gebhart/patrepeval huggingface dataset:
Regulation of ABCA1 expression and cholesterol efflux during adipose differentiation of 3T3-L1 cells (2003)

Adipose cells specialized in energy storage, contain large intracellular triglyceride-rich lipid droplets, are enriched with free cholesterol, and express sterol-regulated transcription factors such as liver X receptor (LXR). The recent identification of the LXR-dependent ATP binding cassette transporter A1 (ABCA1) pathway for cholesterol release from peripheral cells has led us to address the question of the expression and function of ABCA1 in adipocytes. In 3T3-L1 adipose cells, we observed a strong induction of ABCA1 mRNA during adipose differentiation, but only limited variations in ABCA1 protein. Lipid efflux onto apolipoprotein A-I (apoA-I), which depends on ABCA1, was comparable in adipocytes and preadipocytes, demonstrating a differential regulation of ABCA1 mRNA and cholesterol efflux. We also found that total cell cholesterol remained stable during differentiation of 3T3-L1 cells, but membrane cholesterol was lower in adipocytes than in preadipocytes, suggesting redistribution of cholesterol to the lipid droplet. Finally, we show that under standard lipolytic stimulation, 3T3-L1 adipocytes do not release cholesterol onto apoA-I, a process that required long exposures to lipolytic agents (24 h). In conclusion, despite large induction of ABCA1 mRNA during differentiation, cholesterol efflux through the ABCA1 pathway remains limited in adipocytes and requires prolonged lipolysis. This is consistent with the view of the adipocyte behaving as a cholesterol sink, with plasma cholesterol-buffering properties.
A highly sensitive selection method for directed evolution of homing endonucleases (2005)

Homing endonucleases are enzymes that catalyze DNA sequence specific double-strand breaks and can significantly stimulate homologous recombination at these breaks. These enzymes have great potential for applications such as gene correction in gene therapy or gene alteration in systems biology and metabolic engineering. However, homing endonucleases have a limited natural repertoire of target sequences, which severely hamper their applications. Here we report the development of a highly sensitive selection method for the directed evolution of homing endonucleases that couples enzymatic DNA cleavage with the survival of host cells. Using I-SceI as a model homing endonuclease, we have demonstrated that cells with wild-type I-SceI showed a high cell survival rate of 80-100% in the presence of the original I-SceI recognition site, whereas cells without I-SceI showed a survival rate <0.003%. This system should also be readily applicable for directed evolution of other DNA cleavage enzymes.
Weakly consistent transactions in ROSS (1993)

This paper describes the design of the weak consistency scheme used in ROSS, the EAN object store. ROSS supports nested atomic transactions on distributed and replicated objects. The weak consistency method falls into the family of optimistic protocols. After a partitioning, execution of transactions proceeds normally. If write-write conflicts are detected when partitions later merge, transactions may be rolled back to ensure consistency. One-copy serializability is not provided. This approach is particularly well suited to a common class of database applications where there is limited interdependency between objects. A distributed name service is one such application.
Urea cycle defects: Management and outcome (2005)

This paper reviews the clinical presentation of 217 patients with urea cycle defects, including 121 patients with neonatal-onset forms and 96 patients with late-onset forms. Long-term outcome of these patients is also reported with the severity of the neonatal forms of these disorders, mostly for ornithine carbamoyltransferase-deficient males. Patients with late-onset forms may present at any age and carry a 28% mortality rate and a subsequent risk of subsequent disabilities.
The Staphylococci Phages Family: An Overview (2012)

Due to their crucial role in pathogenesis and virulence, phages of Staphylococcus aureus have been extensively studied. Most of them encode and disseminate potent staphylococcal virulence factors. In addition, their movements contribute to the extraordinary versatility and adaptability of this prominent pathogen by improving genome plasticity. In addition to S. aureus, phages from coagulase-negative Staphylococci (CoNS) are gaining increasing interest. Some of these species, such as S. epidermidis, cause nosocomial infections and are therefore problematic for public health. This review provides an overview of the staphylococcal phages family extended to CoNS phages. At the morphological level, all these phages characterized so far belong to the Caudovirales order and are mainly temperate Siphoviridae. At the molecular level, comparative genomics revealed an extensive mosaicism, with genes organized into functional modules that are frequently exchanged between phages. Evolutionary relationships within this family, as well as with other families, have been highlighted. All these aspects are of crucial importance for our understanding of evolution and emergence of pathogens among bacterial species such as Staphylococci.
Increasing the value of atomic force microscopy process metrology using a high-accuracy scanner, tip characterization, and morphological image analysis (1996)

Atomic force microscopes are being used increasingly for process metrology. As a case study, the measurement by atomic force microscope of a soda lime glass optical disk patterned using optical lithography and reactive plasma etching is examined. The atomic force microscope used for this measurement has a highly accurate scanner system. The X, Y, and Z axes are calibrated using laser interferometry. To determine the shape of the tip used a commercially available tip calibration artifact was imaged both before and after the measurement. The image was corrected for the tip shape using mathematical morphology. The value of the atomic force microscope measurement is defined to be the impacts of the metrology on the product or process. It is shown that the value of atomic force microscopy process metrology on an optical disk is increased by using an accurate scanner, tip characterization, and morphological image analysis; however, the cost per measurement is increased as well. In general, the characteristics of the metrology required depends on the specific manufacturing process being supported.
Interleukin‐6 concentrations in the serum of patients with AIDS‐associated Kaposi's sarcoma during treatment with interferon‐alpha (1991)

Interleukin-6 (IL-6) levels were determined in the serum of 14 HIV-1-infected patients with Kaposi's sarcoma, 10 HIV-1-infected patients without symptoms, and 10 healthy male subjects. IL-6 levels were also determined in the serum of the 14 patients with Kaposi's sarcoma during treatment with high-dose human recombinant interferon-alpha (IFN alpha). Serum IL-6 levels were significantly higher in the patients with Kaposi's sarcoma than in the HIV-infected patients without symptoms and the controls. There was no consistent pattern of changes of IL-6 levels during IFN alpha treatment. These results support the view that IL-6 is a cytokine involved in the pathogenesis of AIDS-associated Kaposi's sarcoma, but appear to argue against an effect of IFN alpha on the production or release of IL-6 as an important mechanism of action of IFN alpha.
Mechanism of protection from primary bovine viral diarrhea virus infection. I. The effects of dexamethasone. (1976)

A series of investigations was designed to study the role of cellular immunity and passive antibody in protecting neonatal calves from primary bovine viral diarrhea virus infection. Administration of corticosteroids (dexamethasone) in doses capable of suppressing cellular immunity markedly potentiated systemic bovine viral diarrhea virus infection in calves which lacked bovine viral diarrhea passive neutralizing antibody. Immunosuppressed calves did not form neutralizing antibody to bovine viral diarrhea virus and developed a fatal viremia. Calves with high levels of passive bovine viral diarrhea neutralizing antibodies were protected from the effect of corticosteroids. The results suggest an essential role for humoral passive antibody, but not for cellular immunity, in protection from primary systemic bovine viral diarrhea virus infection in calves.
Computer-Aided Diagnosis of Hepatic Fibrosis: Preliminary Evaluation of MRI Texture Analysis Using the Finite Difference Method and an Artificial Neural Network (2007)

Computer algorithm analysis of equilibrium phase images was found to reflect the degree of fibrosis most accurately. MR image texture analysis performed using the computer algorithm was found to have a potential usefulness for the diagnosis of hepatic fibrosis.
Recognition of Lewis x Derivatives Present on Mucins by Flagellar Components of Pseudomonas aeruginosa (2001)

Pseudomonas aeruginosa binds to human respiratory mucins by mechanisms involving flagellar component-receptor interactions. The adhesion of P. aeruginosa strain PAK is mediated by the flagellar cap protein, FliD, without the involvement of flagellin. Two distinct types of FliD proteins have been identified in P. aeruginosa: A type, found in strain PAK, and B type, found in strain PAO1. In the present work, studies performed with the P. aeruginosa B-type strain PAO1 indicate that both the FliD protein and the flagellin of this strain are involved in the binding to respiratory mucins. Using polyacrylamide-based fluorescent glycoconjugates in a flow cytometry assay, it was previously demonstrated that P. aeruginosa recognizes Le(x) (or Lewis x) derivatives found at the periphery of human respiratory mucins. The aim of the present work was therefore to determine whether these carbohydrate epitopes (or glycotopes) are receptors for FliD proteins and flagellin. The results obtained by both flow cytometry and a microplate adhesion assay indicate that the FliD protein of strain PAO1 is involved in the binding of glycoconjugates bearing Le(x) or sialyl-Le(x) determinants, while the binding of flagellin is restricted to the glycoconjugate bearing Le(x) glycotope. In contrast, the type A cap protein of P. aeruginosa strain PAK is not involved in the binding to glycoconjugates bearing Le(x), sialyl-Le(x), or sulfosialyl-Le(x) glycotopes. This study demonstrates a clear association between a specific Pseudomonas adhesin and a specific mucin glycotope and demonstrates that fine specificities exist in mucin recognition by P. aeruginosa.
Inhibition of growth of human tumor cells in nude mice by a metalloproteinase inhibitor (1994)

The effects of a new metalloproteinase inhibitor, BEI6627B [L-N-(N-hydroxy-2-isobutylsuccinynamoyl)-seryl-L-valine, MW: 375.2] isolated from microbial cultures, on human tumor cell growth in nude mice were investigated. BE16627B inhibited metalloproteinases in enzyme assays, as well as gelatinolysis and collagenolysis in cell cultures. BE16627B at 100 μg/ml showed no apparent cytotoxicity to human tumor cells in culture and its LD50 in mice was more than 1,000 mg/kg (i.p.). The effects of BE16627B on the in vivo growth of 1 human tumor cell lines were examined: HT1080 fibrosarcoma, which overproduces metalloproteinases, and HCT116 colon carcinoma, which barely secretes metalloproteinases. When BE16627B was administered to mice at 2 mg/mouse/day by an osmotic pump implanted s.c. for 3 weeks from 1 week after i.v. inoculation of HT1080 cells, the number and size of nodules of HT1080 cells on the lung surface were reduced to 24.3 and 46.4%, respectively, of those of controls, and the increase in lung weight due to tumor-cell growth was inhibited 85.5% without body-weight loss. Moreover, BE16627B inhibited 71.2% of the growth of HT1080 cells inoculated s.c. into mice under the same conditions, but did not significantly inhibit the s.c. growth of HCT116 human colon-carcinoma cells. Thus, BE16627B inhibited metalloproteinase-dependent human tumor-cell growth as well as lung colonization without showing cytotoxicity in nude mice.
Molluscicidal and antibacterial compounds fromPetunia hybrida (1999)

Three novel and six known petuniasterones were isolated from the aerial parts of Petunia hybrida (Solanaceae). In addition, chromatography yielded four groups of novel 2,3,4,6-tetra-O-acylated sucrose ester isomers. The sucrose esters showed molluscicidal and bactericidal activities. Petuniasterones had different molluscicidal activities, depending on the side-chains. © 1999 Society of Chemical Industry
Cell proliferation in childhood acute leukemia. Comparison of Ki-67 and proliferating cell nuclear antigen immunocytochemical and DNA flow cytometric analysis (1992)

The proliferative activity of bone marrow leukemia cells was determined by DNA flow cytometric (FCM) analysis and labeling index (LI) of Ki-67 monoclonal antibodies and proliferating cell nuclear antigen (PCNA) autoantibodies in 73 children with acute leukemia. LI of Ki-67 varied greatly from patient to patient (range, 0.4% to 42.2%; mean, 18.8%) and differed significantly between acute lymphoblastic leukemia (ALL) and acute nonlymphoblastic leukemia (ANLL). In ALL, the Ki-67 LI showed a positive correlation with the S-phase fraction (SPF) determined by DNA FCM analysis, whereas, in ANLL, there was a discrepancy between the Ki-67 LI and SPF. In contrast, LI of PCNA varied less among the patients (range, 57.2% to 100%; mean, 90.3%), and the value was always higher than that of the Ki-67 LI in individual patients. A significant relationship between PCNA LI and the percentage of blast cells was found in peripheral blood leukocytes from patients with leukemia. These results suggest that the Ki-67 LI reflects differences in the proliferative activity depending on the subtype of the disease and that the PCNA LI is useful as a marker of proliferating cells.
A common function for mRNA 5' and 3' ends in translation initiation in yeast. (1995)

The mRNA poly(A) tail and its associated poly(A) binding protein (Pab1p) are ubiquitous in eukaryotes. The function of the poly(A) tail is to stabilize mRNA and to stimulate its translation. The development of a poly(A)- and cap-dependent yeast in vitro translation system has allowed us to understand how poly(A) stimulates translation. We find that Pab1p but not the cap binding protein eIF-4E is required for poly(A) tail-dependent translation, and that the Pab1p-poly(A) tail complex functions to recruit the 40S ribosomal subunit to the mRNA. These data introduce a new step into the pathway of translation initiation and merge the translational functions of the two ends of mRNA.
An algorithm for maze searching with azimuth input (2002)

The performance of systems for sensor-based robot motion planning is known to depend heavily on the basic search algorithms used. Typically, these are provable graph search schemes modified into maze search algorithms by taking into account the topology of the physical objects in the workspace-for example, the fact that the boundary of a 2-dimensional object is a simple closed curve. Although several maze search algorithms are already available, more are needed to improve the performance and fill gaps in required properties. This work presents a new algorithm that possesses properties not covered so far, and then assesses its performance. The algorithm allows one to use directional input information (such as azimuth angles) rather than the usual Cartesian coordinates; it also allows the robot to "cut corners" on its way to the target, thus shortening the path.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of Immunotoxins Bearing a Single Saporin Molecule with Multiple Toxin Conjugates (2003)

Immunotoxins (IT) constructed by conventional chemical means using heterobifunctional crosslinking reagents such as [N-succinimidyl 3-(2-pyridyldithio) propionate (SPDP) or 4-succinimidyloxycarbonyl-α methyl-α-(2-pyridyldithio) toluene (SMPT) are heterogeneous with regard to the site of attachment of toxin to antibody and to the number of toxin molecules linked per antibody molecule (1, 2). Such constructs inevitably contain mixtures of hybrid molecules comprised of one antibody molecule coupled covalently via a disulfide bond to one, two, or even three toxin moieties (3). Such heterogeneity makes it difficult to accurately evaluate the pharmacologic and therapeutic properties of this class of molecule. A number of independent reports have in the past demonstrated that ITs containing more than one toxin moiety per unit antibody molecule are significantly more potent in vitro for the respective antigen expressing target cell (3, 4). While this has been shown to be generally true for IT performance in vitro, the same has not been consistently demonstrable in vivo. For instance, Ghetie et al. have shown that anti-CD19 and anti-CD25 ricin A-chain (RTA) ITs containing two RTA moieties per unit antibody show an increased potency for target-antigen-expressing cell lines in vitro, compared with ITs containing a single RTA moiety (5). However, in SCID mice bearing the human B-cell lymphoma cell line Daudi, the IT containing two RTA performed no better therapeutically than the IT containing just one RTA molecule. In the same report, an anti-CD22 RTA-IT containing two RTA molecules was not only seven times more potent in vitro but also significantly better therapeutically in the same SCID mouse model of human lymphoma (5).
Diffusion-Weighted MRI for Verification of Electroporation-Based Treatments (2011)

Clinical electroporation (EP) is a rapidly advancing treatment modality that uses electric pulses to introduce drugs or genes into, e.g., cancer cells. The indication of successful EP is an instant plasma membrane permeabilization in the treated tissue. A noninvasive means of monitoring such a tissue reaction represents a great clinical benefit since, in case of target miss, retreatment can be performed immediately. We propose diffusion-weighted magnetic resonance imaging (DW-MRI) as a method to monitor EP tissue, using the concept of the apparent diffusion coefficient (ADC). We hypothesize that the plasma membrane permeabilization induced by EP changes the ADC, suggesting that DW-MRI constitutes a noninvasive and quick means of EP verification. In this study we performed in vivo EP in rat brains, followed by DW-MRI using a clinical MRI scanner. We found a pulse amplitude-dependent increase in the ADC following EP, indicating that (1) DW-MRI is sensitive to the EP-induced changes and (2) the observed changes in ADC are indeed due to the applied electric field.
Radial Distortion Refinement by Inverse Mapping-Based Extrapolation (2006)

"Caltech Calibration Toolbox" by Jean-Yves Bouguet is one of the most famous open-source calibration tools. Although it works well for general camera lenses, it reveals problems in case of wide-angle lens. This paper analyzes the problem and shows that the insufficient calibration of radial distortion is caused by lease-square based polynomial fitting. To overcome the problem, this paper proposes novel refinement method using inverse mapping-based extrapolation. The proposed method is expected to be an efficient supplement and is opened to the public in the appendix as a short Matlab script
The reactions of three bis(viologen) tetraquaternary salts and their reduced radicals (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe reactions of three bis(viologen) tetraquaternary salts and their reduced radicalsStephen J. Atherton, K. Tsukahara, and R. G. WilkinsCite this: J. Am. Chem. Soc. 1986, 108, 12, 3380–3385Publication Date (Print):June 1, 1986Publication History Published online1 May 2002Published inissue 1 June 1986https://pubs.acs.org/doi/10.1021/ja00272a037https://doi.org/10.1021/ja00272a037research-articleACS PublicationsRequest reuse permissionsArticle Views389Altmetric-Citations35LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
MWL fraction with a high concentration of lignin-carbohydrate linkages: Isolation and 2D NMR spectroscopic analysis (2007)

Abstract A preparation enriched in lignin-carbohydrate fragments (LCC-AcOH) was isolated in the course of purification of loblolly pine crude milled wood lignin (MWL). The preparation contained approximately equal amounts of lignin and carbohydrates, with high amounts of arabinose and galactose compared to their levels in wood. LCC-AcOH was investigated by 2D 1 H- 13 C (HMQC and HMBC) correlation NMR techniques and quantitative 13 C NMR. The HMQC spectra allowed direct detection of phenyl glycoside, ester and benzyl ether lignin-carbohydrates linkages in high amounts. The assignment of these structures was supported by the HMBC technique. It is noteworthy that in the ester lignin-carbohydrate linkages, a uronic acid residue was attached not to the benzylic position of lignin, as commonly believed, but to the γ-position of the side chain.
Expression of Cytokine mRNA in Gastric Mucosa withHelicobacter pyloriInfection (1995)

These findings suggest that some cytokines, especially IL-7 and IL-8, play some roles in H. pylori-associated gastritis.
Altered hypothalamic function in response to glucose ingestion in obese humans. (1999)

The hypothalamus plays a central role in the regulation of energy intake and feeding behavior. However, the presence of a functional abnormality in the hypothalamus in humans that may be related to excess energy intake and obesity has yet to be demonstrated in vivo. We, therefore, used functional magnetic resonance imaging (fMRI) to monitor hypothalamic function after oral glucose intake. The 10 obese (34 +/- 2 years of age, BMI 34.2 +/- 1.3 kg/m2) and 10 lean (32 +/- 4 years of age, BMI 22.0 +/- 0.9 kg/m2) subjects with normal glucose tolerance ingested 75 g of glucose while a midsagittal slice through the hypothalamus was continuously imaged for 50 min using a conventional T2*-weighted gradient-echo pulse sequence. After glucose ingestion, lean subjects demonstrated an inhibition of the fMRI signal in the areas corresponding to the paraventricular and ventromedial nuclei. In obese subjects, this inhibitory response was markedly attenuated (4.8 +/- 1.3 vs. 7.0 +/- 0.6% inhibition, P < 0.05) and delayed (9.4 +/- 0.5 vs. 6.4 +/- 0.5 min, P < 0.05) compared with that observed in lean subjects. The time taken to reach the maximum inhibitory response correlated with the fasting plasma glucose (r = 0.75, P < 0.001) and insulin (r = 0.47, P < 0.05) concentrations in both lean and obese subjects. These results demonstrate in vivo, for the first time, the existence of differential hypothalamic function in lean and obese humans that may be secondary to obesity.