical for the progression of multiple types of cancers. We report here the discovery of raloxifene and bazedoxifene as novel inhibitors of IL-6/GP130 protein-protein interactions (PPIs) using multiple ligand simultaneous docking (MLSD) and drug repositioning approaches. Multiple drug scaffolds were simultaneously docked into hot spots of GP130 D1 domain by MLSD to compete with the key interacting residues of IL-6, followed by tethering to generate virtual hit compounds. Similarity searches of virtual hits on drug databases identified raloxifene and bazedoxifene as potential inhibitors of IL-6/GP130 interaction. In cancer cell assays both compounds bind to GP130 and demonstrated selective inhibition of IL-6 induced STAT3 phosphorylation and were significantly more potent than the previously reported natural product inhibitor MDL-A. The identified drugs represent a new class of lead compounds with piperidine, benzothiophene, and indole scaffolds to inhibit IL-6 induced homodimerization of GP130. Besides potential direct usage for clinic trials, the two compounds can also serve as lead compounds for optimization to speed the development of drugs selectively targeting the IL-6/GP130/STAT3 cancer signaling pathway.
The molecular dissection of Fc gamma receptor mediated phagocytosis (1995)

Because hematopoietic cells express multiple Fc gamma receptor isoforms, the role of the individual Fc gamma receptors in phagocytosis has been difficult to define. Transfection of Fc gamma receptors into COS-1 cells, which lack endogeneous Fc gamma receptors but have phagocytic potential, has proved valuable for the study of individual Fc gamma receptor function. Using this model system, we have established that a single class of human Fc gamma receptor mediates phagocytosis in the absence of other Fc receptors and that isoforms from each Fc gamma receptor class mediate phagocytosis, although the requirements for phagocytosis differ. In investigating the relationship between structure and function for Fc gamma receptor mediated phagocytosis, the importance of the cytoplasmic tyrosines of the receptor or its associated gamma chain has been established. For example, two cytoplasmic YXXL sequences, in a configuration similar to the conserved tyrosine-containing motif found in Ig gene family receptors, are important for phagocytosis by the human Fc gamma receptor, Fc gamma RIIA. Fc gamma RI and Fc gamma RIIIA do not possess cytoplasmic tyrosines but transmit a phagocytic signal through interaction with an associated gamma subunit that contains two YXXL sequences in a conserved motif required for phagocytosis. The human Fc gamma RII isoforms Fc gamma RIIB1 and Fc gamma RIIB2 do not induce phagocytosis and have only a single YXXL sequence. Cross-linking the phagocytic Fc gamma receptors induces tyrosine phosphorylation of either Fc gamma RIIA or the gamma chain, and treatment with tyrosine kinase inhibitors reduces both phagocytosis and phosphorylation of the receptor tyrosine residues. Activation of protein tyrosine kinases follows Fc gamma receptor engagement of IgG-coated cells. The data indicate that coexpression of the protein tyrosine kinase Syk, which is associated with the gamma chain in monocytes/macrophages, is important for phagocytosis mediated by Fc gamma RI and Fc gamma RIIIA. Furthermore, phosphatidylinositol-3 kinase is required for phagocytosis mediated by Fc gamma RIIA as well as for phagocytosis mediated by Fc gamma RI/gamma and Rc gamma RIIIA/gamma.
In vitro analysis of virus-associated RNA I (VAI RNA): inhibition of the double-stranded RNA-activated protein kinase PKR by VAI RNA mutants correlates with the in vivo phenotype and the structural integrity of the central domain (1994)

Adenoviruses use the virus-encoded virus-associated RNA (VAI RNA) as a defense against cellular antiviral response by blocking the activation of the interferon-induced, double-stranded RNA-activated protein kinase PKR. The structure of VAI RNA consists of two long, imperfectly base-paired duplex regions connected by a complex short stem-loop at the center, referred to as the central domain. By using a series of adenovirus mutants with linker-scan mutations in the VAI RNA gene, we recently showed that the critical elements required for function in the VAI RNA molecule are in the central domain and that these same elements of the central domain are also involved in binding to PKR. In virus-infected cells, VAI RNA interacts with latent kinase, which is bound to ribosomes; this interaction takes place in a complex milieu. To more fully understand the relationship between structure and function and to determine whether the in vivo phenotype of these mutants can be reproduced in vitro, we have now analyzed these mutant VAI alleles for their ability to block the activation of a partially purified PKR from HeLa cells. We have also derived the structure of these mutants experimentally and correlated the structure with function. Without exception, when the structure of the short stem-loop of the central domain was perturbed, the mutants failed to inhibit PKR. Structural disruptions elsewhere in the central domain or in the long duplex regions of the molecule were not deleterious for in vitro function. Thus, these results support our previous findings and underscore the importance of the elements present in the central domain of the VAI RNA for its function. Our results also suggest that the interaction between PKR and VAI RNA involves a precise secondary (and tertiary) structure in the central domain. It has been suggested that VAI RNA does not activate PKR in virus-infected cells because of mismatches in the imperfectly base-paired long duplex regions. We constructed mutant VAI genes in which the imperfectly base-paired duplex regions were converted to perfectly base-paired regions and assayed in vitro for the activation of PKR. As with the wild-type VAI RNA, these mutants failed to activate PKR in vitro, while they were able to block the activation of PKR better than did the wild type. These results suggest that the failure of VAI RNA to activate PKR is not the result of mismatches in the long duplex regions.(ABSTRACT TRUNCATED AT 400 WORDS)
New Knockout Mice Point to Molecular Basis of Memory (1997)

Neurobiologists have pinpointed the roots of memory in laboratory mice, by plucking out key proteins or adding an excess of them in particular clusters of brain cells. These feats at last offer direct confirmation of the reigning theory of how we remember and show how molecular changes affect the patterns of electrical activity that memories are made of.
k-Space Deep Learning for Accelerated MRI (2018)

The annihilating filter-based low-rank Hankel matrix approach (ALOHA) is one of the state-of-the-art compressed sensing approaches that directly interpolates the missing k-space data using low-rank Hankel matrix completion. The success of ALOHA is due to the concise signal representation in the k-space domain thanks to the duality between structured low-rankness in the k-space domain and the image domain sparsity. Inspired by the recent mathematical discovery that links convolutional neural networks to Hankel matrix decomposition using data-driven framelet basis, here we propose a fully data-driven deep learning algorithm for k-space interpolation. Our network can be also easily applied to non-Cartesian k-space trajectories by simply adding an additional regridding layer. Extensive numerical experiments show that the proposed deep learning method consistently outperforms the existing image-domain deep learning approaches.