gebhart/patrepeval huggingface dataset:
Chylomicrons promote intestinal absorption of lipopolysaccharides (2008)

Recent data suggest that dietary fat promotes intestinal absorption of lipopolysaccharides (LPS) from the gut microflora, which might contribute to various inflammatory disorders. The mechanism of fat-induced LPS absorption is unclear, however. Intestinal-epithelial cells can internalize LPS from the apical surface and transport LPS to the Golgi. The Golgi complex also contains newly formed chylomicrons, the lipoproteins that transport dietary long-chain fat through mesenteric lymph and blood. Because LPS has affinity for chylomicrons, we hypothesized that chylomicron formation promotes LPS absorption. In agreement with our hypothesis, we found that CaCo-2 cells released more cell-associated LPS after incubation with oleic-acid (OA), a long-chain fatty acid that induces chylomicron formation, than with butyric acid (BA), a short-chain fatty acid that does not induce chylomicron formation. Moreover, the effect of OA was blocked by the inhibitor of chylomicron formation, Pluronic L-81. We also observed that intragastric triolein (TO) gavage was followed by increased plasma LPS, whereas gavage with tributyrin (TB), or TO plus Pluronic L-81, was not. Most intestinally absorbed LPS was present on chylomicron remnants (CM-R) in the blood. Chylomicron formation also promoted transport of LPS through mesenteric lymph nodes (MLN) and the production of TNFalpha mRNA in the MLN. Together, our data suggest that intestinal epithelial cells may release LPS on chylomicrons from cell-associated pools. Chylomicron-associated LPS may contribute to postprandial inflammatory responses or chronic diet-induced inflammation in chylomicron target tissues.
Cytoplasmic lipid droplets are translocated into the lumen of the Chlamydia trachomatis parasitophorous vacuole (2008)

The acquisition of host-derived lipids is essential for the pathogenesis of the obligate intracellular bacteria Chlamydia trachomatis. Current models of chlamydial lipid acquisition center on the fusion of Golgi-derived exocytic vesicles and endosomal multivesicular bodies with the bacteria-containing parasitophorous vacuole ("inclusion"). In this study, we describe a mechanism of lipid acquisition and organelle subversion by C. trachomatis. We show by live cell fluorescence microscopy and electron microscopy that lipid droplets (LDs), neutral lipid storage organelles, are translocated from the host cytoplasm into the inclusion lumen. LDs dock at the surface of the inclusion, penetrate the inclusion membrane and intimately associate with reticulate Bodies, the replicative form of Chlamydia. The inclusion membrane protein IncA, but not other inclusion membrane proteins, cofractionated with LDs and accumulated in the inclusion lumen. Therefore, we postulate that the translocation of LDs may occur at IncA-enriched subdomains of the inclusion membrane. Finally, the chlamydial protein Lda3 may participate in the cooption of these organelles by linking cytoplasmic LDs to inclusion membranes and promoting the removal of the LD protective coat protein, adipocyte differentiation related protein (ADRP). The wholesale transport of LDs into the lumen of a parasitophorous vacuole represents a unique mechanism of organelle sequestration and subversion by a bacterial pathogen.
Bone regeneration of porous β‐tricalcium phosphate (Conduit™ TCP) and of biphasic calcium phosphate ceramic (Biosel®) in trabecular defects in sheep (2007)

In this study bone regeneration between porous beta-tricalcium phosphate (Conduit TCP) and biphasic calcium phosphate ceramic (Biosel), with a hydroxyapatite/beta-TCP ratio of 75/25, was compared. The ceramic particles were implanted in sheep trabecular bone for 3, 12, and 26 weeks. Histomorphometrical analysis revealed that Conduit degraded significantly during time and only 36% of the material was left at 26 weeks implantation time. Biosel, in contrast, remained nearly intact. The degradation of Conduit was due to dissolution as well as cell-mediated. Biosel showed a high cellular intervention, although this material did not degrade. Both materials were osteoconductive. The amount of newly formed bone appeared greater in the Conduit group after 26 weeks (46% +/- 8% as compared to 37% +/- 8% for Biosel), but this difference was not significant. Bone distribution over the defect was homogeneous in Conduit, whereas Biosel showed significantly more bone in the periphery of the defect after 26 weeks in comparison to the center. In conclusion, both ceramics are biocompatible and osteoconductive. Degradation showed a difference in amount and in cellular events, with more degraded Conduit TCP with less cellular intervention as compared to Biosel.
HLA Matching for Bone Marrow Transplantation — How Much Is Enough? (2001)

Despite the very large number of volunteers willing to donate bone marrow for unrelated recipients (currently numbering over 7 million worldwide), many candidate recipients still cannot obtain marrow because no HLA-matched volunteer can be found. The major histocompatibility complex (MHC), a group of closely linked genes on chromosome 6, encodes the class I and class II HLA molecules, which, in concert with T-cell receptors, make possible the immune recognition of foreign antigens. HLA molecules are also alloantigens that can trigger immune recognition and graft rejection in unmatched recipients.1 HLA antigens in allografts, in allogeneic leukocytes in transfusions, and in fetal . . .
Naltrindole-5'-isothiocyanate: a nonequilibrium, highly selective .delta.-opioid receptor antagonist (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNaltrindole-5'-isothiocyanate: a nonequilibrium, highly selective .delta.-opioid receptor antagonistP. S. Portoghese, M. Sultana, and A. E. TakemoriCite this: J. Med. Chem. 1990, 33, 6, 1547–1548Publication Date (Print):June 1, 1990Publication History Published online1 May 2002Published inissue 1 June 1990https://pubs.acs.org/doi/10.1021/jm00168a004https://doi.org/10.1021/jm00168a004research-articleACS PublicationsRequest reuse permissionsArticle Views188Altmetric-Citations59LEARN 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
Control strategies of thermostatically controlled appliances in a competitive electricity market (2005)

This paper discusses setpoint-control strategies for thermostatically controlled appliances (TCAs) in a competitive electricity market, with the electric water heater load used as an example. By varying the TCA thermostat settings, the TCA power consumption can be shifted from the high-price period to the low-price period to reduce the peak-load and energy cost. Economic benefits and impacts on distribution feeder load shapes when applying different setpoint-control strategies are studied.
Characterization of Escherichia coli lysis using a family of chimeric E-L genes (1998)

Gene E-L, a chimeric lysis construct from bacteriophages ΦX174 and MS2 lysis proteins E and L, respectively, was subjected to internal deletions to create a series of new E-L clones with altered lysis or killing properties. The lytic activities of the parental genes E, L, E-L and the internal truncated forms of E-L were investigated in this study to characterize the different lysis mechanisms, based on differences in the architecture of the different membrane spanning domains. Electron microscopy and release of marker enzymes for the cytoplasmic and periplasmic spaces revealed that two different lysis mechanisms can be distinguished depending on penetrating of the proteins either the inner membrane or the inner and outer membranes of Escherichia coli. Several candidates, which share efficient lysis properties, have biotechnological applications in terms of cell disruption.
Cytokine pathways and interactions in alopecia areata (2013)

Alopecia areata (AA) is an autoimmune disease resulting in the premature arrest of the follicular growth cycle clinically resulting in patchy, non-scarring hair loss. The presence of a dense follicular T cell infiltrate and variations in cytokines have led to the hypothesis that T cell activation and alterations in inflammatory mediators are crucial participants in the etiopathogenesis of the disease. Various studies suggest that the AA pathogenesis has a dominant TH1-mediated component, with potential involvement of the TH17 pathway. However, a fully integrated view of intersecting cytokine networks that support the autoimmune response in AA is lacking. A more precise understanding of cytokine pathways in disease is required to rationally explore cytokine targeted treatment strategies. Here, we comprehensively and critically review the current literature to provide a working framework regarding the complexity of T cell-cytokine interactions in AA, emphasizing the areas necessitating further research, particularly for the development of novel therapeutic options.
Electrochemiluminescence of tris(2,2′‐bipyridyl)ruthenium and its applications in bioanalysis: a review (2011)

Electrochemiluminescence (ECL) of tris(2,2'-bipyridyl)ruthenium(II) [Ru(bpy)(3) (2+)] is an active research area and includes the synthesis of ECL-active materials, mechanistic studies and broad applications. Extensive research has been focused on this area, due to its scientific and practical importance. In this mini-review we focus on the bio-related applications of ECL. After a brief introduction to Ru(bpy)(3) (2+) ECL and its mechanisms, its application in constructing an effective bioassay is discussed in detail. Three types of ECL assay are covered: DNA, immunoassay and functional nucleic acid sensors. Finally, future directions for these assays are discussed.
Epstein-Barr virus-derived plasmids replicate only once per cell cycle and are not amplified after entry into cells (1991)

Some possible ways in which replication of plasmids containing the Epstein-Barr virus (EBV) plasmid maintenance origin, oriP, might be controlled were investigated. Virtually all plasmid molecules were found to replicate no more than once per cell cycle, whether replication was observed after stable introduction of the plasmids into cells by drug selection or during the first few cell divisions after introducing the DNA into cells. The presence in the cells of excess amounts of EBNA1, the only viral protein needed for oriP function, did not increase the number of oriP-replicated plasmids maintained by cells under selection. In the cell lines studied, EBNA1 and oriP seem to lack the capacity to override the cellular controls that limit DNA replication to one initiation event per DNA molecule per S phase. The multicopy status of EBV-derived, selectable plasmids appears to result from the initial uptake by cells of large numbers of plasmid molecules, the efficient maintenance of these plasmids, and the pressure of genetic selection against plasmid loss. Other unknown controls must be responsible for the amplification of EBV genomes soon after latent infection of cells.
A CRISPR/Cas9 toolkit for multiplex genome editing in plants (2014)

We developed a toolkit that facilitates transient or stable expression of the CRISPR/Cas9 system in a variety of plant species, which will facilitate plant research, as it enables high efficiency generation of mutants bearing multiple gene mutations.
Validation of Comorbid Conditions on the End-Stage Renal Disease Medical Evidence Report (2000)

Since 1995, the Medical Evidence Report for end-stage renal disease (Form 2728) has been used nationally to collect information on comorbid conditions. To date, these data have not been validated. A national cross-sectional study of 1005 incident dialysis patients (734 hemodialysis and 271 peritoneal dialysis) enrolled between October 1995 and June 1998 was conducted using clinical data to validate 17 comorbid conditions on Form 2728. Sensitivity and specificity were calculated for each condition. The relationship between patient characteristics and sensitivity was assessed in multivariate analysis. Sensitivity was fairly high (0.67 to 0.83) for HIV disease, diabetes, and hypertension; intermediate (0.40 to 0.52) for peripheral vascular disease, neoplasm, myocardial infarction, cerebrovascular disease, coronary artery disease, cardiac arrest, and congestive heart failure; and poor (<0.36) for dysrhythmia, ambulation status, pericarditis, chronic obstructive pulmonary disease, and smoking. Sensitivity did not change significantly over calendar time. The sensitivity of Form 2728 averaged across all 17 conditions was 0.59 (95% confidence interval, 0.43 to 0.75). The average sensitivity was 0.10 greater in peritoneal dialysis than hemodialysis patients. 0.11 greater in diabetic patients than nondiabetic patients, and 0.04 less with each added comorbid condition. The specificity was very good for hypertension (0.91) and excellent (>0.95) for the other 16 conditions. Comorbid conditions are significantly underreported on Form 2728, but diagnoses are not falsely attributed to patients. Scientific research, quality of care comparisons, and payment policies that use Form 2728 data should take into account these limitations. Considerable effort should be expended to improve Form 2728 coding if it is to provide accurate estimates of total disease burden in end-stage renal disease patients.
Introduction to Imaging Brain Tumor Metabolism with Positron Emission Tomography (PET) (1995)

The need for prompt and detailed evaluation of cancers and their treatment is requiring increasingly sophisticated methodologies for in vivo assessment. Morphological detail as provided by CT and MRI has yielded significant advances in diagnostic medicine. In spite of such advances, the means of achieving the clinical goals of improved quality and quantity of life in many cancer patients remain elusive. It is becoming increasingly evident that only with the addition of complementary physiological and biochemical data will further advances occur. While neither in vivo morphological imaging with CT or MRI nor physiological imaging with PET or MRS can provide the resolution of microscopic or cellular level assessment, all can provide macroscopic or regional data. With PET, however, exploration of the kinetics or chemical processes occurring at the cellular level is providing a "biological resolution" not heretofore achieved with in vivo imaging. Application of this complementary morphological and biochemical diagnostic information will likely lead to significant advances in patient management in the immediate future, most of which would probably not be achievable using any individual technique. Efficacy studies should be performed, however, when introducing any new high-technology methodology into clinical practice. A number of retrospective and prospective trials on PET applications in clinical oncology are ongoing sponsored by organizations such as the Institute for Clinical PET and the Western PET Association. Detailed studies also are underway to estimate the "cost" of delivery of PET services to the community (146). Numerous PET feasibility studies in animal models have demonstrated that no one radiotracer serves as the best agent for tumor imaging in all cases. Such studies with radiolabeled amino acids, sugars, and nucleoside derivatives, representatives of the major classes of biomolecules, have demonstrated variable tumor uptake dependent on such parameters as the type of cancer, organ of origin, animal host, and chemical structure of the radioligand. Detailed analysis of tracer uptake using multiple ligands in a variety of animal tumor models and clinical patients suggests that while given types of cancers may be better imaged with certain radiotracers, the use of multitracer imaging provides the specific details necessary for appropriate interpretation of tumor status. In addition, in cases where the diagnosis is uncertain, such information could have a significant impact on patient management by reducing the diagnostic differential. In spite of the many successes achieved with FDG in brain tumor imaging, the most well-known example of the problems that can arise with PET image interpretation is with the use of this agent.(ABSTRACT TRUNCATED AT 400 WORDS)
Distributed application configuration (2002)

This paper presents Olan, a language and a run time support intended to facilitate the design, configuration and evolution of distributed applications made up of heterogeneous software components. Configuration covers two phases: for the application builder the identification of the software components and the description of their interconnections and communications; for the application administrator and maintainer the accurate use of system resources provided by the target environment, such as the placement of components on nodes. The main benefit of Olan is to provide a single unified description of distributed applications, adequate for construction, management, and evolution. The overall description is independent from the components' implementation, so that the configuration process, e.g. the production of different versions of an implementation, is decoupled from the programming process. The features of the configuration language and the functions of the runtime support system are illustrated through the example of a distributed teleconferencing application.
Decreased plasma endothelin-1 levels in children with sickle cell disease treated with hydroxyurea. (2005)

Plasma endothelin-1 (ET-1) is elevated in patients with sickle cell disease (SCD). Hydroxyurea (HU) is the only drug with demonstrated clinical efficacy in SCD. Here we show that treatment with HU results in a decreased concentration of circulating ET-1 which is not correlated with the HU-induced increase in HbF level. Blunting of the ET-1 vasoconstrictive stimulus could contribute to the beneficial effects of HU.
Cleavage of the Murine Leukemia Virus Transmembrane Env Protein by Human Immunodeficiency Virus Type 1 Protease: Transdominant Inhibition by Matrix Mutations (1998)

We have identified mutations in the human immunodeficiency virus type 1 (HIV-1) matrix protein (MA) which block infectivity of virions pseudotyped with murine leukemia virus (MuLV) envelope (Env) glycoproteins without affecting infectivity conferred by HIV-1 Env or vesicular stomatitis virus G glycoproteins. This inhibition is very potent and displays a strong transdominant effect; infectivity is reduced more than 100-fold when wild-type and mutant molecular clones are cotransfected at a 1:1 ratio. This phenomenon is observed with both ecotropic and amphotropic MuLV Env. The MA mutations do not affect the incorporation of MuLV Env into virions. We demonstrate that in HIV-1 virions pseudotyped with MuLV Env, the HIV-1 protease (PR) efficiently catalyzes the cleavage of the p15(E) transmembrane (TM) protein to p12(E). Immunoprecipitation analysis of pseudotyped virions reveals that the mutant MA blocks this HIV-1 PR-mediated cleavage of MuLV TM. Furthermore, the transdominant inhibition exerted by the mutant MA on wild-type infectivity correlates with the relative level of p15(E) cleavage. Consistent with the hypothesis that abrogation of infectivity imposed by the mutant MA is due to inhibition of p15(E) cleavage, mutant virions are significantly more infectious when pseudotyped with a truncated p12(E) form of MuLV Env. These results indicate that HIV-1 Gag sequences can influence the viral PR-mediated processing of the MuLV TM Env protein p15(E). These findings have implications for the development of HIV-1-based retroviral vectors pseudotyped with MuLV Env, since p15(E) cleavage is essential for activating membrane fusion and virus infectivity.
DNA-Repair Defects and Olaparib in Metastatic Prostate Cancer (2015)

Treatment with the PARP inhibitor olaparib in patients whose prostate cancers were no longer responding to standard treatments and who had defects in DNA-repair genes led to a high response rate. (Funded by Cancer Research UK and others; ClinicalTrials.gov number, NCT01682772; Cancer Research UK number, CRUK/11/029.).
Conditioning stochastic groundwater flow models on head data (1995)

The authors present a new method for conditioning realizations of the logarithm Y of transmissivity on head data. Each realization is conditioned by subtracting a linear combination of certain basis functions, each corresponding to a measurement, obtained by a process based on co-kriging. The required cross covariance between head and Y can be numerically computed very efficiently using the adjoint method. The coefficients in the linear combination are chosen to try to minimize the differences between computed and measured heads. The most efficient methods for such non-linear optimization problems are those that exploit information about the second derivatives of the function being minimized. The authors show how these second derivatives can be computed very efficiently using the adjoint method for certain classes of finite-element schemes. The authors illustrate their method by application to the WIPP-2 test case of the international INTRAVAL project. They show that the match between computed and measured heads is greatly improved. They compare the method with approaches that use pilot points. The method is exact if the variability of the Y field and the deviations of the measured heads form the values computed for the mean of the Y field are both small, whereas pilot-point methodsmore » are only approximate. However, the method may be more expensive computationally. Finally, they discuss the extension of their method to conditioning on transient head data and to dealing with boundary conditions.« less
High-speed regular expression matching engine using multi-character NFA (2008)

An approach is presented for high throughput matching of regular expressions (regexes) by first converting them into corresponding Non-deterministic Finite Automata (NFAs) which are then configured onto a FPGA. The key novel feature is a technique that, for any given regex, constructs an NFA that processes multiple characters per clock cycle. An efficient algorithm is proposed that outputs an NFA which processes twice the number of characters as the input one. A technique is also proposed that implements the range match operation (e.g. [a–z]) efficiently. A program has been written that implements above ideas to convert regexes into NFAs specified in a structural Hardware Design Language (HDL), which are then mapped onto a FPGA. Performance is evaluated using real world regexes (Snort ruleset). The results demonstrate the practical utility of the approach. For example, for a set of 2,691 regexes, while the standard 1-character NFA obtains a throughput of 1.25 Gbps, our 4-character NFA achieves a throughput of 3.63 Gbps, while requiring only 20% more LUTs and 6% less flip-flops.