gebhart/patrepeval huggingface dataset:
The role of Krüppel-like factors in the reprogramming of somatic cells to induced pluripotent stem cells. (2009)

The potential for clinical application of pluripotent embryonic stem cells is immense but hampered by moral and ethical complications. Recent advances in the reprogramming of somatic cells by defined factors to a state that resemble embryonic stem cells have created tremendous excitement in the field. Four factors, Sox2, Oct4, Klf4 and c-Myc, when exogenously introduced into somatic cells, can lead to the formation of induced pluripotent stem (iPS) cells that have the capacity for self-renewal and differentiation into tissues of all three germ layers. In this review, we focus on the role of Krüppel-like factors (KLFs) in regulating somatic cell reprogramming. KLFs are zinc finger-containing transcription factors with diverse biological functions. We first provide an overview of the KLF family of regulatory proteins, paying special attention to the established biological and biochemical functions of KLF4 and KLF5. We then review the role of KLFs in somatic cell reprogramming and delineate the putative mechanism by which KLFs participates the establishment and self-renewal of iPS cells. Further research is likely to provide additional insight into the mechanisms of somatic cell reprogramming and refinement of the technique with which to generate clinically relevant iPS cells.
Ultraviolet irradiation of spray-dried porcine plasma does not affect the growth performance of nursery pigs when compared with nonirradiated bovine plasma1 (2017)

Ultraviolet light irradiation of spray-dried porcine plasma (SDPP) decreases the risk of disease transmission, but it may decrease the activity of bioactive components in SDPP. Therefore, the objectives of this study were to determine growth performance, morbidity, and mortality responses of nursery pigs fed UV-irradiated SDPP (UV-SDPP) compared with nonirradiated spray-dried bovine plasma (SDBP). Pigs ( = 480; 6.09 ± 2.4 kg initial BW) were blocked by initial BW, and blocks were assigned to pens. the sex ratio was equalized within blocks and pens. Pens were randomly assigned to 1 of 5 dietary treatments (8 pigs/pen and 12 replicates/treatment) in a 3-phase feeding program (phase 1 = d 0 to 13, phase 2 = d 14 to 27, and phase 3 = d 28 to 55). Dietary treatments included a control diet without UV-SDPP or SDBP and diets containing 3% UV-SDPP, 3% SDBP, 6% UV-SDPP, or 6% SDBP during phase 1. Diets were formulated to meet or exceed nutrient requirements and contained the same concentrations of standardized ileal digestible Lys and Lys:ME ratio within phases. Pigs were provided ad libitum access to diets throughout the 55-d experiment. Dietary inclusion rates during phase 2 were reduced to 1.5% UV-SDPP, 1.5% SDBP, 3% UV-SDPP, and 3% SDBP, and all pigs were fed a common diet without UV-SDPP or SDBP during phase 3. Growth performance data were analyzed as a 2 × 2 factorial arrangement of treatments with a control within a completely randomized block design to evaluate the main effects of plasma processing (UV irradiated vs. nonirradiated) and dietary inclusion level, and block, room, and pen were random effects. In phase 1, there were no differences in G:F among treatments, but pigs fed 6% UV-SDPP and 6% SDBP had greater ( < 0.01) ADG (0.11 vs. 0.08 kg/d) and ADFI (0.17 vs. 0.15 kg/d) than pigs fed the control, 3% SDBP, and 3% UV-SDPP diets. After phase 1 (d13), feeding UV-SDPP or SDBP increased ( = 0.02) the BW of pigs. In phases 2 and 3 and the overall feeding period (d 0 to 55), there were no differences in ADG, ADFI, and G:F among dietary treatments. There was a linear decrease ( < 0.01) in mortality of nursery pigs as dietary inclusion rate of SDBP and UV-SDPP increased. In conclusion, feeding SDBP or UV-SDPP diets improved ADG and ADFI during the first 2 wk after weaning due to improved feed consumption, and UV irradiation appeared to have no detrimental effects on the feeding value of SDPP.
Anaerobic Treatment of High Sulfate Wastewater with Oxygenation to Control Sulfide Toxicity (2003)

In this study, oxidation-reduction potential (ORP) was employed to regulate oxygen dosing for online sulfide toxicity control during anaerobic treatment of high sulfate wastewater. The experiment was conducted in an upflow anaerobic filter, which was operated at a constant influent total organic carbon of 6,740 mg/L [equivalent to a chemical oxygen demand (COD) of 18,000 mg/L], but with different influent sulfates of 1,000, 3,000, and 6,000 mg/L. The reactor was initially run at natural ORP (the system’s ORP without oxygenation) of about -290 to -300mV and then was followed by oxygenation to raise ORP by +25mV above the natural level for each influent sulfate level. At 6,000 mg/L sulfate under the natural ORP, methanogenesis was severely inhibited due to sulfide toxicity, and the anaerobic process was almost totally upset. Upon oxygenation by raising ORP to -265mV, the dissolved sulfide was quickly reduced to 12.2 mg S/L with a concomitant improvement in methane yield by 45.9%. If oxygen was not totally used up by sulfide oxidation, the excess oxygen was consumed by facultative bacteria which had been found to stabilize about 13.5% of the influent COD. Both sulfide oxidation and facultative activity acted as a shield to protect the anaerobes from an excessive oxygen exposure. This study showed that direct oxygenation of the recirculated biogas was effective to oxidize sulfide, and the use of ORP to regulate the oxygen dosing was practical and reliable during anaerobic treatment of high sulfate wastewater.
Maximum Likelihood Estimation in the Birth-and-Death Process (1975)

Maximum likelihood estimation of the parameters $\lambda$ and $\mu$ of a simple (linear) birth-and-death process observed continuously over a fixed time interval is studied. Asymptotic distributions for large initial populations and for large periods of observation are derived and some nonstandard results appear. The result problem of estimation from the discrete skeleton of the process is also discussed.
An Efficient and Portable Web Server (1999)

This paper presents the design of a new Web server architecture called the asymmetric multi-process eventdriven (AMPED) architecture, and evaluates the performance of an implementation of this architecture, the Flash Web server. The Flash Web server combines the high performance of single-process event-driven servers on cached workloads with the performance of multiprocess and multi-threaded servers on disk-bound workloads. Furthermore, the Flash Web server is easily portable since it achieves these results using facilities available in all modern operating systems. The performance of different Web server architectures is evaluated in the context of a single implementation in order to quantify the impact of a server’s concurrency architecture on its performance. Furthermore, the performance of Flash is compared with two widelyused Web servers, Apache and Zeus. Results indicate that Flash can match or exceed the performance of existing Web servers by up to 50% across a wide range of real workloads. We also present results that show the contribution of various optimizations embedded in Flash.
SNP genotyping with fluorescence polarization detection (2002)

When a fluorescent molecule is excited by plane polarized light, the fluorescence emitted is also polarized. The degree of fluorescence polarization (FP) detected, under constant temperature and solvent viscosity, is proportional to the molecular weight of the dye molecule. By monitoring the FP of a fluorescent dye, one can detect significant changes in the molecular weight of the molecule without separation or purification. Because the size of the probe is altered in the course of a number of single nucleotide polymorphism (SNP) genotyping reactions, FP is therefore an excellent detection mechanism for these assays. Indeed, FP detection can be used in SNP genotyping with the primer extension TaqMan((R)) and Invader((R)) assays. Use of FP detection makes it possible to reduce the cost of TaqMan((R)) and Invader((R)) probes by abrogating the need for a fluorescence quencher. Moreover, inexpensive, unpurified, and unlabeled probes are used in the primer extension reaction with FP detection. As an end-point detection mechanism, FP detection is suitable for high-throughput SNP genotyping.
Corneal Endothelial Cytotoxicity of Riboflavin/UVA Treatment in vitro (2003)

Recently, we have developed collagen crosslinking induced by combined riboflavin/UVA treatment, thus increasing the biomechanical rigidity of the cornea to treat progressive keratoconus. The present safety study was performed to evaluate possible cytotoxic effects of combined riboflavin/UVA treatment on the corneal endothelium in vitro. Endothelial cell cultures from porcine corneas were treated with 500 microM riboflavin solution, exposed to various endothelial UVA irradiances (370 nm) ranging from 0.1 to 1.6 mW/cm2 for 30 min and evaluated 24 h later using trypan blue staining and Yopro fluorescence staining. The effect of either treatment alone (UVA irradiation ranging from 0.2 to 6 mW/cm2) was also tested. An abrupt cytotoxic threshold irradiance level was found at 0.35 mW/cm2 after combined treatment with riboflavin plus UVA irradiation and at 4 mW/cm2 with UVA irradiation alone. Riboflavin alone was not toxic. A cytotoxic effect of the combined riboflavin/UVA treatment on corneal endothelial cells is to be expected with a corneal thickness of less than 400 microm. Therefore, pachymetry should be routinely performed before riboflavin/UVA treatment to exclude patients at risk.
The Direct Catalytic Asymmetric Three-Component Mannich Reaction (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTThe Direct Catalytic Asymmetric Three-Component Mannich ReactionBenjamin ListView Author Information Departments of Molecular Biology and Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 Cite this: J. Am. Chem. Soc. 2000, 122, 38, 9336–9337Publication Date (Web):September 7, 2000Publication History Received1 June 2000Published online7 September 2000Published inissue 1 September 2000https://pubs.acs.org/doi/10.1021/ja001923xhttps://doi.org/10.1021/ja001923xrapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views17896Altmetric-Citations681LEARN 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 SUBJECTS:Aldehydes,Aldol reactions,Amines,Chemical reactions,Ketones Get e-Alerts
Pitch-based carbon fiber with low modulus and high heat conduction (2001)

Quite a wide variety of properties can be given to pitch-based carbon fiber by controlling its graphite crystal. Herein introduced are characteristics and applications of the low modulus carbon fiber and the high modulus,high heat conduction carbon fiber, both of which could not be produced from the PAN carbon fiber. These new fiber products manufactured and marketed by Nippon Graphite Fiber have unique characteristics hitherto unseen in other materials.
Adoptive T cell immunotherapy strategies for the treatment of patients with ovarian cancer. (2010)

Ovarian cancer is the leading cause of cancer death among gynecological malignances. Despite the initial successful multimodality therapy with cytoreductive surgery and subsequent combination chemotherapy, most patients with advanced disease will ultimately relapse and become incurable. For this reason novel therapeutic approaches for the treatment of this malignancy are urgently needed. Adoptive transfer of genetically modified autologous tumor-reactive T cells is a promising novel antitumor therapy for many cancers. T cells may be genetically modified ex vivo to express chimeric antigen receptors (CARs), which are artificial T cell receptors targeted to specific tumor antigens. The resulting T cells are thus programmed to recognize tumor cells. Ovarian carcinomas in particular appear to be suited to this therapeutic approach based on the fact that these tumors are relatively immunogenic, inducing an endogenous T cell response. Furthermore, the degree to which this endogenous T cell mediated immune response is evident correlates to long-term patient prognosis following surgery and chemotherapy. To this end, adoptive T cell immunotherapy strategies for the treatment of ovarian carcinomas appear to be particularly promising and are currently being investigated at several centers in both pre-clinical and clinical settings.
Number and continuous proliferative pattern of transplanted primitive immunohematopoietic stem cells. (1988)

We estimated numbers of transplantable primitive stem cells (PSCs) and found evidence that the same PSC continuously produced circulating erythrocytes and lymphocytes. These estimations used the binomial formula on data from recipients of identical portions of marrow mixtures containing two distinguishable cell types. Analysis of variance was used to compare repeated tests within each recipient. Values of pi s or pi c, probabilities that two independently sampled cells were descended from the same PSC, were also estimated, as this does not require the unverified condition that all PSCs contribute equally to the differentiated cell population. Several months after transplantation, erythrocytes were descended from only a single PSC per 1-2 X 10(5) marrow cells injected, several times rarer than previously reported. Percentages of erythrocyte and lymphocyte types in each recipient were closely correlated, with r values ranging from 0.86 to 0.94, in groups receiving 2-8 X 10(5) marrow cells; apparently the same precursors repopulated both myeloid and lymphoid lines in each recipient, as expected of true PSCs. Our data did not fit the clonal succession model, which predicts sequential activation of new PSCs and deactivation of old. Between 76 and 154 days, differentiated erythrocyte precursors were probably exhausted, with no evidence for new precursor activation or for further change between 154 and 250 days. The percentage of newly produced erythrocytes (reticulocytes) of each donor type varied little when individual recipients were followed between 165 and 295 days after transplantation, and variances within recipients were similar at marrow doses from 8 to 200 X 10(5) cells, further contradicting models of sequential activation and deactivation of PSC clones. Thus, transplanted PSCs were continually active during much of the recipient's lifespan.
Interleukin-27 directly induces differentiation in hematopoietic stem cells (2007)

Interleukin (IL)-27, one of the most recently discovered IL-6 family cytokines, activates both the signal transducer and activator of transcription (STAT)1 and STAT3, and plays multiple roles in pro- and anti-inflammatory immune responses. IL-27 acts on various types of cells including T, B, and macrophage through the common signal-transducing receptor gp130 and its specific receptor WSX-1, but the effect of IL-27 on hematopoietic stem cells (HSCs) remains unknown. Here, we show that IL-27 together with stem cell factor (SCF) directly acts on HSCs and supports their early differentiation in vitro and in vivo. CD34(-/low)c-Kit(+)Sca-1(+)lineage marker(-) (CD34(-)KSL) cells, a population highly enriched in mouse HSCs, were found to express both IL-27 receptor subunits. In vitro cultures of CD34(-)KSL cells with IL-27 and SCF resulted in an expansion of progenitors including short-term repopulating cells, while some of their long-term repopulating activity also was maintained. To examine its in vivo effect, transgenic mice expressing IL-27 were generated. These mice exhibited enhanced myelopoiesis and impaired B lymphopoiesis in the bone marrow with extramedullary hematopoiesis in the spleen. Moreover, IL-27 similarly acted on human CD34(+) cells. These results suggest that IL-27 is one of the limited cytokines that play a role in HSC regulation.
Unusually infrequent cleavage with several endonucleases and physical map construction of Bacillus subtilis bacteriophage phi 1 DNA (1981)

HaeIII, BalI, StuI, BamHI, SlaI, and EcoRII did not cut the genome of Bacillus subtilis phage phi 1 at all, whereas ThaI, BglII, EcoRI, SalI, and Bsu1247I cut the genome once or twice. The physical map of the phi 1 genome was constructed with the latter restriction endonucleases.
Capillary electrophoresis on microchip (2000)

Capillary electrophoresis and related techniques on microchips have made great strides in recent years. This review concentrates on progress in capillary zone electrophoresis, but also covers other capillary techniques such as isoelectric focusing, isotachophoresis, free flow electrophoresis, and micellar electrokinetic chromatography. The material and technologies used to prepare microchips, microchip designs, channel geometries, sample manipulation and derivatization, detection, and applications of capillary electrophoresis to microchips are discussed. The progress in separation of nucleic acids and proteins is particularly emphasized.
Engineering Escherichia coli for Increased Productivity of Serine-Rich Proteins Based on Proteome Profiling (2003)

Variations in proteome profiles of Escherichia coli in response to the overproduction of human leptin, a serine-rich (11.6% of total amino acids) protein, were examined by two-dimensional gel electrophoresis. The levels of heat shock proteins increased, while those of protein elongation factors, 30S ribosomal protein, and some enzymes involved in amino acid biosynthesis decreased, after leptin overproduction. Most notably, the levels of enzymes involved in the biosynthesis of serine family amino acids significantly decreased. Based on this information, we designed a strategy to enhance the leptin productivity by manipulating the cysK gene, encoding cysteine synthase A. By coexpression of the cysK gene, we were able to increase the cell growth rate by approximately twofold. Also, the specific leptin productivity could be increased by fourfold. In addition, we found that cysK coexpression can improve the production of another serine-rich protein, interleukin-12 beta chain, suggesting that this strategy may be useful for the production of other serine-rich proteins as well. The approach taken in this study should be useful in designing a strategy for improving recombinant protein production.
The contrast sensitivity of retinal ganglion cells of the cat (1966)

1. Spatial summation within cat retinal receptive fields was studied by recording from optic-tract fibres the responses of ganglion cells to grating patterns whose luminance perpendicular to the bars varied sinusoidally about the mean level. 2. Summation over the receptive fields of some cells (X-cells) was found to be approximately linear, while for other cells (Y-cells) summation was very non-linear. 3. The mean discharge frequency of Y-cells (unlike that of X-cells) was greatly increased when grating patterns drifted across their receptive fields. 4. In twenty-one X-cells the relation between the contrast and spatial frequency of drifting sinusoidal gratings which evoked the same small response was measured. In every case it was found that the reciprocal of this relation, the contrast sensitivity function, could be satisfactorily described by the difference of two Gaussian functions. 5. This finding supports the hypothesis that the sensitivities of the antagonistic centre and surround summating regions of ganglion cell receptive fields fall off as Gaussian functions of the distance from the field centre. 6. The way in which the sensitivity of an X-cell for a contrast-edge pattern varied with the distance of the edge from the receptive field centre was determined and found to be consistent with the cell's measured contrast sensitivity function. 7. Reducing the retinal illumination produced changes in the contrast sensitivity function of an X-cell which suggested that the diameters of the summating regions of the receptive field increased while the surround region became relatively ineffective.
Identification and Characterization of Microcin S, a New Antibacterial Peptide Produced by Probiotic Escherichia coli G3/10 (2012)

Escherichia coli G3/10 is a component of the probiotic drug Symbioflor 2. In an in vitro assay with human intestinal epithelial cells, E. coli G3/10 is capable of suppressing adherence of enteropathogenic E. coli E2348/69. In this study, we demonstrate that a completely novel class II microcin, produced by probiotic E. coli G3/10, is responsible for this behavior. We named this antibacterial peptide microcin S (MccS). Microcin S is coded on a 50.6 kb megaplasmid of E. coli G3/10, which we have completely sequenced and annotated. The microcin S operon is about 4.7 kb in size and is comprised of four genes. Subcloning of the genes and gene fragments followed by gene expression experiments enabled us to functionally characterize all members of this operon, and to clearly identify the nucleotide sequences encoding the microcin itself (mcsS), its transport apparatus and the gene mcsI conferring self immunity against microcin S. Overexpression of cloned mcsI antagonizes MccS activity, thus protecting indicator strain E. coli E2348/69 in the in vitro adherence assay. Moreover, growth of E. coli transformed with a plasmid containing mcsS under control of an araC PBAD activator-promoter is inhibited upon mcsS induction. Our data provide further mechanistic insight into the probiotic behavior of E. coli G3/10.
Idiotype Immunization Combined With Granulocyte-Macrophage Colony-Stimulating Factor in Myeloma Patients Induced Type I, Major Histocompatibility Complex–Restricted, CD8- and CD4-Specific T-Cell Responses (1998)

Abstract Idiotypic structures expressed on the myeloma Ig protein might be regarded as a tumor-specific antigen. Five patients with IgG myeloma were immunized with the purified serum M-component by repeated intradermal injections together with soluble granulocyte-macrophage colony-stimulating factor (GM-CSF). All patients developed an idiotype (Id)-specific T-cell immunity, defined as blood T cells predominantly secreting interferon-γ (IFN-γ) and interleukin-2 (IL-2) (type I cells). Id-specific DNA synthesis was induced in one patient. Delayed-type hypersensitivity against the Id was not evoked. The specific IFN-γ/IL-2 T-cell response was inhibited (46% to 100%) by a major histocompatibility complex (MHC) class I monoclonal antibody (MoAb) in all five patients. A 5% to 37% inhibition by an MHC class II MoAb was seen in four patients. CD4+ as well as CD8+ T cells enriched by magnetic microbeads contained Id-specific cells. The T cells recognized peptides corresponding to the complementarity-determining regions 1, 2, and 3 of the heavy chain of the Id. There was a transient rise of B cells producing IgM anti-idiotypic antibodies in all patients. The results indicate that immunization of myeloma patients using the autologous M-component and soluble GM-CSF may evoke an Id-specific predominantly MHC class I–restricted type I T-cell response.