gebhart/patrepeval huggingface dataset:
A pathway‐specific transcriptional activator regulates late steps of clavulanic acid biosynthesis in <i>Streptomyces clavuligerus</i> (1998)

A Streptomyces clavuligerus gene (designated claR) located downstream from the gene encoding clavaminate synthase in the clavulanic acid biosynthetic gene cluster is involved in regulation of the late steps in clavulanic acid biosynthesis. Nucleotide sequence analysis and database searching of ClaR identified a significant similarity to the helix-turn-helix motif (HTH) region of LysR transcriptional regulators. A gene replacement mutant disrupted in claR was unable to produce clavulanic acid, suggesting that claR is essential for clavulanic acid biosynthesis. Furthermore, the accumulation of clavaminic acid in the claR mutant suggested that ClaR regulates the late steps in the clavulanic acid pathway, i.e. those involved in the conversion of clavaminic acid to clavulanic acid. Transcriptional analysis using RNA isolated from the wild type and the claR mutant showed that the expression of the putative late genes, but not the early genes, was regulated by ClaR. High-resolution S1 nuclease analysis of claR suggested that it is expressed as a monocistronic transcript and also as a bicistronic transcript along with the late gene orf-9. The transcription start site of the monocistronic claR transcript was identified as a C residue 155 nucleotides upstream from the claR start codon.
Photoresist developer reclamation technology and system (2002)

A tetramethylammonium hydroxide (TMAH) generally used as photoresist developer for manufacturing LSIs and LCDs is recovered from developer waste (spent developer) using an electrodialysis (ED) method, and purified by ion exchange (IE) technologies. Reclaimed developer features analytically the same purity as commercial fresh one. This reclamation system can achieve a stably high TMAH recovery rate of more than 80%. Furthermore, it has the great advantages of saving operating costs, which amounts to 66.2% (for LSI) and 78.3% (for LCD) total cost reduction compared with conventional no reclamation system in a case study, as well as reducing environmental load.
Adaptive streaming over Content Centric Networks in mobile networks using multiple links (2013)

This paper presents the usage of Content Centric Networking (CCN) for adaptive multimedia streaming in mobile environments, leveraging the recent ISO/IEC MPEG Dynamic Adaptive Streaming over HTTP (DASH) standard. The performance of DASH over CCN is evaluated using real-world mobile bandwidth traces and compared to previous evaluations of different DASH-based as well as proprietary systems. As there are no client-server connections in CCN, it offers the possibility to transfer data from multiple sources as well as over multiple links in parallel, which is definitely an important feature, e.g., for mobile devices offering multiple network links. This functionality is used and evaluated in this paper in combination with DASH, making it possible to dynamically choose the best performing link for media streaming, which is a clear advantage over DASH using HTTP and the TCP/IP protocol stack. The evaluation therefore investigates DASH over CCN in two scenarios using synthetic and real-world mobile bandwidth traces respectively, showing a significantly better performance than conventional DASH using only one connection.
SERS probes for the detection and imaging of biochemical species on the nanoscale (2006)

We have developed novel surface enhanced Raman scattering (SERS)-based nanoimaging probes for dynamic chemical imaging in a non-scanning format. These probes have been developed for obtaining sub-diffraction limited chemical measurements of various biochemical species (e.g., lipids, proteins, etc.) as well as biological organisms (e.g., bacteria, etc.). They combine qualitative and quantitative information obtained from SERS with the imaging capabilities of coherent fiber optic bundles. Nanoimaging probes are fabricated from coherent fiber optic bundles composed of 30,000 individual 4 μm diameter fiber elements. Using a CO<sub>2</sub> laser based micropipette puller, bundles are tapered on one end resulting in the formation of equi-diameter individual elements tens of nanometers to hundreds of nanometers in diameter. Employing these probes, inherent image magnification and submicron spatial resolution is possible. Across these tapered probe tips, uniformly roughened surface features are creating by HF acid etching. These surface features consist of six cladding peaks that surround each individual fiber elements' core, which are uniform in size, shape, structure, and spacing. SERS active surfaces are created on the tapered tips of the probes by selectively depositing silver onto these cladding peaks, creating an array of highly ordered uniform silver islands across these nanoimaging probes' surfaces. This fabrication process results in a high degree of uniformity in SERS enhancement across the image surface of the probes (< 3.0% RSD), which is essential for reproducible quantitative imaging applications. Further SERS enhancement and specific excitation wavelength tuning can be achieved by controlling the spacing between silver islands and the overall size of the silver islands uniformly arrayed across these SERS probe tips. Characterization and imaging of biochemical species and model compounds using these SERS nanoimaging probes is presented in this manuscript.
Novel bradykinins and their precursor cDNAs from European yellow‐bellied toad (<i>Bombina variegata</i>) skin (2002)

Two novel bradykinin-related peptides (Ala3,Thr6)-bradykinin and (Val1,Thr3,Thr6)-bradykinin, were identified by a systematic sequencing study of peptides in the defensive skin secretion of the yellow-bellied toad, Bombina variegata. These peptides are the first amphibian skin bradykinins to exhibit amino acid substitutions at the Pro3 position of the bradykinin nonapeptide. Previously reported bradykinins from other Bombina species were not detected. Respective precursor cDNAs, designated BVK-1 and BVK-2, respectively, were cloned from a skin library by 3'- and 5'-RACE reactions. BVK-1 contained an open-reading frame of 97 amino acids encoding a single copy of (Ala3,Thr6)-bradykinin and similarly, the open-reading frame of BVK-2 consisted of 96 amino acids encoding a single copy of (Val1,Thr3,Thr6)-bradykinin. Synthetic replicates of each novel bradykinin were found to be active on mammalian arterial and small intestinal smooth muscle preparations. The structural diversity of bradykinins in amphibian defensive skin secretions may be related to defence against specific predators.
Enhanced Catalytic Activity and Stability of the Oxygen Evolution Reaction on Tetravalent Mixed Metal Oxide (2020)

The oxygen evolution reaction (OER) is a crucial energy conversion reaction for achieving a sustainable society. Highly active OER catalysts were reported in Fe–Co mixed oxides such as perovskite-type Ba0.5Sr0.5Co0.8Fe0.2O3−δ (BSCF) and brownmillerite-type Ca2FeCoO5. The synergistic effects of Fe–Co mixing on the OER activity are expected in these oxides. However, the details have not been discussed yet because of their structure randomness. In this study, we examine Fe–Co mixing effects on OER catalytic activity for several perovskite and brownmillerite oxides with trivalent and tetravalent Fe and Co ions. Regardless of crystal structures and valence states, the Fe–Co mixing enhances the OER activities compared to the parent compounds. In particular, CaFe0.5Co0.5O3, a perovskite oxide consisting of Fe4+ and Co4+ ions, displays a significant increase in OER activity, which is comparable to BSCF, together with the enhancement of stability. The electronic state of CaFe0.5Co0.5O3 obtained by density-functional theory calculation with the special quasirandom structure model exhibits the existence of active sites with smaller charge-transfer energies than the parent compounds, CaFeO3 and CaCoO3. This finding proposes that the various structural and electronic environments around transition metal ions induced by random distributions of constituent metals contributes to dispersed electronic band structures, leading to highly active sites.
A Systems Approach to Optimize the Operation of a Refrigeration Unit at a Chemical Plant (2005)

This paper focuses on the ongoing system level\nanalysis and the optimization results of two steamturbine\ndriven refrigeration units at the Dow\nChemical company Peroxymerics (PXC) plant\nlocated at St. Charles Operations in Hahnville, LA.\nSix-sigma has been accepted as a corporate-wide\nphilosophy at the Dow Chemical Company, and this\nmethodology was applied to this refrigeration system\noptimization at the plant. Process refrigeration at the\nplant comprises of two individual systems that\noperate at different temperature levels and serve a\nmyriad of process loads as well as provide chilled\nwater for the plant. The total plant capacity is ~6,500\nrefrigeration tons and has a total charge of 225,000\nlbs of refrigerant - R134a. Two steam turbines drive\nthe refrigerant compressors. The utility cost structure\nis interlaced with costs and credits for the supply and\nreturn steam to the plant headers. As a first step\ntowards a systems approach for optimization of the\nrefrigeration unit operation, Dow Chemical Company\ncontracted with Hudson Technologies to undertake a\nfeasibility study. After the projects were completed,\noperational data was then collected and analyzed to\nquantify the cost savings and level of optimization.\nTrending certain key parameters indicated ongoing\nperformance and closely monitored system\ndegradation.
Biological pacemaker created by minimally invasive somatic reprogramming in pigs with complete heart block (2014)

Somatic reprogramming by reexpression of the embryonic transcription factor T-box 18 (TBX18) converts cardiomyocytes into pacemaker cells. We hypothesized that this could be a viable therapeutic avenue for pacemaker-dependent patients afflicted with device-related complications, and therefore tested whether adenoviral TBX18 gene transfer could create biological pacemaker activity in vivo in a large-animal model of complete heart block. Biological pacemaker activity, originating from the intramyocardial injection site, was evident in TBX18-transduced animals starting at day 2 and persisted for the duration of the study (14 days) with minimal backup electronic pacemaker use. Relative to controls transduced with a reporter gene, TBX18-transduced animals exhibited enhanced autonomic responses and physiologically superior chronotropic support of physical activity. Induced sinoatrial node cells could be identified by their distinctive morphology at the site of injection in TBX18-transduced animals, but not in controls. No local or systemic safety concerns arose. Thus, minimally invasive TBX18 gene transfer creates physiologically relevant pacemaker activity in complete heart block, providing evidence for therapeutic somatic reprogramming in a clinically relevant disease model.
Cell-Cell Fusion Induced by the Avian Reovirus Membrane Fusion Protein Is Regulated by Protein Degradation (2004)

The p10 fusion-associated small transmembrane protein of avian reovirus induces extensive syncytium formation in transfected cells. Here we show that p10-induced cell-cell fusion is restricted by rapid degradation of the majority of newly synthesized p10. The small ectodomain of p10 targets the protein for degradation following p10 insertion into an early membrane compartment. Paradoxically, conservative amino acid substitutions in the p10 ectodomain hydrophobic patch that eliminate fusion activity also increase p10 stability. The small amount of p10 that escapes intracellular degradation accumulates at the cell surface in a relatively stable form, where it mediates cell-cell fusion as a late-stage event in the virus replication cycle. The unusual relationship between a nonstructural viral membrane fusion protein and the replication cycle of a nonenveloped virus has apparently contributed to the evolution of a novel mechanism for restricting the extent of virus-induced cell-cell fusion.
Improving the Accuracy of Mean DGD Estimates by Analysis of Second-Order PMD Statistics (2004)

The authors propose a novel technique to improve accuracy in measurements of the mean differential group delay (DGD) of optical fiber. Using the statistics of the second-order polarization-mode dispersion and averaging properly, they find a 30% reduction in measurement uncertainty, which is equivalent to doubling the measurement's optical bandwidth. The authors motivate the necessity for proper averaging by first demonstrating that the conventional conversions of "mean-square" to "mean" DGD lead to (correctable) systematic errors for finite bandwidth measurements.
Hierarchical Ordered Assembly of Genetically Modifiable Viruses into Nanoridge‐in‐Microridge Structures (2019)

Hierarchically assembled nanomaterials can find a variety of applications in medicine, energy, and electronics. Here, an automatically controlled dip-pulling method is developed and optimized to generate an unprecedented ordered nano-to-micro hierarchical nanoridge-in-microridge (NiM) structure from a bacteria-specific human-safe virus, the filamentous phage with or without genetically displaying a foreign peptide. The NiM structure is pictured as a window blind with each lath (the microridge) made of parallel phage bundles (the nanoridges). It is independent of the substrate materials supporting it. Surprisingly, it can induce the bidirectional differentiation of stem cells into neurons and astrocytes within a short timeframe (only 8 d) not seen before, which is highly desired because both neurons and astrocytes are needed simultaneously in treating neurodegenerative diseases. Since phages can direct tissue regeneration, template materials formation, sense molecules, and build electrodes, the NiM structures displaying different peptides and on varying materials hold promise in many technologically important fields.
A Hybrid Technique for Coupling Chemical Kinetics and Hydrodynamics Computations in Multi-Phase Reacting Flow Systems (1997)

Abstract A hybrid technique to couple hydrodynamics and chemical kinetics calculations in a multi-phase, multi-species, turbulent reacting flow simulation has been developed. It divides a flow simulation into two parts: a reacting flow hydrodynamic simulation with a small but sufficient number of lumped reactions to compute flow field properties followed by a many subspecies (of order 10 to 100) reaction kinetics and transport calculation. This technique has been incorporated in a computational fluid dynamics (CFD) code to predict concentrations of many subspecies in a reacting flow where complex chemical reactions take place, and it can be applied to many applications such as combustors. The application presented in this paper is the flow simulation of a fluid catalytic cracking (FCC) riser reactor. Applying the technique in the FCC riser application has shown that it can be used to identify critical processes and operating parameters including the trends and relationships that are necessary to the improve the quality and quantity of FCC products.
Molecular cloning and characterization of a new receptor for galanin (1997)

Galanin (GAL) is a widely distributed neuropeptide with diverse biological effects including modulation of hormone release, antinociception and modification of feeding behavior. Its effects are mediated through G-protein-coupled receptors (GPCR) for which only a single type has been cloned, GAL receptor 1 (GALR1). We describe the cloning of a second galanin receptor type, GALR2, from rat hypothalamus. The GALR2 amino acid sequence is 38% identical to GALR1 and is pharmacologically similar to GALR1 when expressed in COS-7 cells. GALR2 is encoded by a single gene containing at least one intron and expressed in a diverse range of tissues.
Inverse Methods for Reconstruction of Channel Taps in OFDM Systems (2012)

We describe a novel pilot-aided method for estimation of doubly selective wireless channels in OFDM systems. We compute the first few Fourier coefficients of each channel tap from the pilot information. We then estimate the BEM coefficients of the channel taps from their respective Fourier coefficients using a recently developed inverse reconstruction method. For a system with L channel taps, the proposed method uses O(L log L) operations and O(L) memory per OFDM symbol. We validate our method by simulating a system conforming to the IEEE 802.16e standard.
Back-propagation learning in expert networks (1992)

Expert networks are event-driven, acyclic networks of neural objects derived from expert systems. The neural objects process information through a nonlinear combining function that is different from, and more complex than, typical neural network node processors. The authors develop back-propagation learning for acyclic, event-driven networks in general and derive a specific algorithm for learning in EMYCIN-derived expert networks. The algorithm combines back-propagation learning with other features of expert networks, including calculation of gradients of the nonlinear combining functions and the hypercube nature of the knowledge space. It offers automation of the knowledge acquisition task for certainty factors, often the most difficult part of knowledge extraction. Results of testing the learning algorithm with a medium-scale (97-node) expert network are presented.
High-resolution (Doppler-limited) spectroscopy using quantum-cascade distributed-feedback lasers (1998)

Lasing characteristics were evaluated for distributed-feedback quantum-cascade (QC) lasers operating in a continuous mode at cryogenic temperatures. These tests were performed to determine the QC lasers’ suitability for use in high-resolution spectroscopic applications, including Doppler-limited molecular absorption and pressure-limited lidar applications. By use of a rapid-scan technique, direct absorbance measurements of nitric oxide (NO) and ammonia NH3 were performed with several QC lasers, operating at either 5.2 or 8.5 µm. Results include time-averaged linewidths of better than 40??MHz and long-term laser frequency reproducibility, even after numerous temperature cycles, of 80??MHz or better. Tuning rates of 2.5 cm-1 in 0.6??ms can be easily achieved. Noise-equivalent absorbance of 3×10-6 was also obtained without optimizing the optical arrangement.
Orthogonal-Polarization Heterodyne OSNR Monitoring Insensitive to Polarization-Mode Dispersion and Nonlinear Polarization Scattering (2007)

An in-band optical signal-to-noise-ratio (OSNR) monitoring technique that utilizes the polarization orthogonality and heterodyne mixing is proposed. The technique is not only insensitive to polarization-mode dispersion but also robust to nonlinear polarization scattering induced by interchannel cross-phase modulation. Moreover, the technique places no special requirements on the signal properties, such as modulation format and bit rate. The monitoring technique is demonstrated experimentally in both linear and nonlinear systems
An Approach To A Versatile Focal Plane Array Test Facility (1989)

The CECOM Center for Night Vision and Electro-Optics (C2NVEO) infrared nfrared Focal Plane Array test facility is being upgraded to improve speed and test capability. Prior to the upgrade,the test station was capable of testing FPA's, but it did not meet present and future testing needs. Deficiencies such as; high system noise, inflexible dewar configuration, Limited levels of automation, in addition to the inability to perform focussed spot and FPA spectral responsivity measurements were reasons to improve the test station. It was important during this development that the ability to characterize a diverse variety of Infrared (IR) Focal Plane Array designs, sizes, formats, materials, and applications be maintained or increased. Considerations relating to this will be discussed. In the future, the test station will be able to test HgCdTe and PtSi arrays on a much larger scale than at present and test other new technologies as well. The goal is to be able to fully characterize one Focal Plane Array per day.
Two-Stage, Integrated, Geothermal-CO2 Storage Reservoirs: An Approach for Sustainable Energy Production, CO<sub>2</sub>-Sequestration Security, and Reduced Environmental Risk (2012)

We introduce a hybrid two-stage energy-recovery approach to sequester CO{sub 2} and produce geothermal energy at low environmental risk and low cost by integrating geothermal production with CO{sub 2} capture and sequestration (CCS) in saline, sedimentary formations. Our approach combines the benefits of the approach proposed by Buscheck et al. (2011b), which uses brine as the working fluid, with those of the approach first suggested by Brown (2000) and analyzed by Pruess (2006), using CO{sub 2} as the working fluid, and then extended to saline-formation CCS by Randolph and Saar (2011a). During stage one of our hybrid approach, formation brine, which is extracted to provide pressure relief for CO{sub 2} injection, is the working fluid for energy recovery. Produced brine is applied to a consumptive beneficial use: feedstock for fresh water production through desalination, saline cooling water, or make-up water to be injected into a neighboring reservoir operation, such as in Enhanced Geothermal Systems (EGS), where there is often a shortage of a working fluid. For stage one, it is important to find economically feasible disposition options to reduce the volume of brine requiring reinjection in the integrated geothermal-CCS reservoir (Buscheck et al. 2012a). During stage two, which begins as CO{sub 2} reaches the production wells; coproduced brine and CO{sub 2} are the working fluids. We present preliminary reservoir engineering analyses of this approach, using a simple conceptual model of a homogeneous, permeable CO{sub 2} storage formation/geothermal reservoir, bounded by relatively impermeable sealing units. We assess both the CO{sub 2} sequestration capacity and geothermal energy production potential as a function of well spacing between CO{sub 2} injectors and brine/CO{sub 2} producers for various well patterns and for a range of subsurface conditions.
Facile Noninvasive Retinal Gene Delivery Enabled by Penetratin (2016)

Gene delivery to the posterior segment of the eye is severely hindered by the impermeability of defensive barriers; therefore, in clinical settings, genomic medicines are mainly administered by intravitreal injection. We previously found that penetratin could transport the covalently conjugated fluorophore to the fundus oculi by topical instillation. In this study, gene delivery systems enabled by penetratin were designed based on electrostatic binding to target the retina via a noninvasive administration route and prepared with red fluorescent protein plasmid (pRFP) and/or poly(amidoamine) dendrimer of low molecular weight (G3 PAMAM). Formulation optimization, structure confirmation, and characterization were subsequently conducted. Penetratin alone showed limited ability to condense the plasmid but had powerful uptake and transfection by corneal and conjunctival cells. G3 PAMAM was nontoxic to the ocular cells, and when introduced into the penetratin-incorporated complex, the plasmid was condensed more compactly. Therefore, further improved cellular uptake and transfection were observed. After being instilled in the conjunctival sac of rats, the intact complexes penetrated rapidly from the ocular surface into the fundus and resided in the retina for more than 8 h, which resulted in efficient expression of RFP in the posterior segment. Intraocular distribution of the complexes suggested that the plasmids were absorbed into the eyes through a noncorneal pathway during which penetratin played a crucial role. This study provides a facile and friendly approach for intraocular gene delivery and is an important step toward the development of noninvasive gene therapy for posterior segment diseases.