gebhart/patrepeval huggingface dataset:
Characterization and comparative sequence analysis of replication origins from three large Bacillus thuringiensis plasmids (1991)

The replication origins of three large Bacillus thuringiensis plasmids, derived from B. thuringiensis HD263 subsp. kurstaki, have been cloned in Escherichia coli and sequenced. The replication origins, designated ori 43, ori 44, and ori 60, were isolated from plasmids of 43, 44, and 60 MDa, respectively. Each cloned replication origin exhibits incompatibility with the resident B. thuringiensis plasmid from which it was derived. Recombinant plasmids containing the three replication origins varied in their ability to transform strains of B. thuringiensis, Bacillus megaterium, and Bacillus subtilis. Analysis of the derived nucleotide and amino acid sequences indicates that the replication origins are nonhomologous, implying independent derivations. No significant homology was found to published sequences of replication origins derived from the single-stranded DNA plasmids of gram-positive bacteria, and shuttle vectors containing the three replication origins do not appear to generate single-stranded DNA intermediates in B. thuringiensis. The replication origin regions of the large plasmids are each characterized by a single open reading frame whose product is essential for replication in B. thuringiensis. The putative replication protein of ori 60 exhibits partial homology to the RepA protein of the Bacillus stearothermophilus plasmid pTB19. The putative replication protein of ori 43 exhibits weak but extensive homology to the replication proteins of several streptococcal plasmids, including the open reading frame E replication protein of the conjugative plasmid pAM beta 1. The nucleotide sequence of ori 44 and the amino acid sequence of its putative replication protein appear to be nonhomologous to other published replication origin sequences.
Facile -C−H Bond Activation in Phosphinoamine Ligands Resulting in Regio- and Stereoselective C−C Coupling with Terminal Acetylenes (1998)

Novel C−C coupling products are afforded from the reaction of tris(pyrazolyl)borate ruthenium complexes, containing the phosphinoamine ligands Ph2PCH2CH2NMe2, Ph2PCH2CH2NEt2, and Ph2PCH2CH2NiPr2, with terminal acetylenes (see scheme). The coupling takes place regioselectively at the γ-carbon atom of the phosphinoamine ligand and, depending on the steric requirments of R, either at the internal or terminal carbon atom of the acetylene molecule. All these reactions proceed in a highly diastereoselective fashion.
Extension for Stateful PCE to allow Optional Processing of PCEP Objects (2000)

This document introduces a mechanism to mark some Path Computation
Element (PCE) Communication Protocol (PCEP) objects as optional during
PCEP messages exchange for the Stateful PCE model to allow relaxing
some constraints.
Adducts of chlorohydroxyfuranones and of aldehyde conjugates. (1999)

The work reported here concerned the structural determination of adducts formed in reactions of nucleosides with chlorohydroxyfuranones and with conjugates of malonaldehyde and acetaldehyde. The chlorohydroxyfuranones are bacterial mutagens produced during chlorine disinfection of drinking-water, malonaldehyde is the major end-product of lipid peroxidation, and acetaldehyde is the major metabolite of ethanol. Exogenous sources of acetaldehyde are, for example, tobacco smoke and automobile emissions. The chlorohydroxyfuranones were found to form substituted and unsubstituted cyclic etheno adducts with adenosine, cytidine and guanosine and substituted cyclic propeno adducts with adenosine. The malonaldehyde-acetaldehyde conjugates reacted with adenosine to produce a strongly fluorescent dihydropyridine purine derivative and a substituted propenoformyl adenosine derivative. Most of the adducts identified in this study are new, and their mutagenic properties are as yet unknown.
Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection (2023)

Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from transcriptome sequencing (RNA-seq) data sets of <i>in vitro</i> infections and autopsy lung tissues of COVID-19 patients. Four genomic hot spots were identified for DVG recombination, and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single-cell RNA-seq analysis indicated the interferon (IFN) stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the next-generation sequencing (NGS) data set from a published cohort study and observed a significantly higher amount and frequency of DVG in symptomatic patients than those in asymptomatic patients. Finally, we observed exceptionally diverse DVG populations in one immunosuppressive patient up to 140 days after the first positive test of COVID-19, suggesting for the first time an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and into how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection. <b>IMPORTANCE</b> Defective viral genomes (DVGs) are generated ubiquitously in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide the potential for them to be used in novel antiviral therapies and vaccine development. SARS-CoV-2 DVGs are generated through the recombination of two discontinuous genomic fragments by viral polymerase complex, and this recombination is also one of the major mechanisms for the emergence of new coronaviruses. Focusing on the generation and function of SARS-CoV-2 DVGs, these studies identify new hot spots for nonhomologous recombination and strongly suggest that the secondary structures within viral genomes mediate the recombination. Furthermore, these studies provide the first evidence for IFN stimulation activity of <i>de novo</i> DVGs during natural SARS-CoV-2 infection. These findings set up the foundation for further mechanism studies of SARS-CoV-2 recombination and provide evidence to harness the immunostimulatory potential of DVGs in the development of a vaccine and antivirals for SARS-CoV-2.
Green scalable aerosol synthesis of porous metal–organic frameworks (2013)

Benchmarked micro or nanosized HKUST-1, ZIF-8 and Fe3(BTC)2 as well as template-assisted Fe3(BTC)2 metal-organic frameworks (MOFs) of various morphologies were synthesized via a green and scalable aerosol route. Their high space time yields make this continuous method very promising for the industrial production and shaping of MOFs.
Performance simulation of 2D photonic-crystal devices fabricated by pattern-integrated interference lithography (2014)

Pattern-integrated interference lithography (PIIL) has recently been proposed as a rapid, single-step, and wafer-scale fabrication technique for custom-modified one-, two- and three-dimensional periodic structures. Among these structures, photonic-crystal devices have significant potential applications. In this work, we simulate the fabrication of two-dimensional photonic-crystal devices by PIIL using a rigorous vector modeling and realistic photolithographic conditions. We also model the etched patterns in silicon and evaluate the photonic-crystal motif-area and motif-displacement errors. We further calculate the device intensity transmission spectra and show that the performance of PIIL-produced devices are comparable to, and in some cases are superior to, that of their idealized equivalents.
Rock Type Modeling: An Effective Method to Determine Reservoir Quality Rock to Discretize Net Pay in Lower Guadalupe Formation, Abanico Field, Colombia (2012)

Abstract The quality of a reservoir rock is determined, among other factors by porosity, permeability and the connection between the pores, known as pore throat radii. The determination of the values of this last parameter is important for estimating the flow and storage capacity of the reservoir rock. The aim of this study is the determination of quality rock types in the lower member in Guadalupe Geological Formation in Abanico Field. To achieve this goal were identified pore throats radii in 3 cores taken in the central and north area of the Abanico Field. Winland, the mid-70's, showed a statistical correlation between the optimal flow through the rocks and the radii of pore throats, when 35% of the pore space of a rock is saturated with a phase that does not wet, during capillary pressure test by mercury injection. For his part, Pittman, achievement extends the study of Winland, which development an empirical set of equations, through the use of a system of multiple regression statistical analysis. This is job was based on Pittman equations. Pittman calculated the pore thorat radii that correspond to the 35 th percentile, which was extended to a spread of mercury saturations percentiles (between 10 and 75%). Using this methodology it was determined that the dominant pore throat radius in the samples studied for the Lower Guadalupe Formation, corresponds to a mercury saturation of 45% (R45). This result is relevant because from of testing was determined the percentage of pore volume that contributes to the flow capacity of the rock and the percentage of pore volume that provides storage capacity. Integrating the capillary-pressure data with well log information from the production history, it was determined that the hydraulic unit Lower Guadalupe is primarily Macro-porous type with pre throat radii between 2 and 10 microns, with minor variations Mega-porous rocks (&amp;gt; 10 microns), Meso-Porous (0.5–2 microns), Micro-porous (0.1–0.5μm) and Nano-porous (&amp;lt;0.1), allowing the generation of iso-quality rock maps, which show in an areal way, areas with the best thicknesses which are related directly to the production of hydrocarbons in the Lower Guadalupe Formation, being a key parameter in the characterization of rock-fluid system.
Generalize or Die: Operating Systems Support for Memristor-Based Accelerators (2017)

The deceleration of transistor feature size scaling has motivated growing adoption of specialized accelerators implemented as GPUs, FPGAs, ASICs, and more recently new types of computing such as neuromorphic, bio-inspired, ultra low energy, reversible, stochastic, optical, quantum, combinations, and others unforeseen. There is a tension between specialization and generalization, with the current state trending to master slave models where accelerators (slaves) are instructed by a general purpose system (master) running an Operating System (OS). Traditionally, an OS is a layer between hardware and applications and its primary function is to manage hardware resources and provide a common abstraction to applications. Does this function, however, apply to new types of computing paradigms? This paper revisits OS functionality for memristor-based accelerators. We explore one accelerator implementation, the Dot Product Engine (DPE), for a select pattern of applications in machine learning, imaging, and scientific computing and a small set of use cases. We explore typical OS functionality, such as reconfiguration, partitioning, security, virtualization, and programming. We also explore new types of functionality, such as precision and trustworthiness of reconfiguration. We claim that making an accelerator, such as the DPE, more general will result in broader adoption and better utilization.
Structure/Function Analysis of Human Interleukin 5 and its Receptor (1995)

We have performed a detailed structure-function analysis of human interleukin 5 (hIL5) and its receptor. By testing a hIL5 mutant panel in a solid phase binding assay and a proliferation assay using hIL5 dependent cell-lines, areas on hIL5 involved in either the receptor alpha-subunit interaction or in receptor activation were identified. Epitope mapping data of a neutralizing and a non-neutralizing monoclonal antibody were in agreement with the mutant analysis. hIL5 binding areas on the IL5R alpha-subunit were identified by interspecies chimaera analysis. Finally, hIL5 mutants with reduced receptor activation potential have antagonistic properties.
Interferon (IFN) beta acts downstream of IFN-gamma-induced class II transactivator messenger RNA accumulation to block major histocompatibility complex class II gene expression and requires the 48-kD DNA-binding protein, ISGF3-gamma. (1995)

Interferon (IFN) gamma, a cardinal proinflammatory cytokine, induces expression of the gene products of the class II locus of the major histocompatibility complex (MHC), whereas IFN-alpha or -beta suppresses MHC class II expression. The mechanism of IFN-beta-mediated MHC class II inhibition has been unclear. Recently, a novel factor termed class II transactivator (CIITA) has been identified as essential for IFN-gamma-induced MHC class II transcription. We studied the status of IFN-gamma-induced CIITA messenger RNA (mRNA) accumulation and CIITA-driven transactivation in IFN-beta-treated cells and used cell lines that had defined defects in the type I IFN response pathway to address the roles of IFN signaling components in the inhibition of MHC class II induction. IFN-beta treatment did not suppress IFN-gamma-induced accumulation of CIITA mRNA. After cells were stably transfected with CIITA, endogenous MHC class II genes were constitutively expressed, and MHC class II promoters, delivered by transfection, were actively transcribed in CIITA-expressing cells. Expression of these promoters was significantly impaired by pretreatment with IFN-beta. These results suggest that IFN-beta acts downstream of CIITA mRNA accumulation, and acts in part by reducing the functional competence of CIITA for transactivating MHC class II promoters. IFN stimulated gene factor 3 (ISGF3) gamma was essential for IFN-beta to mediate inhibition of MHC class II induction, regardless of whether MHC class II transcription was stimulated by IFN-gamma or directly by CIITA expression. Results of these experiments suggest that inhibition of MHC class II in IFN-beta-treated cells requires expression of gene(s) directed by the ISGF3-IFN-stimulated response element pathway, and that these gene product(s) may act by blocking CIITA-driven transcription of MHC class II promoters.
Ultrathin Si capping layer suppresses charge trapping in HfOxNy∕Ge metal-insulator-semiconductor capacitors (2007)

In this study the authors investigated the Ge outdiffusion characteristics of HfOxNy∕Ge metal-insulator-semiconductor capacitors to determine their charge trapping behavior. Capping the Ge substrate with an ultrathin Si layer inhibits the incorporation of Ge into the high-k bulk dielectric in the form of GeOx, thereby diminishing the resultant oxide charge trapping. The thermal stability of the entire capacitor structure was also improved after performing an additional Si passivation process.
Improved MUSIC algorithm for estimation of time delays in asynchronous DS-CDMA systems (2002)

An algorithm for time delay estimation in an asynchronous direct-sequence code-division multiple access (DS-CDMA) system which exploits the structure of the system better than previously known algorithms, is presented. The different algorithms are compared through simulation and asymptotic analysis (large number of vector samples). For a typical scenario it is shown that the proposed algorithm decreases the standard deviation of the time delay errors with a factor of approximately 2.
Plasma reactor dry cleaning strategy after TaC, MoN, WSi, W, and WN etching processes (2009)

Reproducibility of plasma etching processes is a critical issue for metal/high-k gate stack patterning because of progressive modification of the reactor wall conditions. Periodic dry cleaning of the etching chamber in appropriate plasma chemistry allows the achievement of acceptable reproducibility. The authors have used quasi in situ x-ray photoelectron spectroscopy to analyze the coatings formed on the walls of an industrial inductively coupled plasma reactor during the etching of TaC, MoN, WSi, W, and WN materials in various chemistries. Metallic residues containing Ta, Mo, or W are generally detected after the etching process, and the main factors responsible for their deposition are identified. They have then investigated the best plasma chemistry to clean each of these deposits. It is concluded that fluorine-based cleaning (eventually preceded by a chlorine cleaning step if Hf-based high-k dielectric is introduced in the stack) is efficient to remove the coatings formed on the reactor walls after metal gate stack etching. However, AlFx (YFx) residues are formed on the Al2O3 (Y2O3) reactor walls. Alternatively, the authors show that an efficient reactor cleaning strategy providing good wafer-to-wafer reproducibility (without AlFx or YFx residues) is a two-step SF6∕Cl2 process followed by SiCl4∕Cl2 plasma, whatever the materials in the high-k metal gate stack (poly-Si, TiN, TaC, TaN, MoN, W, WN, WSi, and HfO2).
Performance Analysis of NOMA in Training-Based Multiuser MIMO Systems (2017)

This paper considers the use of non-orthogonal-multiple-access (NOMA) in multiuser MIMO systems in practical scenarios where channel state information (CSI) is acquired through pilot signaling. A new NOMA scheme that uses shared pilots is proposed. Achievable rate analysis is carried out for different pilot signaling schemes, including both uplink and downlink pilots. The achievable rate performance of the proposed NOMA scheme with shared pilot within each group is compared with the traditional orthogonal access scheme with orthogonal pilots. Our proposed scheme is a generalization of the orthogonal scheme, and can be reduced to the orthogonal scheme when appropriate power allocation parameters are chosen. Numerical results show that when downlink CSI is available at the users, our proposed NOMA scheme outperforms orthogonal schemes. However with more groups of users present in the cell, it is preferable to use multi-user beamforming instead of NOMA.
Periodic Trends in Organic Functionalization of Group IV Semiconductor Surfaces (2009)

Organic functionalization of group IV semiconductor surfaces provides a means to precisely control the interfacial properties of some of the most technologically important electronic materials in use today. The 2 x 1 reconstructed group IV (100) surfaces in ultrahigh vacuum, in particular, have a well-defined surface that allows adsorbate-surface interactions to be studied in detail. Surface dimers containing a strong sigma- and weak pi-bond form upon reconstruction of the group IV (100) surfaces, imparting a rich surface reactivity, which allows useful analogies to be made between reactions at the surface and those in classic organic chemistry. To date, most studies have focused on single substrates and a limited number of adsorbate functional groups. In this Account, we bring together experimental and theoretical results from several studies to investigate broader trends in thermodynamics and kinetics of organic molecules reacted with group IV (100)-2 x 1 surfaces. By rationalizing these trends in terms of simple periodic properties, we aim to provide guidelines by which to understand the chemical origin of the observed trends and predict how related molecules or functionalities will react. Results of experimental and theoretical studies are used to show that relative electronegativities and orbital overlap correlate well with surface-adsorbate covalent bond strength, while orbital overlap together with donor electronegativity and acceptor electron affinity correlate with surface-adsorbate dative bond strength. Using such simple properties as predictive tools is limited, of course, but theoretical calculations fill in some of the gaps. The predictive power inherent in periodic trends may be put to use in designing molecules for applications where controlled attachment of organic molecules to semiconductor surfaces is needed. Organic functionalization may facilitate the semiconductor industry's transition from traditional silicon-based architectures to other materials, such as germanium, that offer better electrical properties. Potential applications also exist in other fields ranging from organic and molecular electronics, where control of interfacial properties may allow coupling of traditional semiconductor technology with such developing technologies, to biosensors and nanoscale lithography, where the functionality imparted to the surface may be used directly. Knowledge of thermodynamic and kinetic trends and the fundamental basis of these trends may enable effective development of new functionalization strategies for such applications.
Faraday communications. Ultrasonic monitoring of crystallization in an oil-in-water emulsion (1990)

We present a simple reliable method based on ultrasonic propagation for monitoring crystallization and melting of the dispersed oil phase in emulsion droplets. The sensitivity of the technique is illustrated for an n-hexadecane-in-water emulsion by comparing ultrasonic velocity data with densities over the temperature range 0–30 °C.
GliZ, a Transcriptional Regulator of Gliotoxin Biosynthesis, Contributes toAspergillus fumigatusVirulence (2006)

Gliotoxin is a nonribosomal peptide produced by Aspergillus fumigatus. This compound has been proposed as an A. fumigatus virulence factor due to its cytotoxic, genotoxic, and apoptotic properties. Recent identification of the gliotoxin gene cluster identified several genes (gli genes) likely involved in gliotoxin production, including gliZ, encoding a putative Zn(2)Cys(6) binuclear transcription factor. Replacement of gliZ with a marker gene (DeltagliZ) resulted in no detectable gliotoxin production and loss of gene expression of other gli cluster genes. Placement of multiple copies of gliZ in the genome increased gliotoxin production. Using endpoint survival data, the DeltagliZ and a multiple-copy gliZ strain were not statistically different from the wild type in a murine pulmonary model; however, both the wild-type and the multiple-copy gliZ strain were more virulent than DeltalaeA (a mutant reduced in production of gliotoxin and other toxins). A flow-cytometric analysis of polymorphonuclear leukocytes (PMNs) exposed to supernatants from wild-type, DeltagliZ, complemented DeltagliZ, and DeltalaeA strains supported a role for gliotoxin in apoptotic but not necrotic PMN cell death. This may indicate that several secondary metabolites are involved in A. fumigatus virulence.
Synthesis of Multi-substituted Pyrazoles Utilizing the N-Alkylated 3-Hydroxy-3-propargyl- or allenylisoindolines (2003)

to di-, tri-,
Cover Feature: Spray‐Flame‐Prepared LaCo1–xFexO3 Perovskite Nanoparticles as Active OER Catalysts: Influence of Fe Content and Low‐Temperature Heating (ChemElectroChem 12/2020) (2020)

The Cover Feature shows a spray-flame reactor used to synthesize perovskite catalyst nanoparticles. The blue methane/oxygen pilot flame at the bottom ignites a combustible precursor aerosol injected via a centric nozzle. Nanoparticle formation downstream of the reaction zone leads to metastable, highly active LaCo1–xFexO3 perovskite catalysts with improved oxygen evolution reaction activity. The image was taken by Samer Suleiman. More information can be found in the Aricle by B. Alkan et al.
Edge compensated transform coding (2002)

Transform based image compression has difficulty with image regions containing edges. Edge compensated transform coding (ECTC) addresses this problem by preprocessing to remove edges. This preprocessing is adapted to transform coding. The edge information is sent in a side channel and the edges are replaced at the receiver. Subjective improvement is demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>