gebhart/patrepeval huggingface dataset:
Multicopy Integration and Expression of Heterologous Genes in <i>Methylobacterium extorquens</i> ATCC 55366 (2006)

High-level expression of chromosomally integrated genes in Methylobacterium extorquens ATCC 55366 was achieved under the control of the strong M. extorquens AM1 methanol dehydrogenase promoter (PmxaF) using the mini-Tn7 transposon system. Stable maintenance and expression of the integrated genes were obtained in the absence of antibiotic selective pressure. Furthermore, using this technology, a multicopy integration protocol for M. extorquens was also developed. Chromosomal integration of one to five copies of the gene encoding the green fluorescent protein (gfp) was achieved. The multicopy-based expression system permitted expression of a preset number of gene copies. A unique specific Tn7 integration locus in the chromosome of M. extorquens, known as the Tn7 attachment site (attTn7 site), was identified. This single attTn7 site was identified in an intergenic region between glmS, which encodes the essential enzyme glucosamine-6-phosphate synthetase, and dhaT, which encodes 1,3-propanediol dehydrogenase. The fact that the integration event is site specific and the fact that the attTn7 site is a noncoding region of the chromosome make the mini-Tn7 transposon system very useful for insertion of target genes and subsequent expression. In all transformants tested, expression and segregation of the transforming gene were stable without generation of secondary mutations in the host. In this paper, we describe single and multicopy chromosome integration and stable expression of heterologous genes (bgl [beta-galactosidase], est [esterase], and gfp [green fluorescent protein]) in M. extorquens.
Elevated Expression of CKS1B at 1q21 Is Highly Correlated with Short Survival in Myeloma. (2004)

Abstract The variability in survival among patients with myeloma can range from months to >10 years. Patients at highest risk are best identified by the presence or absence of an abnormal karyotype found by conventional cytogenetics. However, this test only accounts for ~15% of the variability in outcome. Thus, many patients who present with no cytogenetic abnormalities experience rapid relapse and early death. To better define high-risk disease and also potentially identify specific genetic mechanisms that give rise to this poor survival, we analyzed the gene expression patterns in freshly isolated plasma cells from 40 newly diagnosed myeloma patients who were then treated with high-dose therapy and tandem stem cell transplants. Patients were separated into two groups of 20. Those in the “short-survival” group all died within 900 days of therapy initiation due to disease progression. Patients in the “long-survival” group had all survived >1453 days since therapy initiation. RNA from plasma cells was labeled and hybridized to the U133Plus2.0 microarray containing ~33,000 genes. The expression value was transformed by the log base 2 and each sample was normalized to give a mean of 0 and a variance of 1. Chi-square analyses and t-tests were performed to identify genes whose expression patterns were unique to each group. Kaplan-Meier analysis of overall survival using expression level quartiles was used to demonstrate links to outcome. A total of 1770 probe sets were significantly differentially expressed between the two groups (P <.05). A total of 1025 (58%) of the probe sets were up-regulated in the short-survival group. The chromosomal map positions of all 1770 probe sets were determined; 19% mapped to chromosome 1. Of the 1770 probe sets, 84 demonstrating a >2-fold difference in expression were further analyzed with Kaplan-Meier survival analyses. In this test, 18 probe sets representing 17 genes were highly significant (P <.0001). Of the 17 genes identified, 10 map to chromosome 1; all 4 genes from the p arm were down-regulated while all 6 genes from the q arm were up-regulated in the short-survival group. We have previously demonstrated that jumping 1q and amplification of genes from 1q21 represent common genetic lesions in myeloma. We then examined by FISH, BCL2 and IL-6R showed highly variable over-expression in patient subsets, unrelated to outcome. CKS1B, an evolutionarily conserved protein that interacts genetically and physically with cyclin-dependent kinases and promotes mitosis, is located very near the 1q21 amplification and is over-expressed in myelomas with a short survival. Using FISH analysis with probes specific for these genes, we will determine if over-expression is due to gene amplification. Given the important role of CKS1B in controlling mitosis and the emerging role of D-type cyclins in myelomagenesis, this gene represents a strong candidate for a gene whose over-expression, possibly as a result of gene amplification, may impart a highly aggressive phenotype on malignant plasma cells.
Piezoelectric Properties of Hot-Pressed Lead Titanate Zirconate Family Ceramics (1981)

Piezoelectric properties of hot-pressed Pb(Zn 1/3 Nb 2/3 )O 3 –Pb(Sn 1/3 Nb 2/3 )O 3 –PbTiO 3 –PbZrO 3 quaternary ceramics are described. The ceramics exhibited high coupling coefficient and high dielectric constant. A small addition of MnO 2 to the quaternary ceramics increased markedly mechanical quality factor ( Q M =1400), and coercive field ( E c =20 kV/cm). The ceramics made it possible to produce high frequency transducer for large strain and high output voltage.
Long Duration Testing of Type C Thermocouples at 1500 ?C (2008)

Experience with Type C thermocouples operating for long periods in the 1400 to 1600 °C temperature range indicate that significant decalibration occurs, often leading to expensive downtime and material waste. As part of an effort to understand the mechanisms causing drift in these thermocouples, the Idaho National Laboratory conducted a long duration test at 1500 °C containing eight Type C thermocouples. As report in this document, results from this long duration test were adversely affected due to oxygen ingress. Nevertheless, results provide key insights about the impact of precipitate formation on thermoelectric response. Post-test examinations indicate that thermocouple signal was not adversely impacted by the precipitates detected after 1,000 hours of heating at 1,500 °C and suggest that the signal would not have been adversely impacted by these precipitates for longer durations (if oxygen ingress had not occurred in this test).
Genetic Characterization of 2 Novel Feline Caliciviruses Isolated from Cats with Idiopathic Lower Urinary Tract Disease (2002)

Feline caliciviruses (FCVs) are potential etiologic agents in feline idiopathic lower urinary tract disease (I-LUTD). By means of a modified virus isolation method, we examined urine obtained from 28 male and female cats with nonobstructive I-LUTD, 12 male cats with obstructive I-LUTD, and 18 clinically healthy male and female cats. All cats had been routinely vaccinated for FCV. Two FCVs were isolated; I (FCV-U1) from a female cat with nonobstructive I-LUTD, and another (FCV-U2) from a male cat with obstructive I-LUTD. To determine the genetic relationship of FCV-U1 and FCV-U2 to other FCVs. capsid protein gene RNA was reverse transcribed into cDNA, amplified, and sequenced. Multiple amino acid sequence alignments and phylogenetic trees were constructed for the entire capsid protein, hypervariable region E, and the more conserved (nonhypervariable) regions A, B, D, and F. When compared to 23 other FCV isolates with known biotypes, the overall amino acid sequence identity of the capsid protein of FCV-U1 and FCV-U2 ranged from 83 to 96%; identity of hypervariable regions C and E ranged from 58 to 85%. Phylogenetically, FCV-U1 clearly separated from other FCV strains in phenograms based on nonhypervariable regions. In contrast, FCV-U2 consistently segregated with the Urbana strain in all phenograms. Clustering of isolates by geographic origin was most apparent in phenograms based on nonhypervariable regions. No clustering of isolates by biotype was apparent in any phenograms. Our results indicate that FCV-UI and FCV-U2 are genetically distinct from other known vaccine and field strains of FCV.
Large-scale distributed Internet-based discovery mechanism for dynamic spectrum allocation (2014)

Scarcity of frequencies and the demand for more bandwidth is likely to increase the need for devices that utilize the available frequencies more efficiently. Radios must be able to dynamically find other users of the frequency bands and adapt so that they are not interfered, even if they use different radio protocols. As transmitters far away may cause as much interference as a transmitter located nearby, this mechanism can not be based on location alone. Central databases can be used for this purpose, but require expensive infrastructure and planning to scale. In this paper, we propose a decentralized protocol and architecture for discovering radio devices over the Internet. The protocol has low resource requirements, making it suitable for implementation on limited platforms. We evaluate the protocol through simulation in network topologies with up to 2.3 million nodes, including topologies generated from population patterns in Norway. The protocol has also been implemented as proof-of-concept in real Wi-Fi routers.
A Novel Ferroelectric Superlattice Based Multi-Level Cell Non-Volatile Memory (2019)

We demonstrate a novel ferroelectric (FE) superlattice based multi-level cell (MLC) memory, which outperforms previous multi-state FE memory implemented using partial polarization switching, from the standpoint of device-to-device variation. We show that the FE superlattice consisting of alternate FE and dielectric (DE) thin layers provides a scalable approach for MLC implementation because: 1) the superlattice constructs controlled layer-by-layer polarization switching in the constituent FE layers; 2) the number of FE layers equals the number of stored bits; and, finally, (3) the switching of all the domains in a given coercive field (E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</sub> ) distribution associated with one isolated peak suppresses the variation induced by partial polarization switching. Based on these, we experimentally demonstrate a 2-bit/cell FE superlattice memory and simulate a 3-bit/cell memory with excellent device-to-device variation.
<title>Fabrication of phase-shifting masks employing multilayer films</title> (1994)

The design and fabrication of phase shifting masks using multi-layer films are summarized. Mask blanks consist of fused silica substrates coated with a top chrome layer, an SiO<SUB>2</SUB> phase layer, and an etch-stop layer. The layer thicknesses are designed to give a (pi) -phase shift at 248 nm (or at 365 nm), and equal and maximal transmission at etched and non-etched regions. The chrome layer is patterned by e-beam resist and is etched by reactive ion etching (RIE) with Cl<SUB>2</SUB> chemistry. The SiO<SUB>2</SUB> layer is patterned by another e-beam resist in registration with first chrome pattern and is etched by RIE with CHF<SUB>3</SUB> chemistry. Two materials were investigated as the etch stop layer, namely Al<SUB>2</SUB>O<SUB>3</SUB> and HfO<SUB>2</SUB>, with the latter having advantageous properties. It is shown that a 20% processing window is achieved in this type of PSM for a 5 degree phase accuracy as in contrast to quartz etched PSM in which the etched depth and uniformity has to be controlled to within 2.5% for a similar phase accuracy.
Cloning of latex bêta-1,3-glucanase cDNA and characterisation of the recombinant protein (2001)

Latex allergy affects only about 0.1% of the general population in Europe1-3, although healthcare workers in the Europe and America who frequently use latex examination and surgical gloves are more likely to be allergic to latex. Reports from Europe and the USA give prevalence figures between 2.4 to 17%4,5. Hundreds of proteins are found in natural rubber latex. Of these, only a small handful are allergenic. There has been much interest in identifying the proteins in Hevea latex responsible for latex allergy and much effort was expended on isolating and purifying the allergenic proteins from Hevea latex or latex products6. Also of considerable interest to researchers is the cloning of the cDNA that encode the protein allergens7. Successful DNA cloning would enable production of the recombinant protein that can then be used in immunoassays and in various immunological investigations such as epitope mapping. The International Union of Immunological Societies (IUIS) recognises eleven allergenic proteins (Hev b 1 to Hev b 11) of natural rubber latex from Hevea brasiliensis. Among these, Hev b 28 is a major allergen that has been detected in latex gloves9. This paper reports the cloning of Hev b 2 and the production of the recombinant protein. Some of its enzymic and immunological characterisatics are described.
DolphinAtack: Inaudible Voice Commands (2017)

Speech recognition (SR) systems such as Siri or Google Now have become an increasingly popular human-computer interaction method, and have turned various systems into voice controllable systems(VCS). Prior work on attacking VCS shows that the hidden voice commands that are incomprehensible to people can control the systems. Hidden voice commands, though hidden, are nonetheless audible. In this work, we design a completely inaudible attack, DolphinAttack, that modulates voice commands on ultrasonic carriers (e.g., f > 20 kHz) to achieve inaudibility. By leveraging the nonlinearity of the microphone circuits, the modulated low frequency audio commands can be successfully demodulated, recovered, and more importantly interpreted by the speech recognition systems. We validate DolphinAttack on popular speech recognition systems, including Siri, Google Now, Samsung S Voice, Huawei HiVoice, Cortana and Alexa. By injecting a sequence of inaudible voice commands, we show a few proof-of-concept attacks, which include activating Siri to initiate a FaceTime call on iPhone, activating Google Now to switch the phone to the airplane mode, and even manipulating the navigation system in an Audi automobile. We propose hardware and software defense solutions. We validate that it is feasible to detect DolphinAttack by classifying the audios using supported vector machine (SVM), and suggest to re-design voice controllable systems to be resilient to inaudible voice command attacks.
Development of a novel recessive genetic male sterility system for hybrid seed production in maize and other cross‐pollinating crops (2015)

We have developed a novel hybridization platform that utilizes nuclear male sterility to produce hybrids in maize and other cross-pollinating crops. A key component of this platform is a process termed Seed Production Technology (SPT). This process incorporates a transgenic SPT maintainer line capable of propagating nontransgenic nuclear male-sterile lines for use as female parents in hybrid production. The maize SPT maintainer line is a homozygous recessive male sterile transformed with a SPT construct containing (i) a complementary wild-type male fertility gene to restore fertility, (ii) an α-amylase gene to disrupt pollination and (iii) a seed colour marker gene. The sporophytic wild-type allele complements the recessive mutation, enabling the development of pollen grains, all of which carry the recessive allele but with only half carrying the SPT transgenes. Pollen grains with the SPT transgenes exhibit starch depletion resulting from expression of α-amylase and are unable to germinate. Pollen grains that do not carry the SPT transgenes are nontransgenic and are able to fertilize homozygous mutant plants, resulting in nontransgenic male-sterile progeny for use as female parents. Because transgenic SPT maintainer seeds express a red fluorescent protein, they can be detected and efficiently separated from seeds that do not contain the SPT transgenes by mechanical colour sorting. The SPT process has the potential to replace current approaches to pollen control in commercial maize hybrid seed production. It also has important applications for other cross-pollinating crops where it can unlock the potential for greater hybrid productivity through expanding the parental germplasm pool.
Thermochemical alkane dehydrogenation catalyzed in solution without the use of a hydrogen acceptor (1997)

W. Xu, G. P. Rosini, K. Krogh-Jespersen, A. S. Goldman, M. Gupta, C. M. Jensen and W. C. Kaska, Chem. Commun., 1997, 2273 DOI: 10.1039/A705105K
Different Methods of Identifying New Antigenic Epitopes of Human Papillomavirus Type 16 E6 and E7 Proteins (2004)

Human papillomavirus (HPV) infection is the most common cause of sexually transmitted viral infection and is the main cause of cervical cancer. Identification of HPV T-cell epitopes would be instrumental not only in our understanding of the protective immune response but also in the development of vaccines and immunotherapies. In contrast to viruses which cause systemic infection, identification of HPV epitopes is technically challenging because HPV causes a localized mucosal infection and the frequency of pathogen-specific T lymphocytes in peripheral blood is expected to be low. Here we describe three new antigenic epitopes (E7 7-15 [TLHEYMLDL], E6 52-61 [FAFRDLCIVY], and E7 79-87 [LEDLLMGTL]) of HPV 16 E6 and E7 proteins which have oncogenic activities. E7 7-15 was identified among peptides previously shown to bind to human leukocyte antigen (HLA)-A2.1 molecule, but it was found likely to be restricted by the HLA-B48 molecule. E6 52-61 (likely to be restricted by HLA-B57) and E7 79-87 (likely to be restricted by HLA-B60) were detected, based on the magnitude of the T-cell immune responses, in another individual. In particular, T-cell clones specific for the E6 52-61 epitope were isolated effectively by magnetically selecting them based on gamma interferon secretion. This is an efficient method of identifying new epitopes of antigens for which the number of specific T lymphocytes in the circulation is expected to be small, and it should be widely applicable in identifying new T-cell epitopes.
Capacity analysis of MediaGrid: a P2P IPTV platform for fiber to the node (FTTN) networks (2007)

This paper studies the conditions under which P2P sharing can increase the capacity of IPTV services over FTTN networks. For a typical FTTN network, our study shows a) P2P sharing is not beneficial when the total traffic in a local video office is low; b) P2P sharing increases the load on FTTN switches and routers in local video offices; c) P2P sharing is the most beneficial when the network bottleneck is experienced in the southbound segment of a local video office (equivalently a northbound segment of an FTTN switch); and d) sharing among all FTTN serving communities is not needed when network congestion problems are solved by using some other technologies such as program pre-caching or replication. Based on the analytical results, design for IPTV services which monitors FTTN network conditions and decides when and how to share videos among peers to maximize the service capacity. Simulations and bounds both validate the potential benefits of the MediaGrid IPTV service platform.
Über Pterinchemie. 72. Mitteilung. Trennung der Diastereomeren (6<i>R</i>)‐ und (6<i>S</i>)‐5,6,7,8‐Tetrahydro‐<scp>L</scp>‐biopterin (1979)

Separation of the Diastereomers (6 R )‐ and (6 S )‐5,6,7,8‐Tetrahydro‐ L ‐biopterin The mixture of the diastereomers of the tetraacetylderivative IV of (6 RS )‐5,6,7,8‐tetrahydro‐ L ‐biopterin could be separated by fractional crystallisation in methanol into the diastereomers IV A and IV B. Hydrolysis with hydrochloric acid gives the pure, diastereomeric, (6 R )‐ and (6 S )‐5,6,7,8‐tetrahydro‐ L ‐biopterins.
Nonlinear Ship–Wave Interaction Model, Part 2: Ship Boundary Condition (2006)

One of the main problems in modeling ship-wave hydrodynamics is solving for the forcing (pressure) at the ship boundary. With an arbitrary ship, singularities occur in evaluating the velocity potential and the velocities on the hull. Inaccuracies in the evaluation of the singular terms in the velocity potential result in discretization errors, numerical errors, and excessive computational costs. In this paper we present a new approach to evaluating the pressure on a ship: evaluating the pressure in the ship normal vector coordinate system. The main advantage of this approach is that p is a smooth function in the ship normal vector coordinate system, enabling us to obtain accurate results very efficiently (i.e., with much less CPU time) without encountering numerical difficulties arising from possible singularities.
Compartmentalized self-replication under fast PCR cycling conditions yields Taq DNA polymerase mutants with increased DNA-binding affinity and blood resistance (2014)

Faster-cycling PCR formulations, protocols, and instruments have been developed to address the need for increased throughput and shorter turn-around times for PCR-based assays. Although run times can be cut by up to 50%, shorter cycle times have been correlated with lower detection sensitivity and increased variability. To address these concerns, we applied Compartmentalized Self Replication (CSR) to evolve faster-cycling mutants of Taq DNA polymerase. After five rounds of selection using progressively shorter PCR extension times, individual mutations identified in the fastest-cycling clones were randomly combined using ligation-based multi-site mutagenesis. The best-performing combinatorial mutants exhibit 35- to 90-fold higher affinity (lower Kd ) for primed template and a moderate (2-fold) increase in extension rate compared to wild-type Taq. Further characterization revealed that CSR-selected mutations provide increased resistance to inhibitors, and most notably, enable direct amplification from up to 65% whole blood. We discuss the contribution of individual mutations to fast-cycling and blood-resistant phenotypes.
Totally distributed key management for dynamic groups in MANETs (2005)

Most existing solutions to group security in mobile ad hoc networks (MANETs) rely on a multicast core based tree (CBT) for key distribution. Such solutions, although suitable for systems with low mobility and static characteristics, are highly unsuitable for dynamic and sparse groups with changing neighborhoods. Also, tree based solutions are prone to a man-in-the-middle attack which might lead to network partitioning. Moreover, a group controller is required to control the key generation process. In this paper, we propose an entirely decentralized key generation mechanism. Using our approach, keys can be established between group members with absolutely no prior communication, as long as the group members are known. The solution relies on threshold cryptography and introduces a novel concept of node-group-key (NGK) mapping. Analytical and simulation results show appreciable performance enhancements.
Nanobubbles Provide Theranostic Relief to Cancer Hypoxia (2016)

Hypoxia is a common motif among tumors, contributing to metastasis, angiogenesis, cellular epigenetic abnormality, and resistance to cancer therapy. Hypoxia also plays a pivotal role in oncological studies, where it can be used as a principal target for new anti-cancer therapeutic methods. Oxygen nanobubbles were designed in an effort to target the hypoxic tumor regions, thus interrupting the hypoxia-inducible factor-1α (HIF-1α) regulatory pathway and inhibiting tumor progression. At less than 100nm, oxygen nanobubbles act as a vehicle for site-specific oxygen delivery, while also serving as an ultrasound contrast agent for advanced imaging purposes. Through in vitro and in vivo studies, it was shown the reversal of 5mC hypomethylation was achieved in the hypoxia-afflicted regions. An obvious increase in the oxygen concentration within hypoxic regions was also observed, implying adequate oxygen dissociation from the nanobubbles to the hypoxic tumor microenvironment. These implications suggest nanobubbles can be used as a means for epigenetic regulation, ultrasound imaging, and cancer therapeutics, thus having a significant impact on new-age cancer treatment methods in oncology.