gebhart/patrepeval huggingface dataset:
Lessons Learned and Experiences Gained in Developing the Waterflooding Concept of a Fractured Basement-Granite Reservoir: A 20-Year Case Study (2011)

Summary Naturally fractured reservoirs (NFRs) represent more than 20% of the world's oil and gas reserves. However, their characterization is complex and presents unique challenges in comparison with conventional reservoirs. It is immensely difficult to achieve the best results in the secondary-recovery process for NFRs. This paper presents a successful development of waterflooding to overcome the complex geological characterization of the White Tiger field, the largest fractured basement reservoir to date on the continental shelf of Vietnam. This reservoir has a complicated geological structure, with high heterogeneity, high temperature, and high closure stress. The total oil initially in place (OIIP) of this field reached nearly 4 billion bbl from 2000 m of oil-bearing thickness, and the field has been produced by more than 100 wells, 10 of which have flowed at the rate of approximately 1,000 B/D. The geological study and fractured model have been carefully investigated in both micro- and macroscale to improve waterflooding performance. The authors have analyzed the advantages and disadvantages of injection systems in this basement reservoir during 20 years of production history, and an artificial water buffer solution has been proposed to improve the waterflooding process. The authors have described the establishment and association of local artificial water buffer in the basement reservoir. An effective method to optimize the injected-water volume has also been discussed. Promising results from the White Tiger field have shown that the average reservoir pressure and total oil recovery have increased significantly in comparison with previous injection schemes. This paper presents useful guidelines to solve some typical problems of waterflooding in fractured basement reservoirs: What can be applied in waterflooding for a fractured basement reservoir? What is the optimal injection rate and injected volume for the fractured basement reservoir? How do we evaluate the probability of high water cut in production wells during the waterflooding process? How do we predict the rise of an artificial water/oil contact (AWOC)?
XML to facilitate management of multi-vendor networks (2001)

Many standards aimed at managing networks currently exist, and yet networks remain notoriously difficult to maintain. Template-based management systems go a long way towards solving this problem. By developing an XML based language to describe network elements, as well as the topology of a network, we can create tools that are free from vendor specific idiosyncrasies, and are capable of managing both today’s networks and those of the future.%%%%%%%%
A Filamentous Phage Associated with Recent Pandemic <i>Vibrio parahaemolyticus</i> O3:K6 Strains (2000)

A specific serotype, O3:K6, of Vibrio parahaemolyticus has recently been causing epidemics of gastroenteritis in Southeast Asia, Japan, and North America. To examine whether the new O3:K6 strains possess characteristics that may exacerbate outbreaks, we compared V. parahaemolyticus O3:K6 strains with non-O3:K6 strains using strains isolated from individuals with traveler's diarrhea at Kansai Airport Quarantine Station, Osaka, Japan. All 24 O3:K6 strains possessed a common plasmid, pO3K6 (DNA size, 8,782 bp, with 10 open reading frames [ORFs]). The gene organization of pO3K6 was similar to that of Vf33, a filamentous phage previously described in V. parahaemolyticus. We isolated a phage (phage f237) from the culture supernatant of V. parahaemolyticus O3:K6 strain KXV237, which formed a turbid plaque on an indicator strain. The genome of f237 was single-stranded DNA, and the double-stranded DNA obtained by treatment of the genome with DNA polymerase was identical to that of pO3K6 when analyzed by agarose gel electrophoresis after HindIII digestion. Furthermore, the N-terminal amino acid sequence of the f237 major coat protein was found in ORF4 of pO3K6. Our results showed that pO3K6 is a replicative form of f237. Among the ORFs found in the f237 genome, the sequence of ORF8 had no significant homology to those of any proteins in databases. ORF8 was located on a region corresponding to the distinctive region of Vf33, and its G+C content was apparently lower than that of the remaining DNA sequence of f237. By colony hybridization, ORF8 was detected only in O3:K6 strains isolated since 1996 and was not found in O3:K6 strains isolated before 1996 and clinical V. parahaemolyticus strains other than those of serotype O3:K6. Thus, this study shows that f237 is exclusively associated with recent V. parahaemolyticus O3:K6 strains. The ORF8 gene can be a useful genetic marker for the identification of the recently widespread O3:K6 strains of V. parahaemolyticus.
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling (2011)

http://Dostielab.biochem.mcgill.ca.
Engineering Nanoparticle-Coated Bacteria as Oral DNA Vaccines for Cancer Immunotherapy (2015)

Live attenuated bacteria are of increasing importance in biotechnology and medicine in the emerging field of cancer immunotherapy. Oral DNA vaccination mediated by live attenuated bacteria often suffers from low infection efficiency due to various biological barriers during the infection process. To this end, we herein report, for the first time, a new strategy to engineer cationic nanoparticle-coated bacterial vectors that can efficiently deliver oral DNA vaccine for efficacious cancer immunotherapy. By coating live attenuated bacteria with synthetic nanoparticles self-assembled from cationic polymers and plasmid DNA, the protective nanoparticle coating layer is able to facilitate bacteria to effectively escape phagosomes, significantly enhance the acid tolerance of bacteria in stomach and intestines, and greatly promote dissemination of bacteria into blood circulation after oral administration. Most importantly, oral delivery of DNA vaccines encoding autologous vascular endothelial growth factor receptor 2 (VEGFR2) by this hybrid vector showed remarkable T cell activation and cytokine production. Successful inhibition of tumor growth was also achieved by efficient oral delivery of VEGFR2 with nanoparticle-coated bacterial vectors due to angiogenesis suppression in the tumor vasculature and tumor necrosis. This proof-of-concept work demonstrates that coating live bacterial cells with synthetic nanoparticles represents a promising strategy to engineer efficient and versatile DNA vaccines for the era of immunotherapy.
Self-organized criticality (1999)

The concept of self-organized criticality was introduced to explain the behaviour of the sandpile model. In this model, particles are randomly dropped onto a square grid of boxes. When a box accumulates four particles they are redistributed to the four adjacent boxes or lost off the edge of the grid. Redistributions can lead to further instabilities with the possibility of more particles being lost from the grid, contributing to the size of each avalanche. These model 'avalanches' satisfied a power-law frequency-area distribution with a slope near unity. Other cellular-automata models, including the slider-block and forest-fire models, are also said to exhibit self-organized critical behaviour. It has been argued that earthquakes, landslides, forest fires, and species extinctions are examples of self-organized criticality in nature. In addition, wars and stock market crashes have been associated with this behaviour. The forest-fire model is particularly interesting in terms of its relation to the critical-point behaviour of the site-percolation model. In the basic forest-fire model, trees are randomly planted on a grid of points. Periodically in time, sparks are randomly dropped on the grid. If a spark drops on a tree, that tree and adjacent trees burn in a model fire. The fires are the `avalanches' and they are found to satisfy power-law frequency-area distributions with slopes near unity. This forest-fire model is closely related to the site-percolation model, that exhibits critical behaviour. In the forest-fire model there is an inverse cascade of trees from small clusters to large clusters, trees are lost primarily from model fires that destroy the largest clusters. This quasi steady-state cascade gives a power-law frequency-area distribution for both clusters of trees and smaller fires. The site-percolation model is equivalent to the forest-fire model without fires. In this case there is a transient cascade of trees from small to large clusters and a power-law distribution is found only at a critical density of trees.
Enhancing application robustness in cloud data centers (2011)

We propose OX, a runtime system that uses application-level availability constraints and application topologies discovered on the fly to enhance resilience to infrastructure anomalies for cloud applications. OX allows application owners to specify groups of highly available virtual machines, following component roles and replication semantics. To discover application topologies, OX monitors network traffic among virtual machines, transparently. Based on this information, OX builds on-line topology graphs for applications and incrementally partitions these graphs across the infrastructure to enforce availability constraints and optimize communication between virtual machines. We evaluate OX in a realistic cloud setting using a mix of Hadoop and YCSB/Cassandra workloads. We show how OX increases application robustness, by protecting applications from network interference effects and rack-level failures. 1
A survey of image retargeting techniques (2010)

Advances in imaging technology have made the capture and display of digital images ubiquitous. A variety of displays are used to view them, ranging from high-resolution computer monitors to low-resolution mobile devices, and images often have to undergo changes in size and aspect ratio to adapt to different screens. Also, displaying and printing documents with embedded images frequently entail resizing of the images to comply with the overall layout. Straightforward image resizing operators, such as scaling, often do not produce satisfactory results, since they are oblivious to image content. In this work, we review and categorize algorithms for contentaware image retargeting, i.e., resizing an image while taking its content into consideration to preserve important regions and minimize distortions. This is a challenging problem, as it requires preserving the relevant information while maintaining an aesthetically pleasing image for the user. The techniques typically start by computing an importance map which represents the relevance of every pixel, and then apply an operator that resizes the image while taking into account the importance map and additional constraints. We intend this review to be useful to researchers and practitioners interested in image retargeting.
The Israeli strain IS-98-ST1 of West Nile virus as viral model for West Nile encephalitis in the Old World (2004)

West Nile virus (WNV) recently became a major public health concern in North America, the Middle East, and Europe. In contrast with the investigations of the North-American isolates, the neurovirulence properties of Middle-Eastern strains of WNV have not been extensively characterized. Israeli WNV strain IS-98-ST1 that has been isolated from a white stork in 1998, was found to be highly neuroinvasive in adult C57BL/6 mice. Strain IS-98-ST1 infects primary neuronal cells from mouse cortex, causing neuronal death. These results demonstrate that Israeli strain IS-98-ST1 provides a suitable viral model for WNV-induced disease associated with recent WNV outbreaks in the Old World.
In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9 (2020)

In vivo mutagenesis systems accelerate directed protein evolution but often show restricted capabilities and deleterious off-site mutations on cells. To overcome these limitations, here we report an in vivo platform to diversify specific DNA segments based on protein fusions between various base deaminases (BD) and the T7 RNA polymerase (T7RNAP) that recognizes a cognate promoter oriented towards the target sequence. Transcriptional elongation of these fusions generates transitions C to T or A to G on both DNA strands and in long DNA segments. To delimit the boundaries of the diversified DNA, the catalytically dead Cas9 (dCas9) is tethered with custom-designed crRNAs as a "roadblock" for BD-T7RNAP elongation. Using this T7-targeted dCas9-limited in vivo mutagenesis (T7-DIVA) system, rapid molecular evolution of the antibiotic resistance gene TEM-1 is achieved. While the efficiency is demonstrated in E. coli, the system can be adapted to a variety of bacterial and eukaryotic hosts.
Do different conditioning regimens really make a difference? (2012)

Over the past 15 years, the use of reduced-intensity/nonmyeloablative conditioning regimens before allogeneic hematopoietic stem cell transplantation has been increasing. Despite major disparities in the level of myeloablation, intensity of immunosuppression (including great diversity of in vivo T-cell depletion), and postgraft immunomodulation, the different approaches have contributed jointly to a modification of the stage of allogeneic stem cell transplantation: transplantation-related procedure mortality has been decreased dramatically, allowing allogeneic immunotherapy to be used in previously excluded populations, including elderly patients, young but clinically unsuitable patients, patients with lymphoid malignancies or solid tumors, and patients without an HLA-identical related or unrelated donor. Together, these diverse regimens have provided one of the biggest breakthroughs since the birth of allogeneic BM transplantation. However, consensus on how to reach the optimal goal of minimal transplantation-related mortality with maximum graft-versus-tumor effect is far from being reached, and further studies are needed to define optimal conditioning and immunomodulatory regimens that can be integrated to reach this goal. These developments, which will most likely vary according to different clinical situations, have to be compared continuously with advances achieved in traditional allogeneic transplantation and nontransplantation treatments. However, the lack of prospective comparative trials is and will continue to make this task challenging.
Cloning, expression in <i>Escherichia coli</i> and characterization of the recombinant Neu5Acα2,6Galβ1,4GlcNAc-specific high-affinity lectin and its mutants from the mushroom <i>Polyporus squamosus</i> (2004)

Lectin from the mushroom Polyporus squamosus (PSL) has a unique carbohydrate-binding specificity for sialylated glycoconjugates containing Neu5Acalpha2,6Galbeta1,4Glc/GlcNAc trisaccharide sequences of asparagine-linked glycoproteins. In the present study, we elucidate the molecular basis for its binding specificity as well as establish a consistent source of this useful lectin using a bacterial expression system. cDNA cloning revealed that PSL contains a ricin B chain-like (QXW)(3) domain at its N-terminus that is composed of three homologous subdomains (alpha, beta and gamma). A recombinant lectin was expressed in Escherichia coli as a fully active, soluble form. It agglutinated rabbit erythrocytes and showed the highest affinity for Neu5Acalpha2,6Galbeta1,4GlcNAc, but not for the sialyl alpha2,3-linked isomer. We also investigated the structure-function relationship of PSL. A monomeric C-terminal deletion mutant lacking 40% of the lectin's molecular mass retained sugar-binding activity, indicating that the carbohydrate-binding sites are situated in the N-terminal portion of the lectin, whereas the C-terminal portion probably functions in oligomerization and structural stabilization. Mutant constructs that have single amino acid substitutions in the putative sugar-binding sites, based on sequence alignment with the ricin B-chain, indicate that the beta and gamma subdomains are most probably sugar-binding sites. The recombinantly expressed lectin will be a valuable reagent for the detection of the Neu5Acalpha2,6Galbeta1,4GlcNAc sequence of asparagine-linked glycans.
APAREL—A parse-request language (1969)

APAREL is described: this language is an extension to an algorithmic language (PL/I) that provides the pattern-matching capabilities normally found only in special purpose languages such as SNOBOL4 and TMG. This capability is provided through parse-requests stated in a BNF-like format. These parse-requests form their own programming language with special sequencing rules. Upon successfully completing a parse-request, an associated piece of PL/I code is executed. This code has available for use, as normal PL/I strings, the various pieces (at all levels) of the parse. It also has available, as normal PL/I variables, the information concerning which of the various alternatives were successful. Convenient facilities for multiple input-output streams, the initiation of sequences of parse-requests as a subroutine, and parse-time semantic checks are also included. APAREL has proven convenient in building a powerful SYNTAX and FUNCTION macro system, an algebraic language preprocessor debugging system, an on-line command parser, a translator for Dataless Programming, and as a general string manipulator.
Naive CD8<sup>+</sup> T‐cell precursors display structured TCR repertoires and composite antigen‐driven selection dynamics (2015)

Basic parameters of the naive antigen (Ag)-specific T-cell repertoire in humans remain poorly defined. Systematic characterization of this 'ground state' immunity in comparison with memory will allow a better understanding of clonal selection during immune challenge. Here, we used high-definition cell isolation from umbilical cord blood samples to establish the baseline frequency, phenotype and T-cell antigen receptor (TCR) repertoire of CD8(+) T-cell precursor populations specific for a range of viral and self-derived Ags. Across the board, these precursor populations were phenotypically naive and occurred with hierarchical frequencies clustered by Ag specificity. The corresponding patterns of TCR architecture were highly ordered and displayed partial overlap with adult memory, indicating biased structuring of the T-cell repertoire during Ag-driven selection. Collectively, these results provide new insights into the complex nature and dynamics of the naive T-cell compartment.
Direct drive electrical power take-off for offshore marine energy converters (2005)

This paper investigates the issues associated with converting the energy produced by marine renewable energy converters, namely wave and tidal stream devices, into electricity using direct drive electrical power take-off, without use of complex pneumatic, hydraulic or other mechanical linkages. In order to demonstrate the issues, two alternative topologies of linear electrical machines are investigated: the linear vernier hybrid permanent magnet machine and the air-cored tubular permanent magnet machine. The electrical characteristics of these machines are described and compared in the context of mechanical integration. Potential solutions to the issues of sealing, corrosion and lubrication are discussed taking into account the electrical properties of the two topologies.
Horizontal Transfer of Tetracycline Resistance among <i>Chlamydia</i> spp. In Vitro (2009)

ABSTRACT There are no examples of stable tetracycline resistance in clinical strains of Chlamydia trachomatis . However, the swine pathogen Chlamydia suis is commonly tetracycline resistant, both in America and in Europe. In tested U.S. strains, this resistance is mediated by a genomic island carrying a tet (C) allele. In the present study, the ability of C. suis to mobilize tet (C) into other chlamydial species was examined. Differently antibiotic resistant strains of C. suis , C. trachomatis , and Chlamydia muridarum were used in coculture experiments to select for multiply antibiotic resistant progeny. Coinfection of mammalian cells with a naturally occurring tetracycline-resistant strain of C. suis and a C. muridarum or C. trachomatis strain containing selected mutations encoding rifampin (rifampicin) or ofloxacin resistance readily produced doubly resistant recombinant clones that demonstrated the acquisition of tetracycline resistance. The resistance phenotype in the progeny from a C. trachomatis L2/ofl R - C. suis R19/tet R cross resulted from integration of a 40-kb fragment into a single ribosomal operon of a recipient, leading to a merodiploid structure containing three rRNA operons. In contrast, a cross between C. suis R19/tet R and C. muridarum MoPn/ofl R led to a classical double-crossover event transferring 99 kb of DNA from C. suis R19/tet R into C. muridarum MoPn/ofl R . Tetracycline resistance was also transferred to recent clinical strains of C. trachomatis . Successful crosses were not obtained when a rifampin-resistant Chlamydophila caviae strain was used as a recipient for crosses with C. suis or C. trachomatis . These findings provide a platform for further exploration of the biology of horizontal gene transfer in Chlamydia while bringing to light potential public health concerns generated by the possibility of acquisition of tetracycline resistance by human chlamydial pathogens.
Room-Temperature Lasing from Monolithically Integrated GaAs Microdisks on Silicon (2018)

Additional functionalities on semiconductor microchips are progressively important in order to keep up with the ever-increasing demand for more powerful computational systems. Monolithic III–V integration on Si promises to merge mature Si CMOS processing technology with III–V semiconductors possessing superior material properties, e.g., in terms of carrier mobility or band structure (direct band gap). In particular, Si photonics would strongly benefit from an integration scheme for active III–V optoelectronic devices in order to enable low-cost and power-efficient electronic–photonic integrated circuits. We report on room-temperature lasing from AlGaAs/GaAs microdisk cavities monolithically integrated on Si(001) using a selective epitaxial growth technique called template-assisted selective epitaxy. The grown gain material possesses high optical quality without indication of threading dislocations, antiphase boundaries, or twin defects. The devices exhibit single-mode lasing at T < 250 K and lasing thresholds between 2 and 18 pJ/pulse depending on the cavity size (1–3 μm in diameter).