bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Transcription Factor Analysis of Undifferentiated Single Human Embryonic Stem Cells
Authors: Ståhlberg Anders , Bengtsson Martin , Hemberg Martin , Semb Henrik 
Published: October 2009

Abstract
Background: Human embryonic stem cells (hESCs) require expression of transcription factor genes POU5F1 (POU class 5 homeobox 1), NANOG (Nanog homeobox), and SOX2 [SRY (sex determining region Y)-box 2] to maintain their capacity for self-renewal and pluripotency. Because of the heterogeneous nature of cell populations, it is desirable to study the gene regulation in single cells. Large and potentially important fluctuations in a few cells cannot be detected at the population scale with microarrays or sequencing technologies. We used single-cell gene expression profiling to study cell heterogeneity in hESCs.
Methods: We collected 47 single hESCs from cell line SA121 manually by glass capillaries and 57 single hESCs from cell line HUES3 by flow cytometry. Single hESCs were lysed and reverse-transcribed. Reverse-transcription quantitative real-time PCR was then used to measure the expression POU5F1, NANOG, SOX2, and the inhibitor of DNA binding genes ID1, ID2, and ID3. A quantitative noise model was used to remove measurement noise when pairwise correlations were estimated.
Results: The numbers of transcripts per cell varied &gt;100-fold between cells and showed lognormal features. POU5F1 expression positively correlated with ID1 and ID3 expression (P &lt; 0.05) but not with NANOG or SOX2 expression. When we accounted for measurement noise, SOX2 expression was also correlated with ID1, ID2, and NANOG expression (P &lt; 0.05).
Conclusions: We demonstrate an accurate method for transcription profiling of individual hESCs. Cell-to-cell variability is large and is at least partly nonrandom because we observed correlations between core transcription factors. High fluctuations in gene expression may explain why individual cells in a seemingly undifferentiated cell population have different susceptibilities for inductive cues.
Identification and characterisation of a novel GHR defect disrupting the polypyrimidine tract and resulting in GH insensitivity
Authors: David A , Miraki-Moud F , Shaw N J , Savage M O , Clark A J L , Metherell L A 
Published: October 2009

ObjectiveGH insensitivity (GHI) is caused in the majority of cases by impaired function of the GH receptor (GHR). All but one knownGHRmutation are in the coding sequence or the exon/intron boundaries. We identified and characterised the first intronic defect occurring in the polypyrimidine tract of theGHRin a patient with severe GHI.DesignWe investigated the effect of the novel defect on mRNA splicing using anin vitrosplicing assay and a cell transfection system.MethodsGHRwas analysed by direct sequencing. To assess the effect of the novel defect, two heterologous minigenes (wild-type and mutant L1-GHR8-L2) were generated by insertingGHRexon 8 and its flanking wild-type or mutant intronic sequences into a well-characterised splicing reporter (Adml-par L1–L2).32P-labelled pre-mRNA was generated from the two constructs and incubated in HeLa nuclear extracts or HEK293 cells.ResultsSequencing of theGHRrevealed a novel homozygous defect in the polypyrimidine tract of intron 7 (IVS7-6T>A). This base change does not involve the highly conserved splice site sequences, and is not predictedin silicoto affect GHR mRNA splicing. Nevertheless, skipping of exon 8 from the mutant L1-GHR8-L2 mRNA was clearly demonstrated in thein vitrosplicing assay and in transfected HEK293 cells.ConclusionDisruption of theGHRpolypyrimidine tract causes aberrant mRNA splicing leading to a mutant GHR protein. This is predicted to lack its transmembrane and intracellular domains and, thus, be incapable of transducing a GH signal.
Analysis of Injection/Falloff Data From Horizontal Wells
Authors: Boughrara Amina A. , Reynolds Albert C. 
Published: October 2009

Summary
We have constructed new approximate analytical solutions for injection and falloff pressure response that include thermal effects that arise when flooding a reservoir with water that has a temperature considerably lower than that of the reservoir. We have developed an optimization code based on the Levenberg-Marquardt algorithm and coupled it with our new approximate analytical solutions to obtain a procedure for data analysis where our approximate analytical solutions are used as the forward model in the nonlinear regression. We demonstrate that we can generate estimates of absolute permeabilities, the well skin factor, the length of the well and relative premeabilities by matching data to analytical solutions by minimization of a weighted least squares objective function. The relative permeability curves are constructed assuming a power law parametrization. In the horizontal well case, we show that the absolute permeabilities in the three principal directions can be resolved separately, provided the duration of the test is sufficiently long.
A New Organic Gel System for Water Control: a Computed Tomography Study
Authors: Al-Muntasheri Ghaithan A. , Zitha Pacelli L.J. , Nasr-El-Din Hisham A. 
Published: October 2009

SummaryBecause of their thermal stability, organically cross-linked gels have been used in conformance treatments for high-temperature applications. Most of these gels consist of a polyacrylamide-based polymer and an organic cross-linker. Polyethyleneimine (PEI) has been used as an organic cross-linker for polyacrylamide-based copolymers.Allison and Purkaple (1988) reported that PEI can form aqueous gels with simple polyacrylamide (PAM) at room temperature. In a previous study (Al-Muntasheri et al. 2008), we have shown that PEI can form ringing gels with polyacrylamide homopolymers at temperatures up to 130°C (266°F). In addition, the gelation kinetics of this system was reported up to 140°C (285°F). However, the placement of this system in porous media was not examined.In this study, the displacement of this gel system was visualized with computed tomography (CT) in sandstone cores. A permeability reduction of more than 94% was realized at 23°C for cores shut in at 50°C and 45°C.In addition to CT visualization, this study reports on the bulk testing of this system over a wide range of concentrations of PAM and PEI. Visual observation revealed the formation of stable gels for 3 weeks at 100°C (212°F). These gels were rigid and nonflowing at PAM concentrations of 5, 7, and 9 wt% cross-linked with PEI at concentrations from 0.5 to 3 wt%.
Active management of third stage of labor: evidence versus practice
Authors: OLADAPO OLUFEMI T. , AKINOLA OLUWAROTIMI I. , FAWOLE ADENIRAN O. , ADEYEMI ADEWALE S. , ADEGBOLA OMOLOLU , LOTO OLABISI M. , FABAMWO ADETOKUNBO O. , ALAO MOSES O. , SOTUNSA JOHN O. ,   for the Nigerian AMTSL Group
Published: October 2009

AbstractObjective. To determine the correct use of active management of third stage of labor (AMTSL) (using the full complement of existing standard definitions) and compare the outcomes of third stage of labor in women who received AMTSL (according to these definitions) with those who did not. Design. Observational, cross‐sectional survey. Setting. Seven tertiary centers in southwest Nigeria. Population. Women undergoing non‐instrumental vaginal deliveries. Methods. Prospective direct observations of childbirth procedures. AMTSL was defined according to Cochrane review, ICM/FIGO (International Confederation of Midwives/International Federation of Gynecology and Obstetrics), and WHO (World Health Organization) recommendations. Main outcome measures. Use of AMTSL and its components and outcome of third stage of labor. Results. There was a high rate of compliance with most of the individual components of AMTSL. The use of AMTSL varied widely with the definition applied and tended to decrease with increasing strictness of the criteria (Cochrane review: 88.9%; ICM/FIGO: 42%; WHO: 1.8%). The frequencies of adverse labor outcomes were generally low (postpartum hemorrhage (PPH): 4.9%; severe PPH: 0.8%; retained placenta: 1.9%; uterine inversion: 0.0%). Frequencies of PPH, postpartum anemia, and mean blood loss among women who received AMTSL according to the Cochrane review definition were significantly lower than for those who did not (p < 0.05). There was no significant difference between any of the outcomes for women who received AMTSL according to the ICM/FIGO definition and those who did not. Conclusions. The survey reveals substantial definition‐dependent variation in the providers' adherence to recommended AMTSL practices. The clinical implications of the current practice in this population suggest the need for randomized comparison of various AMTSL packages to determine their comparative effectiveness in the prevention of PPH.
Sodium Benzoate, a Metabolite of Cinnamon and a Food Additive, Reduces Microglial and Astroglial Inflammatory Responses
Authors: Brahmachari Saurav , Jana Arundhati , Pahan Kalipada 
Published: October 2009

Abstract
Upon activation, microglia and astrocytes produce a number of proinflammatory molecules that participate in the pathophysiology of several neurodegenerative disorders. This study explores the anti-inflammatory property of cinnamon metabolite sodium benzoate (NaB) in microglia and astrocytes. NaB, but not sodium formate, was found to inhibit LPS-induced expression of inducible NO synthase (iNOS), proinflammatory cytokines (TNF-α and IL-1β) and surface markers (CD11b, CD11c, and CD68) in mouse microglia. Similarly, NaB also inhibited fibrillar amyloid β (Aβ)-, prion peptide-, double-stranded RNA (polyinosinic-polycytidylic acid)-, HIV-1 Tat-, 1-methyl-4-phenylpyridinium+-, IL-1β-, and IL-12 p402-induced microglial expression of iNOS. In addition to microglia, NaB also suppressed the expression of iNOS in mouse peritoneal macrophages and primary human astrocytes. Inhibition of NF-κB activation by NaB suggests that NaB exerts its anti-inflammatory effect through the inhibition of NF-κB. Although NaB reduced the level of cholesterol in vivo in mice, reversal of the inhibitory effect of NaB on iNOS expression, and NF-κB activation by hydroxymethylglutaryl-CoA, mevalonate, and farnesyl pyrophosphate, but not cholesterol and ubiquinone, suggests that depletion of intermediates, but not end products, of the mevalonate pathway is involved in the anti-inflammatory effect of NaB. Furthermore, we demonstrate that an inhibitor of p21ras farnesyl protein transferase suppressed the expression of iNOS, that activation of p21ras alone was sufficient to induce the expression of iNOS, and that NaB suppressed the activation of p21ras in microglia. These results highlight a novel anti-inflammatory role of NaB via modulation of the mevalonate pathway and p21ras.
Resistance of Human Alveolar Macrophages toBacillus anthracisLethal Toxin
Authors: Wu Wenxin , Mehta Harshini , Chakrabarty Kaushik , Booth J. Leland , Duggan Elizabeth S. , Patel Krupa B. , Ballard Jimmy D. , Coggeshall K. Mark , Metcalf Jordan P. 
Published: October 2009

AbstractThe etiologic agent of inhalational anthrax, Bacillus anthracis, produces virulence toxins that are important in the disease pathogenesis. Current studies suggest that mouse and human macrophages are susceptible to immunosuppressive effects of one of the virulence toxins, lethal toxin (LT). Thus a paradigm has emerged that holds that the alveolar macrophage (AM) does not play a significant role in the innate immune response to B. anthracis or defend against the pathogen as it is disabled by LT. This is inconsistent with animal models and autopsy studies that show minimal disease at the alveolar surface. We examined whether AM are immunosuppressed by LT. We found that human AM were relatively resistant to LT-mediated innate immune cytokine suppression, MEK cleavage, and induction of apoptosis as compared with mouse RAW 264.7 macrophages. Mouse AM and murine bone marrow-derived macrophages were also relatively resistant to LT-mediated apoptosis despite intermediate sensitivity to MEK cleavage. The binding component of LT, protective Ag, does not attach to human AM, although it did bind to mouse AM, murine bone marrow-derived macrophages, and RAW 264.7 macrophages. Human AM do not produce significant amounts of the protective Ag receptor anthrax toxin receptor 1 (TEM8/ANTXR1) and anthrax toxin receptor 2 (CMG2/ANTXR2). Thus, mature and differentiated AM are relatively resistant to the effects of LT as compared with mouse RAW 264.7 macrophages. AM resistance to LT may enhance clearance of the pathogen from the alveolar surface and explain why this surface is relatively free of B. anthracis in animal models and autopsy studies.
Enhanced Tumor Metastasis in Response to Blockade of the Chemokine Receptor CXCR6 Is Overcome by NKT Cell Activation
Authors: Cullen Robyn , Germanov Elitza , Shimaoka Takeshi , Johnston Brent 
Published: October 2009

Abstract
Invariant NKT (iNKT) cells can induce potent antitumor responses in vivo. However, the mechanisms that regulate the effects of iNKT cells are unclear. The chemokine receptor CXCR6, and its ligand CXCL16, have been shown to play critical roles in iNKT cell homeostasis and activation. Thus we investigated the role of CXCR6 in protection against experimental metastasis of B16-F10 melanoma (B16) and Lewis lung carcinoma (LLC) cells to the liver and lungs. Wild-type and CXCR6−/− mice exhibited no differences in tumor cell metastasis to the lungs. However, metastasis of LLC and B16 tumor cells to the liver was enhanced in CXCR6−/− mice. Liver metastasis was also increased in wild-type mice treated with a CXCL16 neutralizing Ab. As Ab treatments did not alter iNKT cell numbers, this implicates a direct role for CXCR6/CXCL16 in regulating antitumor immunity. Cytokine induction was significantly attenuated in CXCR6−/− mice upon systemic iNKT cell activation with the glycolipid Ags α-galactosylceramide (α-GalCer), α-C-GalCer (a Th1 polarizing derivative), or OCH (a Th2 polarizing derivative). Despite differences in the levels of cytokine production, liver and lung metastasis were inhibited significantly in both wild-type and CXCR6−/− mice treated with glycolipids. Single doses of α-GalCer, α-C-GalCer, or OCH were sufficient to prevent liver metastasis and subsequent doses failed to elicit optimal cytokine responses. Our findings implicate a role for CXCR6 in natural immunosurveillance against liver metastasis. However, CXCR6 deficiency could be overcome by systemic iNKT cell activation, demonstrating that even suboptimal iNKT cell activation can protect against metastasis.
Nonfunctional Regulatory T Cells and Defective Control of Th2 Cytokine Production in Natural Scurfy Mutant Mice
Authors: Lahl Katharina , Mayer Christian T. , Bopp Tobias , Huehn Jochen , Loddenkemper Christoph , Eberl Gérard , Wirnsberger Gerald , Dornmair Klaus , Geffers Robert , Schmitt Edgar , Buer Jan , Sparwasser Tim 
Published: October 2009

Abstract
Foxp3+ regulatory T cells (Tregs) are crucial for preventing autoimmunity. We have demonstrated that depletion of Foxp3+ Tregs results in the development of a scurfy-like disease, indicating that Foxp3− effector T cells are sufficient to induce autoimmunity. It has been postulated that nonfunctional Tregs carrying potentially self-reactive T cell receptors may contribute to scurfy (sf) pathogenesis due to enhanced recognition of self. Those cells, however, could not be identified in sf mutants due to the lack of Foxp3 protein expression. To address this issue, we crossed the natural sf mouse mutant with bacterial artificial chromosome transgenic DEREG (depletion of regulatory T cells) mice. Since DEREG mice express GFP under the control of an additional Foxp3 promoter, those crossings allowed proving the existence of “would-be” Tregs, which are characterized by GFP expression in the absence of functional Foxp3. Sf Tregs lost their in vitro suppressive capacity. This correlated with a substantial reduction of intracellular cAMP levels, whereas surface expression of Treg markers was unaffected. Both GFP+ and GFP− sf cells produced high amounts of Th2-type cytokines, reflected also by enhanced Gata-3 expression, when tested in vitro. Nevertheless, sf Tregs could be induced in vitro, although with lower efficiency than DEREG Tregs. Transfer of GFP+ sf Tregs, in contrast to GFP− sf T cells, into RAG1-deficient animals did not cause the sf phenotype. Taken together, natural and induced Tregs develop in the absence of Foxp3 in sf mice, which lack both suppressive activity and autoreactive potential, but rather display a Th2-biased phenotype.
β1 Integrin-Dependent Engulfment of Yersinia enterocolitica by Macrophages Is Coupled to the Activation of Autophagy and Suppressed by Type III Protein Secretion
Authors: Deuretzbacher Anne , Czymmeck Nicole , Reimer Rudolph , Trülzsch Konrad , Gaus Kristin , Hohenberg Heinrich , Heesemann Jürgen , Aepfelbacher Martin , Ruckdeschel Klaus 
Published: October 2009

Abstract
Autophagy is a central lysosomal degradation process that is essential for the maintenance of cellular homeostasis. Autophagy has furthermore emerged as integral part of the host immune response. Autophagic processes promote the separation and degradation of intracellular microorganisms which contributes to the development of innate and adaptive immunity. Some pathogenic microbes have therefore evolved mechanisms to evade or impede autophagy. We analyzed the effects of the enteropathogenic bacterium Yersinia enterocolitica on autophagy in macrophages. Yersiniae use a number of defined adhesins and secreted proteins to manipulate host immune responses. Our results showed that Y. enterocolitica defective in type III protein secretion efficiently activated autophagy in macrophages. Autophagy was mediated by the Yersinia adhesins invasin and YadA and particularly depended on the engagement of β1 integrin receptors. Several autophagy-related events followed β1 integrin-mediated engulfment of the bacteria including the formation of autophagosomes, processing of the marker protein LC3, redistribution of GFP-LC3 to bacteria-containing vacuoles, and the segregation of intracellular bacteria by autophagosomal compartments. These results provide direct evidence for the linkage of β1 integrin-mediated phagocytosis and autophagy induction. Multiple microbes signal through integrin receptors, and our results suggest a general principle by which the sensing of an extracellular microbe triggers autophagy. Owing to the importance of autophagy as host defense response, wild-type Y. enterocolitica suppressed autophagy by mobilizing type III protein secretion. The subversion of autophagy may be part of the Y. enterocolitica virulence strategy that supports bacterial survival when β1 integrin-dependent internalization and autophagy activation by macrophages are deleterious for the pathogen.
CTL Clones Isolated from an HLA-Cw-Mismatched Bone Marrow Transplant Recipient with Acute Graft-Versus-Host Disease
Authors: Sugimoto Kyoko , Murata Makoto , Terakura Seitaro , Naoe Tomoki 
Published: October 2009

Abstract
HLA-Cw disparity in a donor increases the risk of acute graft-vs-host disease (GVHD) after bone marrow transplantation. Acute GVHD is mediated by donor CTLs. However, mismatched HLA-Cw-specific CTLs generated in posttransplant recipients who developed acute GVHD have not been characterized in detail. In this study, CTL clones isolated from a recipient at the onset of acute GVHD who was transplanted from an HLA-A, -B, and -DRB1-matched, HLA-Cw-mismatched (recipient, Cw*0303/Cw*0702; donor, Cw*0801/Cw*0702), unrelated donor were characterized. The seven isolated CTLs, including CD4+, CD8+, and CD4+CD8+ T lymphocytes, lysed recipient cells, HLA-Cw*0303-transfected 721.211 cells, and HLA-Cw*0303-transfected donor cells, but not untransfected 721.211 cells or donor cells. Thus, all CTLs recognized the mismatched Cw*0303 molecule as an alloantigen. The sequences of Cw*0303 and Cw*0801 differ by 16 aas. Stimulation of CTLs by COS cells transfected with Cw*0303 cDNA constructs demonstrated that Cw*0303 mutants in which individual amino acids constituting peptide-binding pockets were substituted with the corresponding Cw*0801 amino acids significantly decreased IFN-γ production by all CTLs, whereas Cw*0303 mutants bearing Cw*0801 amino acids outside the positions constituting peptide-binding pockets stimulated all CTLs to the same degree as the wild-type Cw*0303 construct. These data suggest that all CTLs recognized the Cw molecule in a peptide-dependent manner. ELISPOT revealed that Cw*0303-reactive T cells accounted for one-half of the total of alloreactive T cells in the blood during GVHD. Taken together, non-self Cw-specific CTL clones with a variety of phenotypes and peptide specificities can be generated in posttransplant recipients with acute GVHD.
Genetically Attenuated Parasite Vaccines Induce Contact-Dependent CD8+ T Cell Killing of Plasmodium yoelii Liver Stage-Infected Hepatocytes
Authors: Trimnell Adama , Takagi Akihide , Gupta Megha , Richie Thomas L. , Kappe Stefan H. , Wang Ruobing 
Published: October 2009

Abstract
The production of IFN-γ by CD8+ T cells is an important hallmark of protective immunity induced by irradiation-attenuated sporozoites against malaria. Here, we demonstrate that protracted sterile protection conferred by a Plasmodium yoelii genetically attenuated parasite (PyGAP) vaccine was completely dependent on CD8+ T lymphocytes but only partially dependent on IFN-γ. We used live cell imaging to document that CD8+ CTL from PyGAP-immunized mice directly killed hepatocyte infected with a liver stage parasite. Immunization studies with perforin and IFN-γ knockout mice also indicated that the protection was largely dependent on perforin-mediated effector mechanisms rather than on IFN-γ. This was further supported by our observation that both liver and spleen CD8+ T cells from PyGAP-immunized mice induced massive apoptosis of liver stage-infected hepatocytes in vitro without the release of detectable IFN-γ and TNF-α. Conversely, CD8+ T cells isolated from naive mice that had survived wild-type P. yoelii sporozoite infection targeted mainly sporozoite-traversed and uninfected hepatocytes, revealing an immune evasion strategy that might be used by wild-type parasites to subvert host immune responses during natural infection. However, CTLs from wild-type sporozoite-challenged mice could recognize and kill infected hepatocytes that were pulsed with circumsporozoite protein. Additionally, protection in PyGAP-immunized mice directly correlated with the magnitude of effector memory CD8+ T cells. Our findings implicate CTLs as key immune effectors in a highly protective PyGAP vaccine for malaria and emphasize the critical need to define surrogate markers for correlates of protection, apart from IFN-γ.