gebhart/patrepeval huggingface dataset:
Cloning and Characterization of a Complex DNA Fingerprinting Probe for Candida parapsilosis (2001)

Candida parapsilosis accounts for a significant number of nosocomial fungemias, but in fact, no effective and verified genetic fingerprinting method has emerged for assessing the relatedness of independent isolates for epidemiological studies. A complex 15-kb DNA fingerprinting probe, Cp3-13, was therefore isolated from a library of C. parapsilosis genomic DNA fragments. The efficacy of Cp3-13 for DNA fingerprinting was verified by a comparison of its clustering capacity with those of randomly amplified polymorphic DNA analysis and internally transcribed spacer region sequencing, by testing species specificity, and by assessing its capacity to identify microevolutionary changes both in vitro and in vivo. Southern blot hybridization of EcoRI/SalI-digested DNA with Cp3-13 provides a fingerprinting system that (i) identifies the same strain in independent isolates, (ii) discriminates between unrelated isolates, (iii) separates independent isolates into valid groups in a dendrogram, (iv) identifies microevolution in infecting populations, and (v) is amenable to automatic computer-assisted DNA fingerprint analysis. This probe is now available for epidemiological studies.
Lactoferrin: influences on Langerhans cells, epidermal cytokines, and cutaneous inflammation (2002)

It has been suggested previously that, in addition to other biological roles, lactoferrin (LF) may display antiinflammatory properties secondary to the regulation of cytokine expression. To explore this concept further, we have here examined in human volunteers the influence of recombinant homologous LF on the migration of epidermal Langerhans cells (LC), a process that is known to be dependent upon the local availability of certain proinflammatory cytokines including tumor necrosis factor alpha (TNF-alpha) and interleukin 1beta (IL-1beta). In common with previous studies in mice, it was found that topical administration of LF prior to exposure at the same site to the contact sensitizer diphenylcyclopropenone resulted in a significant reduction of allergen-induced LC migration from the epidermis (measured as a function of the frequency of CD1a+ or HLA-DR+ LC found in epidermal sheets prepared from punch biopsies of the treated skin sites). However, under the same conditions of exposure, LF was unable to influence migration of LC induced by the intradermal administration of TNF-alpha data consistent with the hypothesis that one action of LF in the skin is to regulate the local production of this cytokine. Further support for this hypothesis was derived from experiments conducted with IL-1beta. This cytokine is also able to induce the mobilization of LC following intradermal injection, although in this case, migration is known to be dependent upon the de novo production of TNF-alpha. We observed that prior exposure to LF resulted in a substantial inhibition of IL-1beta-induced LC migration, data again consistent with the regulation of TNF-alpha production by LF. Collectively, these results support the view that LF is able to influence cutaneous immune and inflammatory processes secondary to regulation of the production of TNF-alpha and possibly other cytokines.
Parallel Computing on Wide-Area Clusters: the Albatross Project, (1999)

The aim of the Albatross project is to study applications and programming environments for widearea cluster computers, which consist of multiple clusters connected by wide-area networks. Parallel processing on such systems is useful but challenging, given the large differences in latency and bandwidth between LANs and WANs. We apply application-level optimizations that exploit the hierarchical structure of wide-area clusters to minimize communication over the WANs. In addition, we use highly efficient local-area communication protocols. We illustrate this approach using a highperformance Java system that is implemented on a collection of four Myrinet-based clusters connected by wide-area ATM networks. The optimized applications obtain high speedups on this wide-area system. 1 Introduction As cluster computers become more widely available, it becomes feasible to run parallel applications on multiple clusters at different geographic locations. By using several clusters for a single appli...
Immune response in mice following immunization with DNA encoding fragment C of tetanus toxin (1996)

Tetanus toxin is a potent neurotoxin synthesized by Clostridium tetani. Immunization with fragment C protein, the nontoxic C-terminal domain of tetanus toxin, will protect mice against lethal challenge with tetanus toxin. A synthetic gene encoding fragment C (tetC) had previously been shown to express high levels of fragment C in Saccharomyces cerevisiae. A plasmid, pcDNA3/tetC, which encodes the synthetic tetC gene expressed under the control of the human cytomegalovirus major intermediate-early promoter/enhancer region, was constructed. Expression of fragment C was observed in eukaryotic cells growing in vitro following transfection with pcDNA3/tetC. The immune response induced by intramuscular immunization with pure pcDNA3/tetC DNA was evaluated in a murine model. Anti-fragment C serum immunoglobulin and proliferative responses in splenocytes were observed in BALB/c mice following two immunizations with pcDNA3/tetC. The major immunoglobulin G subclass that recognized fragment C was immunoglobulin G2a, and the stimulated splenocytes secreted high levels of gamma interferon. Immunity to tetanus is dependent on the presence of neutralizing serum antibodies against tetanus toxin. Sufficient anti-fragment C serum immunoglobulins were induced by DNA-mediated immunization to protect mice against lethal challenge with tetanus toxin.
Direct Analysis of RNA after Transfection (1996)

It is possible to transfect mammalian cells with a gene of interest and directly detect the RNA made from that gene 24 to 48 hr later. The ability to analyze the RNA directly allows mutation and functional analysis of an intact gene, as the promoter does not have to be subcloned. This technique is also essential when fusion genes are used. In order to be sure that the level of the reporter protein produced by a fusion gene provides an accurate measure of appropriately initiated RNA from the promoter under study, it is necessary to determine the amount and 5' end of the fusion message. An investigator who verifies this using direct RNA analysis can proceed with some confidence that the level of the reporter protein is a measure of promoter activity. The difficulty in directly analyzing RNA is that the sensitivity of detection is at the limits of present technology. Consequently, the transfection protocol, RNA preparation, and RNA analysis techniques all have to be working near optimum in order for an experiment to work. This overview discusses parameters that must be considered when directly analyzing RNA after a transfection: transfection efficiency, the method of preparation of the RNA, the method of analysis of RNA, and strength of the promoter.
Role of Adiponectin in Preventing Vascular Stenosis (2002)

Obesity is more linked to vascular disease, including atherosclerosis and restenotic change, after balloon angioplasty. The precise mechanism linking obesity and vascular disease is still unclear. Previously we have demonstrated that the plasma levels of adiponectin, an adipose-derived hormone, decreases in obese subjects, and that hypoadiponectinemia is associated to ischemic heart disease. In current the study, we investigated the in vivorole of adiponectin on the neointimal thickening after artery injury using adiponectin-deficient mice and adiponectin-producing adenovirus. Adiponectin-deficient mice showed severe neointimal thickening and increased proliferation of vascular smooth muscle cells in mechanically injured arteries. Adenovirus-mediated supplement of adiponectin attenuated neointimal proliferation. In cultured smooth muscle cells, adiponectin attenuated DNA synthesis induced by growth factors including platelet-derived growth factor, heparin-binding epidermal growth factor (EGF)-like growth factor (HB-EGF), basic fibroblast growth factor, and EGF and cell proliferation and migration induced by HB-EGF. In cultured endothelial cells, adiponectin attenuated HB-EGF expression stimulated by tumor necrosis factor α. The current study suggests an adipo-vascular axis, a direct link between fat and artery. A therapeutic strategy to increase plasma adiponectin should be useful in preventing vascular restenosis after angioplasty.
Identification of Cancer Stem Cells in Dog Glioblastoma (2009)

There is increasing evidence in some malignancies that the tumor clone is heterogeneous in regard to proliferation and differentiation. The cancer stem cell hypothesis implies that not all the cells in the tumor have the same capacity to proliferate and maintain the growth of the tumor. Only a relatively small fraction of cells in the tumor, termed cancer stem cells (CSCs), possess the ability to proliferate and self-renew extensively. In the past decade, several groups have reported the existence of a CSC population in different human brain tumors from both children and adults. We report here the identification of a CSC population from a Boxer dog with glioblastoma multiforme (GBM) that possesses a great capacity for proliferation, self-renewal, and differentiation. This cloned cell line is aneuploid, forms neurospheres in culture, possesses CSC markers, and reproduces the original dog GBM when inoculated into the nude mouse brain.
Development of efficient suicide mechanisms for biological containment of bacteria (1991)

To optimize plasmid containment, we have systematically investigated the factors that limit the killing efficiency of a suicide system based on the relF gene from Escherichia coli controlled by inducible lac promoters and placed on plasmids. In induction experiments with this suicide system, killing efficiency was unaffected by temperature and growth medium; there was no requirement for great promoter strength or high plasmid copy number. We could demonstrate that the factors limiting killing were the mutation rate of the suicide function and the reduced growth rate caused by a basal level of expression of the suicide gene during normal growth, which can give a selective growth advantage to cells with mutated suicide functions. The capacity of the plasmid-carried killing system to contain the plasmid was tested in transformation, transduction, and conjugational mobilization. The rate of plasmid transfer detected in these experiments seemed too high to provide adequate biological containment. As expected from the induction experiments, plasmids that escaped containment in these transfer experiments turned out to be mutated in the suicide function. With lac-induced suicide as a test, the efficiency of the system was improved by tightening the repression of the suicide gene, thereby preventing selection of cells mutated in the killing function. Reduction of the mutational inactivation rate of the suicide system by duplication of the suicide function augmented the efficiency of the suicide dramatically. These results permit the construction of extremely efficient biological containment systems.
IN VIVO DELIVERY OF CASPASE 8 siRNA IMPROVES THE SURVIVAL OF SEPTIC MICE. (2004)

Wesche, D. E.; Chung, C. S.; Lomas-Neira, J.; Gregory, S. H.; Avala, A. Author Information
Coordinated Max-Min SIR Optimization in Multicell Downlink - Duality and Algorithm (2011)

Typical formulations of max-min weighted SIR problems involve either a total power constraint or individual power constraints. These formulations are unable to handle the complexities in multicell networks where each base station can be subject to its own sum power constraint. This paper considers the max-min weighted SIR problem subject to multiple weighted-sum power constraints, where the weights can represent relative power costs of serving different users. First, we derive the uplink-downlink duality principle by applying Lagrange duality to the single-constraint problem. Next, we apply nonlinear Perron-Frobenius theory to derive a closed-form solution for the multiple-constraint problem. Then, by exploiting the structure of the closed-form solution, we relate the multiple-constraint problem with its single-constraint subproblems and establish the dual uplink problem. Finally, we further apply nonlinear Perron-Frobenius theory to derive an algorithm which converges geometrically fast to the optimal solution.
High Affinity Anti-inorganic Material Antibody Generation by Integrating Graft and Evolution Technologies (2010)

Recent advances in molecular evolution technology enabled us to identify peptides and antibodies with affinity for inorganic materials. In the field of nanotechnology, the use of the functional peptides and antibodies should aid the construction of interface molecules designed to spontaneously link different nanomaterials; however, few material-binding antibodies, which have much higher affinity than short peptides, have been identified. Here, we generated high affinity antibodies from material-binding peptides by integrating peptide-grafting and phage-display techniques. A material-binding peptide sequence was first grafted into an appropriate loop of the complementarity determining region (CDR) of a camel-type single variable antibody fragment to create a low affinity material-binding antibody. Application of a combinatorial library approach to another CDR loop in the low affinity antibody then clearly and steadily promoted affinity for a specific material surface. Thermodynamic analysis demonstrated that the enthalpy synergistic effect from grafted and selected CDR loops drastically increased the affinity for material surface, indicating the potential of antibody scaffold for creating high affinity small interface units. We show the availability of the construction of antibodies by integrating graft and evolution technology for various inorganic materials and the potential of high affinity material-binding antibodies in biointerface applications.
Agent based Bandwidth Reservation Routing Technique in Mobile Ad Hoc Networks (2011)

In mobile ad hoc networks (MANETs), inefficient resource allocation causes heavy losses to the service providers and results in inadequate user proficiency. For improving and automating the quality of service of MANETs, efficient resource allocation techniques are required. In this paper, we propose an agent based bandwidth reservation technique for MANET. The mobile agent from the source starts forwarding the data packets through the path which has minimum cost, congestion and bandwidth. The status of every node is collected which includes the bottleneck bandwidth field and the intermediate node computes the available bandwidth on the link. At the destination, after updating the new bottleneck bandwidth field, the data packet is feedback to the source. In resource reservation technique, if the available bandwidth is greater than bottleneck bandwidth, then bandwidth reservation for the flow is done. Using rate monitoring and adjustment methodologies, rate control is performed for the congested flows. By simulation results, we show that the resource allocation technique reduces the losses and improves the network performance.
Molecular weight studies on the active constituents of compound 48/80 (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular weight studies on the active constituents of compound 48/80George W. Read and James F. LenneyCite this: J. Med. Chem. 1972, 15, 3, 320–323Publication Date (Print):March 1, 1972Publication History Published online1 May 2002Published inissue 1 March 1972https://pubs.acs.org/doi/10.1021/jm00273a026https://doi.org/10.1021/jm00273a026research-articleACS PublicationsRequest reuse permissionsArticle Views91Altmetric-Citations40LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Technical Advancement of Carbonate Acid Stimulation Injection (2019)

Abstract Formation damage is the impairment of permeability of rocks inside a petroleum reservoir. This occurs during drilling, production, stimulation and enhanced oil recovery operations, by various mechanisms such as chemical, mechanical, biological and thermal. Near wellbore formation damages have a great impact on productivity of the damaged formation. Acidizing is a stimulation method to remove the effect of near wellbore damage through reacting with damaging materials or the formation rocks (carbonate or sandstone rocks) to restore or improve permeability around the wellbore. Several experiments are conducted to study the effect of temperature and acid concentration combined on the efficiency of matrix acidizing. Three different concentrations scenarios of hydrochloric acid (3%, 15%, and 28%) and 4 different temperatures scenarios (25 °C, 35 °C, 70 °C, and 100 °C) were tested to investigate pore-enlargement success effect on permeability. The purpose of this experiment is to introduce the concept of optimized temperature augmented with optimized acid concentration in carbonate matrix acidulation. Morphology of pore geometry and area measurement software is used. New Advancement in imaging that captured pore area enlargement as big-data necessarily for artificial intelligence modeling. Captured pores before treatment and captured pores after thermal-HCL acid treatment have demonstrated that image processing of the actual acidized rock data can select the optimized recipe concentration of acid that will increase permeability, hence recovery. The results show that matrix acidizing is an effective method to improve permeability and enhance production, as it demonstrates that using less acid concentration with the optimized temperature can result in a favorable and satisfying outcomes.
Comparative antiinflammatory and bone protective effects of two diphosphonates in adjuvant arthritis (1979)

The effects of disodium ethane-1-hydroxy-1,1-diphosphonate (EHDP) and disodium dichloromethane diphosphonate (Cl2MDP) were evaluated in the rat adjuvant model of arthritis to directly compare their ability to inhibit arthritic processes. The results of the experiment indicated that both diphosphonates inhibited osseous changes, pedal inflammation, and the change in body weight gain patterns which are characteristic of this model. The latter effects suggest that diphosphonates may have antinflammatory activity that is not related to their previously known actions on bone. Cl2MDP appeared to be more effective than EHDP in this particular model when all aspects were considered. The relationship of these results to the potential safety of these compounds in clinical situations is discussed.
Lazy decision trees (1996)

Lazy learning algorithms, exemplied by nearest-neighbor algorithms, do not induce a concise hypoth-esis from a given training set; the inductive process is delayed until a test instance is given. Algorithms for constructing decision trees, such as C4.5, ID3, and CART create a single \\best &amp;quot; decision tree during the training phase, and this tree is then used to classify test instances. The tests at the nodes of the con-structed tree are good on average, but there may be better tests for classifying a specic instance. We pro-pose a lazy decision tree algorithm|LazyDT|that conceptually constructs the \\best &amp;quot; decision tree for each test instance. In practice, only a path needs to be constructed, and a caching scheme makes the al-gorithm fast. The algorithm is robust with respect to missing values without resorting to the complicated methods usually seen in induction of decision trees. Experiments on real and articial problems are pre-sented.
Optimization of Lithium Content and Sintering Aid for Maximized Li + Conductivity and Density in Ta‐Doped Li 7 La 3 Zr 2 O 12 (2015)

Ta‐doped cubic phase Li 7 La 3 Zr 2 O 12 ( LLZ ) lithium garnet received considerable attention in recent times as prospective electrolyte for all‐solid‐state lithium battery. Although the conductivity has been improved by stabilizing the cubic phase with the Ta 5+ doping for Zr 4+ in LLZ , the density of the pellet was found to be relatively poor with large amount of pores. In addition to the high Li + conductivity, density is also an essential parameter for the successful application of LLZ as solid electrolyte membrane in all‐solid‐state lithium battery. Systematic investigations carried out through this work indicated that the optimal Li concentration of 6.4 (i.e., Li 6.4 La 3 Zr 1.4 Ta 0.6 O 12 ) is required to obtain phase pure, relatively dense and high Li + conductive cubic phase in Li 7− x La 3 Zr 2− x Ta x O 12 solid solutions. Effort has been also made in this work to enhance the density and Li + conductivity of Li 6.4 La 3 Zr 1.4 Ta 0.6 O 12 further through the Li 4 SiO 4 addition. A maximized room‐temperature (33°C) total (bulk + grain boundary) Li + conductivity of 3.7 × 10 −4 S/cm and maximized relative density of 94% was observed for Li 6.4 La 3 Zr 1.4 Ta 0.6 O 12 added with 1 wt% of Li 4 SiO 4 .
Quantification of Cell Edge Velocities and Traction Forces Reveals Distinct Motility Modules during Cell Spreading (2008)

Actin-based cell motility and force generation are central to immune response, tissue development, and cancer metastasis, and understanding actin cytoskeleton regulation is a major goal of cell biologists. Cell spreading is a commonly used model system for motility experiments -- spreading fibroblasts exhibit stereotypic, spatially-isotropic edge dynamics during a reproducible sequence of functional phases: 1) During early spreading, cells form initial contacts with the surface. 2) The middle spreading phase exhibits rapidly increasing attachment area. 3) Late spreading is characterized by periodic contractions and stable adhesions formation. While differences in cytoskeletal regulation between phases are known, a global analysis of the spatial and temporal coordination of motility and force generation is missing. Implementing improved algorithms for analyzing edge dynamics over the entire cell periphery, we observed that a single domain of homogeneous cytoskeletal dynamics dominated each of the three phases of spreading. These domains exhibited a unique combination of biophysical and biochemical parameters -- a motility module. Biophysical characterization of the motility modules revealed that the early phase was dominated by periodic, rapid membrane blebbing; the middle phase exhibited continuous protrusion with very low traction force generation; and the late phase was characterized by global periodic contractions and high force generation. Biochemically, each motility module exhibited a different distribution of the actin-related protein VASP, while inhibition of actin polymerization revealed different dependencies on barbed-end polymerization. In addition, our whole-cell analysis revealed that many cells exhibited heterogeneous combinations of motility modules in neighboring regions of the cell edge. Together, these observations support a model of motility in which regions of the cell edge exhibit one of a limited number of motility modules that, together, determine the overall motility function. Our data and algorithms are publicly available to encourage further exploration.