bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced growth and recombinant protein production of Escherichia coli by a perfluorinated oxygen carrier in miniaturized fed-batch cultures
Authors: Pilarek Maciej , Glazyrina Julia , Neubauer Peter 
Published: June 2011

Abstract

Background
Liquid perfluorochemicals (PFCs) are interesting oxygen carriers in medicine and biotechnology with a high solubility for oxygen. They have been repeatedly used for improving oxygen transfer into prokaryotic and eukaryotic cell cultures, however their application is still limited. Here we show the great benefit of air/oxygen saturated perfluorodecalin (PFD) for high cell density cultivation of Escherichia coli in microwell plates and their positive effect on the soluble production of a correctly folded heterologously expressed alcohol dehydrogenase.

Results
In EnBase® cultivations the best effect was seen with PFD saturated with oxygen enriched air (appr. 10 μM oxygen per ml) when PFD was added at the time of induction. In contrast the effect of PFD was negligible when it was added already at the time of inoculation. Optimisation of addition time and content of loaded oxygen into the PFD resulted in an increased the cell density by 40% compared to control cultures, and correspondingly also the product yield increased, demonstrated at the example of a recombinant alcohol dehydrogenase.

Conclusions
PFCs are a valuable additive in miniaturized cell culture formats. For production of recombinant proteins in low cell density shaken cultures the addition of oxygen-enriched PFD makes the process more robust, i.e. a high product yield is not any more limited to a very narrow cell density window during which the induction has to be done. The positive effect of PFD was even more obvious when it was added during high cell density cultures. The effect of the PFD phase depends on the amount of oxygen which is loaded into the PFD and which thus is a matter of optimisation.
Transcription and translation of human F11R gene are required for an initial step of atherogenesis induced by inflammatory cytokines
Authors: Azari Bani M , Marmur Jonathan D , Salifu Moro O , Ehrlich Yigal H , Kornecki Elizabeth , Babinska Anna 
Published: June 2011

AbstractBackground -The F11 Receptor (F11R; aka JAM-A, JAM-1) is a cell adhesion protein present constitutively on the membrane surface of circulating platelets and within tight junctions of endothelial cells (ECs). Previous reports demonstrated that exposure of ECs to pro-inflammatory cytokines causes insertion of F11R molecules into the luminal surface of ECs, ensuing with homologous interactions between F11R molecules of platelets and ECs, and a resultant adhesion of platelets to the inflamed ECs. The main new finding of the present report is that the first step in this chain of events is thede-novotranscription and translation of F11R molecules, induced in ECs by exposure to inflammatory cytokines.Methods -The experimental approach utilized isolated, washed human platelet suspensions and cultured human venous endothelial cells (HUVEC) and human arterial endothelial cells (HAEC) exposed to the proinflammatory cytokines TNF-alpha and/or IFN-gamma, for examination of the ability of human platelets to adhere to the inflamed ECs thru the F11R. Our strategy was based on testing the effects of the following inhibitors on this activity: general mRNA synthesis inhibitors, inhibitors of the NF-kappaB and JAK/STAT pathways, and small interfering F11R-mRNA (siRNAs) to specifically silence the F11R gene.Results -Treatment of inflamed ECs with the inhibitors actinomycin, parthenolide or with AG-480 resulted in complete blockade of F11R- mRNA expression, indicating the involvement of NF-kappaB and JAK/STAT pathways in this induction. Transfection of ECs with F11R siRNAs caused complete inhibition of the cytokine-induced upregulation of F11R mRNA and inhibition of detection of the newly- translated F11R molecules in cytokine-inflamed ECs. The functional consequence of the inhibition of F11R transcription and translation was the significant blockade of the adhesion of human platelets to inflamed ECs.Conclusion -These results prove thatde novosynthesis of F11R in ECs is required for the adhesion of platelets to inflamed ECs. Because platelet adhesion to an inflamed endothelium is crucial for plaque formation in non-denuded blood vessels, we conclude that thede-novotranslation of F11R is a crucial early step in the initiation of atherogenesis, leading to atherosclerosis, heart attacks and stroke.
Prediction of plant promoters based on hexamers and random triplet pair analysis
Authors: Azad AKM , Shahid Saima , Noman Nasimul , Lee Hyunju 
Published: June 2011

Abstract

Background
With an increasing number of plant genome sequences, it has become important to develop a robust computational method for detecting plant promoters. Although a wide variety of programs are currently available, prediction accuracy of these still requires further improvement. The limitations of these methods can be addressed by selecting appropriate features for distinguishing promoters and non-promoters.

Methods
In this study, we proposed two feature selection approaches based on hexamer sequences: the Frequency Distribution Analyzed Feature Selection Algorithm (FDAFSA) and the Random Triplet Pair Feature Selecting Genetic Algorithm (RTPFSGA). In FDAFSA, adjacent triplet-pairs (hexamer sequences) were selected based on the difference in the frequency of hexamers between promoters and non-promoters. In RTPFSGA, random triplet-pairs (RTPs) were selected by exploiting a genetic algorithm that distinguishes frequencies of non-adjacent triplet pairs between promoters and non-promoters. Then, a support vector machine (SVM), a nonlinear machine-learning algorithm, was used to classify promoters and non-promoters by combining these two feature selection approaches. We referred to this novel algorithm as PromoBot.

Results
Promoter sequences were collected from the PlantProm database. Non-promoter sequences were collected from plant mRNA, rRNA, and tRNA of PlantGDB and plant miRNA of miRBase. Then, in order to validate the proposed algorithm, we applied a 5-fold cross validation test. Training data sets were used to select features based on FDAFSA and RTPFSGA, and these features were used to train the SVM. We achieved 89% sensitivity and 86% specificity.

Conclusions
We compared our PromoBot algorithm to five other algorithms. It was found that the sensitivity and specificity of PromoBot performed well (or even better) with the algorithms tested. These results show that the two proposed feature selection methods based on hexamer frequencies and random triplet-pair could be successfully incorporated into a supervised machine learning method in promoter classification problem. As such, we expect that PromoBot can be used to help identify new plant promoters. Source codes and analysis results of this work could be provided upon request.
Arthritis is associated with T-cell-induced upregulation of Toll-like receptor 3 on synovial fibroblasts
Authors: Zhu Wenhua , Meng Liesu , Jiang Congshan , He Xiaojing , Hou Weikun , Xu Peng , Du Heng , Holmdahl Rikard , Lu Shemin 
Published: June 2011

Abstract
Introduction
Toll-like receptors (TLRs) are likely to play crucial roles in the pathogenesis of rheumatoid arthritis (RA). The aim of this study was to determine the key TLRs in synovium and explore their roles in the activation of fibroblast-like synoviocytes (FLSs) mediated by T cells in arthritis.

Methods
Pristane-induced arthritis (PIA) was established by subcutaneous injection with pristane at the base of the rat's tail. TLR expression in synovium from PIA rats was detected at different time points by performing real-time PCR. Polyinosinic:polycytidylic acid (poly(I:C)) was intra-articularly administrated to PIA rats, and arthritis was monitored macroscopically and microscopically. Synovial TLR3 was detected by immunohistochemical staining. Rat FLSs were stimulated with pristane-primed T cells or pristane-primed, T-cell conditioned medium. The intervention of TLR3 in FLSs was achieved by specific short-hairpin RNA (shRNA) or an antibody. The migration ability of FLSs was measured by using the scratch test, and gene expression was detected by using real-time PCR. FLSs from RA patients were stimulated with various cytokines and TLR ligands, and TLR3 expression was detected by performing real-time PCR. In addition, with different concentrations of poly(I:C) stimulation, TLR3 expression of FLSs from RA patients and patients with osteoarthritis (OA) was compared.

Results
Synovium TLR3 displayed early and persistent overexpression in PIA rats. TLR3 was expressed in FLSs, and local treatment with poly(I:C) synergistically aggravated the arthritis. Rat FLSs co-cultured with pristane-primed T cells showed strengthened migration ability and significant upregulation of TLR3, IFN-β, IL-6 and matrix metalloproteinase 3 (MMP3) expression, which could also be induced by pristane-primed, T-cell conditioned medium. The upregulation of cytokines and MMPs was blocked by shRNA or TLR3 antibodies. In RA FLSs with cytokine or TLR ligand stimulation, TLR3 expression exhibited remarkable upregulation. Furthermore, RA FLSs showed higher reactivity than OA FLSs to poly(I:C).

Conclusions
TLR3 in the synovium of PIA rats was overexpressed, and activation of the TLR3 signaling pathway could aggravate this arthritis. The induction of TLR3 in FLSs resulted from T cell-derived inflammatory stimulation and could further mediate FLS activation in arthritis. We conclude that TLR3 upregulation of FLSs activated by T cells results in articular inflammation.
Rac2 is required for the formation of neutrophil extracellular traps
Authors: Lim Michael Byung H , Kuiper Jan W P , Katchky Ashley , Goldberg Hailey , Glogauer Michael 
Published: June 2011

ABSTRACTNeutrophils play a critical role as a first line of defense against invading pathogens. Recently, a new defense strategy of neutrophils was described, in which pathogens are trapped and killed by NETs. However, the exact underlying mechanisms leading to the formation of NETs remain elusive. Here, we explored the role of the Rac small GTPases in the formation of NETs using neutrophils that lack Rac1, Rac2, or both isoforms. Efficient NET formation was observed in WT and Rac1null neutrophils. In contrast, NET formation was markedly impaired in cells lacking Rac2 or both Rac2 and Rac1. The defect in NET formation in Rac2null cells was rescued by exogenous ROS sources, suggesting that Rac2-mediated ROS generation is required for NET formation. In addition, we assessed the role of NO in NET formation in mouse neutrophils. Blocking NO production with the NOS inhibitor L-NAME significantly reduced NET formation. Moreover, we show that Rac2null cells produce significantly less NO than Rac1null cells or their WT counterparts. Our data suggest that Rac2 is essential for NET formation via pathways involving ROS and NO.
Comparison of 18F-FDG PET/CT with bone scintigraphy for detection of bone metastasis: a meta-analysis
Authors: Cheng Xu , Li Yongjun , Xu Zhaoqiang , Bao Lihua , Li Dianfu , Wang Jie 
Published: June 2011

Background The skeleton is one of the favorable sites for the metastasis of almost all human malignant neoplasms. An accurate diagnosis of bone metastasis is crucial for the patient's staging and management. Purpose To investigate and compare diagnostic performance of 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) and bone scintigraphy (BS) for detection of bone metastasis in malignancies using meta-analysis. Material and Methods PubMed (Medline included) was searched for relevant articles. We assessed the methodological quality with Quality Assessment of Diagnosis Accuracy Studies (QUADAS) score tool, and used statistical software to obtain pooled estimates of sensitivity, specificity, diagnostic odds ratio (DOR), and summary receiver-operating characteristic (SROC) curve. Results Six studies met inclusion criteria. For 18F-FDG PET/CT, the pooled sensitivity and specificity were 0.934 and 0.975, respectively. The pooled positive likelihood ratio (LR+), negative likelihood ratio (LR–) and diagnostic odds ratio (DOR) were 34.990, 0.068 and 559.02, respectively. The area under the SROC curve was 0.9854. For BS, the pooled sensitivity, specificity, LR + , LR– and DOR were 0.706 (0.642–0.764), 0.911 (0.896–0.926), 13.982 (2.419–80.817), 0.319 (0.143–0.712), and 60.420 (21.393–170.64), respectively. The area under the SROC curve was 0.9386. Conclusion The results indicate that 18F-FDG PET/CT do have both higher sensitivity and specificity than bone scintigraphy for detecting metastatic bone tumor. However, further research is needed to evaluate the diagnostic performance of 18F-FDG PET/CT and BS in each common malignancy.
Entextualizing institutional memories: retelling the academic story
Authors: Cook-Gumperz Jenny 
Published: June 2011

AbstractThis paper explores the making of academic knowledge as discourse. It reports on the closing down of an academic program based on memories reconstructed through narrative interviews of two professors who organized this program. A narrative analysis of the two long interviews contrasting performance styles reveals differences in response by the two professors, even though their position within the institution is nominally the same. Their tales emerge through the multiple layering of their discourse as moral commentaries of their life and times, albeit from two very different perspectives. The narratives unfold through retellings; the tale shifts to a moral commentary on participants' actions that reveals the longevity of institutionally shaped ways of thinking.
Development and Calibration of an Electronic Miniature Cone Penetrometer for Design of Small Piles in Silty Clays
Authors: Cui Xinzhuang 
Published: June 2011

Abstract
For the design of shallowly embedded small size pile under lateral load, a new kind of electronic miniature cone penetrometer is developed. And a novel mini calibration chamber is also designed to form homogeneous soil specimens for miniature cone penetration test (MCPT) in laboratory. A series of MCPTs and pile loading tests in silty clay are carried out. For silty clay, penetration curve has no correlation with cone angles within the tested range of 19° to 32°. The initial segment of penetration curve is linear for silty clay. However, the cone tip resistance tends to be stable when the cone is penetrated to a certain depth. It is implied that the critical depth effect occurs for MCPT of silty clay. For silty clay, the critical depth effect is caused by different soil failure mechanisms under different confining pressures. The lateral bearing capacity and stiffness of small size pile are all directly related to the ultimate cone tip resistance of soil. It is concluded that the miniature cone penetrometer is an effective apparatus for the design of small size shallowly embedded pile.
Media Use and Child Sleep: The Impact of Content, Timing, and Environment
Authors: Garrison Michelle M. , Liekweg Kimberly , Christakis Dimitri A. 
Published: June 2011

BACKGROUND:
Media use has been shown to negatively affect a child's sleep, especially in the context of evening use or with a television in the child's bedroom. However, little is known about how content choices and adult co-use affect this relationship.

OBJECTIVE:
To describe the impact of media content, timing, and use behaviors on child sleep.

METHODS:
These data were collected in the baseline survey and media diary of a randomized controlled trial on media use in children aged 3 to 5 years. Sleep measures were derived from the Children's Sleep Habits Questionnaire. Media diaries captured time, content title, and co-use of television, video-game, and computer usage; titles were coded for ratings, violence, scariness, and pacing. Nested linear regression models were built to examine the impact of timing, content, and co-use on the sleep problem score.

RESULTS:
On average, children consumed 72.9 minutes of media screen time daily, with 14.1 minutes occurring after 7:00 pm. Eighteen percent of parents reported at least 1 sleep problem; children with a bedroom television consumed more media and were more likely to have a sleep problem. In regression models, each additional hour of evening media use was associated with a significant increase in the sleep problem score (0.743 [95% confidence interval: 0.373–1.114]), as was daytime use with violent content (0.398 [95% confidence interval: 0.121–0.676]). There was a trend toward greater impact of daytime violent use in the context of a bedroom television (P = .098) and in low-income children (P = .07).

CONCLUSIONS:
Violent content and evening media use were associated with increased sleep problems. However, no such effects were observed with nonviolent daytime media use.
A Prospective, Controlled Study of the Botanical Compound Mixture LCS101 for Chemotherapy-Induced Hematological Complications in Breast Cancer
Authors: Yaal-Hahoshen Neora , Maimon Yair , Siegelmann-Danieli Nava , Lev-Ari Shahar , Ron Ilan G. , Sperber Fani , Samuels Noah , Shoham Jacob , Merimsky Ofer 
Published: June 2011

Abstract

Background.
This prospective, controlled study evaluated the safety, tolerability, and efficacy of the mixture of botanical compounds known as LCS101 in preventing chemotherapy-induced hematological toxicity in breast cancer patients.

Methods.
Female patients diagnosed with localized breast cancer were randomly allocated to receive treatment with either LCS101 or placebo capsules, in addition to conventional chemotherapy. The study intervention was initiated 2 weeks prior to the initiation of chemotherapy and continued until chemotherapy was completed, with participants receiving 2 g of LCS101 capsules thrice daily. Subjects were assessed for the development of hematological and nonhematological toxicities, as well as the tolerability and safety of the study intervention.

Results.
Sixty-five breast cancer patients were recruited, with 34 allocated to LCS101 and 31 allocated to placebo treatment. Patients in the treatment group developed significantly less severe (grades 2–4) anemia (p &lt; .01) and leukopenia (p &lt; .03) when comparing grades 0–1 with grades 2–4, with significantly less neutropenia (p &lt; .04) when comparing grades 0–2 with grades 3–4. This effect was more significant among patients undergoing a dose-dense regimen. No statistically significant effect was found with respect to nonhematological toxicities, and side effect rates were not significantly different between the groups, with no severe or life-threatening events observed in either group.

Conclusion.
The addition of LCS101 to anthracycline- and taxane-based chemotherapy is safe and well tolerated, and may significantly prevent some chemotherapy-induced hematological toxicities in early breast cancer patients. These results should encourage further larger and more extensive clinical trials.
Gestational Diabetes Mellitus in Relation to Maternal Dietary Heme Iron and Nonheme Iron Intake
Authors: Qiu Chunfang , Zhang Cuilin , Gelaye Bizu , Enquobahrie Daniel A. , Frederick Ihunnaya O. , Williams Michelle A. 
Published: June 2011

OBJECTIVE
Higher heme iron intake is associated with increased type 2 diabetes risk. However, no previous study has evaluated gestational diabetes mellitus (GDM) risk in relation to heme iron intake during pregnancy. We investigated associations of maternal preconceptional and early pregnancy heme and nonheme iron intake with subsequent GDM risk.

RESEARCH DESIGN AND METHODS
We conducted a prospective cohort study of 3,158 pregnant women. A food frequency questionnaire was used to assess maternal diet. Multivariable generalized linear regression models were used to derive estimates of relative risks (RRs) and 95% CIs.

RESULTS
Approximately 5.0% of the cohort developed GDM (n = 158). Heme iron intake was positively and significantly associated with GDM risk (Ptrend = 0.04). After adjusting for confounders, women reporting the highest heme iron intake levels (≥1.52 vs. &lt;0.48 mg per day) experienced a 3.31-fold–increased GDM risk (95% CI 1.02–10.72). In fully adjusted models, we noted that a 1-mg per day increase in heme iron was associated with a 51% increased GDM risk (RR 1.51 [95% CI 0.99–2.36]). Nonheme iron was inversely, though not statistically significantly, associated with GDM risk, and the corresponding RRs were 1.00, 0.83, 0.62, and 0.61 across quartiles of nonheme iron intake (Ptrend = 0.08).

CONCLUSIONS
High levels of dietary heme iron intake during the preconceptional and early pregnancy period may be associated with increased GDM risk. Associations of GDM risk with dietary nonheme iron intake are less clear. Confirmation of these findings by future studies is warranted.
Glomerular Dysfunction and Associated Risk Factors over 4–5 Years following Antiretroviral Therapy Initiation in Africa
Authors:   the DART Trial Team, Stöhr Wolfgang , Reid Andrew , Walker A Sarah , Ssali Francis , Munderi Paula , Mambule Ivan , Kityo Cissy , Grosskurth Heiner , Gilks Charles F , Gibb Diana M , Hakim James 
Published: June 2011

Background The aim of this study was to investigate long-term renal function in HIV-infected adults initiating antiretroviral therapy (ART) with a CD4+ T-cell count <200 cells/mm3 in Africa. Methods This was an observational analysis within the DART trial randomizing 3,316 adults to routine laboratory and clinical monitoring (LCM) or clinically driven monitoring (CDM). Serum creatinine was measured pre-ART (all ≤360 μmol/l), at weeks 4 and 12, then every 12 weeks for 4-5 years; estimated glomerular filtration rate (eGFR) was determined using the Cockcroft-Gault formula. We analysed eGFR changes, and cumulative incidences of eGFR<30 ml/min/1.73 m2 and chronic kidney disease (CKD; <60 ml/min/1.73 m2 or 25% decrease if <60 ml/min/1.73 m2 pre-ART; confirmed >3 months). Results At ART initiation, median CD4+ T-cell count was 86 cells/mm3; 1,492 (45%) participants had mild (60–<90 ml/min/1.73 m2), 237 (7%) moderate (30–<60 ml/min/1.73 m2) and 7 (0.2%) severe (15–<30 ml/min/1.73 m2) decreases in eGFR. First-line ART was zidovudine/lamivudine plus tenofovir (74%), abacavir (9%) or nevirapine (17%). By 4 years, cumulative incidence of eGFR<30 ml/min/1.73 m2 was 2.8% ( n=90) and CKD was 5.0% ( n=162). Adjusted eGFR increases to 4 years were 1, 9 and 6 ml/min/1.73 m2 with tenofovir, abacavir and nevirapine, respectively ( P<0.001), and 4 and 2 ml/min/1.73 m2 for LCM and CDM, respectively ( P=0.005; 2 and 3 ml/min/1.73 m2 to 5 years; P=0.81). Conclusions On all regimens and monitoring strategies, severe eGFR impairment was infrequent; differences in eGFR changes were small, suggesting that first-line ART, including tenofovir, can be given safely without routine renal function monitoring.
La pulsion esthétique
Authors: Chouvel Jean-Marc 
Published: June 2011

Résumé La notion de pulsion élaborée par la psychanalyse ne donne guère de place à la jouissance esthétique, sauf à en faire un substitut ou une « sublimation » de la pulsion sexuelle. Cette manière de concevoir la réalité du phénomène artistique fait trop peu de cas d’une motivation essentielle du vivant, qui tourne autour de la notion de beauté. La musique est plus particulièrement cet art qui nous parle sans que nous en connaissions la langue. Il s’agira de sonder, à travers l’histoire de la pensée – et à travers le miroir du temps – ce qui fait de l’esthétique le moment le plus intense de la manifestation d’un inconscient qui est autant dans notre corps et dans nos sens que dans notre tête, et qui est autant dans le monde qu’en nous-même.