bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specialty Supplement Use and Biologic Measures of Oxidative Stress and DNA Damage
Authors: Kantor Elizabeth D. , Ulrich Cornelia M. , Owen Robert W. , Schmezer Peter , Neuhouser Marian L. , Lampe Johanna W. , Peters Ulrike , Shen Danny D. , Vaughan Thomas L. , White Emily 
Published: August 2013

Abstract
Background: Oxidative stress and resulting cellular damage have been suggested to play a role in the etiology of several chronic diseases, including cancer and cardiovascular disease. Identifying factors associated with reduced oxidative stress and resulting damage may guide future disease-prevention strategies.
Methods: In the VITamins And Lifestyle (VITAL) biomarker study of 209 persons living in the Seattle area, we examined the association between current use of several specialty supplements and oxidative stress, DNA damage, and DNA repair capacity. Use of glucosamine, chondroitin, fish oil, methylsulfonylmethane (MSM), coenzyme Q10 (CoQ10), ginseng, ginkgo, and saw palmetto was ascertained by a supplement inventory/interview, whereas the use of fiber supplements was ascertained by questionnaire. Supplements used by more than 30 persons (glucosamine and chondroitin) were evaluated as the trend across number of pills/week (non-use, &lt;14 pills/week, 14+ pills/week), whereas less commonly used supplements were evaluated as use/non-use. Oxidative stress was measured by urinary 8-isoprostane and PGF2α concentrations using enzyme immunoassays (EIA), whereas lymphocyte DNA damage and DNA repair capacity were measured using the Comet assay. Multivariate-adjusted linear regression was used to model the associations between supplement use and oxidative stress/DNA damage.
Results: Use of glucosamine (Ptrend: 0.01), chondroitin (Ptrend: 0.003), and fiber supplements (P: 0.01) was associated with reduced PGF2α concentrations, whereas CoQ10 supplementation was associated with reduced baseline DNA damage (P: 0.003).
Conclusions: Use of certain specialty supplements may be associated with reduced oxidative stress and DNA damage.
Impact: Further research is needed to evaluate the association between specialty supplement use and markers of oxidative stress and DNA damage. Cancer Epidemiol Biomarkers Prev; 22(12); 2312–22. ©2013 AACR.
Integration of Metabolomics and Transcriptomics Revealed a Fatty Acid Network Exerting Growth Inhibitory Effects in Human Pancreatic Cancer
Authors: Zhang Geng , He Peijun , Tan Hanson , Budhu Anuradha , Gaedcke Jochen , Ghadimi B. Michael , Ried Thomas , Yfantis Harris G. , Lee Dong H. , Maitra Anirban , Hanna Nader , Alexander H. Richard , Hussain S. Perwez 
Published: August 2013

Abstract
Purpose: To identify metabolic pathways that are perturbed in pancreatic ductal adenocarcinoma (PDAC), we investigated gene-metabolite networks with integration of metabolomics and transcriptomics.
Experimental Design: We conducted global metabolite profiling analysis on two independent cohorts of resected PDAC cases to identify critical metabolites alteration that may contribute to the progression of pancreatic cancer. We then searched for gene surrogates that were significantly correlated with the key metabolites, by integrating metabolite and gene expression profiles.
Results: Fifty-five metabolites were consistently altered in tumors as compared with adjacent nontumor tissues in a test cohort (N = 33) and an independent validation cohort (N = 31). Weighted network analysis revealed a unique set of free fatty acids (FFA) that were highly coregulated and decreased in PDAC. Pathway analysis of 157 differentially expressed gene surrogates revealed a significantly altered lipid metabolism network, including key lipolytic enzymes PNLIP, CLPS, PNLIPRP1, and PNLIPRP2. Gene expressions of these lipases were significantly decreased in pancreatic tumors as compared with nontumor tissues, leading to reduced FFAs. More importantly, a lower gene expression of PNLIP in tumors was associated with poorer survival in two independent cohorts. We further showed that two saturated FFAs, palmitate and stearate, significantly induced TRAIL expression, triggered apoptosis, and inhibited proliferation in pancreatic cancer cells.
Conclusions: Our results suggest that impairment in a lipolytic pathway involving lipases, and a unique set of FFAs, may play an important role in the development and progression of pancreatic cancer and provide potential targets for therapeutic intervention. Clin Cancer Res; 19(18); 4983–93. ©2013 AACR.
Subtype-Specific MEK-PI3 Kinase Feedback as a Therapeutic Target in Pancreatic Adenocarcinoma
Authors: Mirzoeva Olga K. , Collisson Eric A. , Schaefer Peter M. , Hann Byron , Hom Yun K. , Ko Andrew H. , Korn W. Michael 
Published: August 2013

Abstract
Mutations in the KRAS oncogene are dominant features in pancreatic ductal adenocarcinoma (PDA). Because KRAS itself is considered “undruggable,” targeting pathways downstream of KRAS are being explored as a rational therapeutic strategy. We investigated the consequences of MAP–ERK kinase (MEK) inhibition in a large PDA cell line panel. Inhibition of MEK activated phosphoinositide 3-kinase in an EGF receptor (EGFR)-dependent fashion and combinations of MEK and EGFR inhibitors synergistically induced apoptosis. This combinatorial effect was observed in the epithelial but not mesenchymal subtype of PDA. RNA expression analysis revealed predictors of susceptibility to the combination, including E-cadherin, HER3, and the miR200-family of microRNAs, whereas expression of the transcription factor ZEB1 was associated with resistance to the drug combination. Knockdown of HER3 in epithelial-type and ZEB1 in mesenchymal-type PDA cell lines resulted in sensitization to the combination of MEK and EGFR inhibitors. Thus, our findings suggest a new, subtype-specific, and personalized therapeutic strategy for pancreatic cancer. Mol Cancer Ther; 12(10); 2213–25. ©2013 AACR.
Transcriptional Regulation of CXCR4 in Prostate Cancer: Significance of TMPRSS2-ERG Fusions
Authors: Singareddy Rajareddy , Semaan Louie , Conley-LaComb M. Katie , St. John Jason , Powell Katelyn , Iyer Matthew , Smith Daryn , Heilbrun Lance K. , Shi Dongping , Sakr Wael , Cher Michael L. , Chinni Sreenivasa R. 
Published: August 2013

Abstract
CXCR4 is a chemokine receptor that mediates invasion and metastasis. CXCR4 expression is transcriptionally regulated in cancer cells and is associated with aggressive prostate cancer phenotypes. Previously, we and others have shown that the transcription factor ERG regulates CXCR4 expression in prostate cancer cells and that androgens modulate CXCR4 expression via increasing ERG expression. Herein, the molecular mechanisms of ERG-mediated CXCR4 promoter activation, phosphorylation of ERG by intracellular kinases and subsequent CXCR4 expression, as well as the status of ERG and CXCR4 in human prostate cancer specimens were investigated. Using multiple molecular strategies, it was demonstrated that (i) ERG expressed in TMPRSS2-ERG fusion positive VCaP cells selectively binds to specific ERG/Ets bindings sites in the CXCR4 promoter; (ii) distal binding sites mediate promoter activation; (iii) exogenously expressed ERG promotes CXCR4 expression; (iv) ERG is phosphorylated at Serine-81 and -215, by both IKK and Akt kinases, and Akt mediates CXCR4 expression; (v) ERG-induced CXCR4 drives CXCL12-dependent adhesion to fibronectin; and (vi) ERG and CXCR4 were coexpressed in human prostate cancer tissue, consistent with ERG-mediated transcriptional activation of CXCR4. These data demonstrate that ERG activates CXCR4 expression by binding to specific ERG/Ets responsive elements and via intracellular kinases that phosphorylate ERG at discrete serine residues.
Implications: These findings provide a mechanistic link between TMPRSS2-ERG translocations and intracellular kinase-mediated phosphorylation of ERG on enhanced metastasis of tumor cells via CXCR4 expression and function in prostate cancer cells. Mol Cancer Res; 11(11); 1349–61. ©2013 AACR.
A Solo-Based Automated Quality Control Algorithm for Airborne Tail Doppler Radar Data
Authors: Bell Michael M. , Lee Wen-Chau , Wolff Cory A. , Cai Huaqing 
Published: August 2013

AbstractAn automated quality control preprocessing algorithm for removing nonweather radar echoes in airborne Doppler radar data has been developed. This algorithm can significantly reduce the time and experience level required for interactive radar data editing prior to dual-Doppler wind synthesis or data assimilation. The algorithm uses the editing functions in the Solo software package developed by the National Center for Atmospheric Research to remove noise, Earth-surface, sidelobe, second-trip, and other artifacts. The characteristics of these nonweather radar returns, the algorithm to identify and remove them, and the impacts of applying different threshold levels on wind retrievals are presented. Verification was performed by comparison with published Electra Doppler Radar (ELDORA) datasets that were interactively edited by different experienced radar meteorologists. Four cases consisting primarily of convective echoes from the Verification of the Origins of Rotation in Tornadoes Experiment (VORTEX), Bow Echo and Mesoscale Convective Vortex Experiment (BAMEX), Hurricane Rainband and Intensity Change Experiment (RAINEX), and The Observing System Research and Predictability Experiment (THORPEX) Pacific Asian Regional Campaign (T-PARC)/Tropical Cyclone Structure-2008 (TCS08) field experiments were used to test the algorithm using three threshold levels for data removal. The algorithm removes 80%, 90%, or 95% of the nonweather returns and retains 95%, 90%, or 85% of the weather returns on average at the low-, medium-, and high-threshold levels. Increasing the threshold level removes more nonweather echoes at the expense of also removing more weather echoes. The low threshold is recommended when weather retention is the highest priority, and the high threshold is recommended when nonweather removal is the highest priority. The medium threshold is a good compromise between these two priorities and is recommended for general use. Dual-Doppler wind retrievals using the automatically edited data compare well to retrievals from interactively edited data.
A Variational Method for Estimating Surface Fluxes with Mass Conservation Constraint
Authors: Li Sen , Zhong Zhong , Guo Weidong , Lu Wei 
Published: August 2013

AbstractOn the basis of the similarity theory of the atmospheric surface layer and the mass conservation principle, a new scheme using a variational method is developed to estimate the surface momentum and sensible and latent heat fluxes. In this scheme, the mass conservation is introduced into the cost function as a weak physical constraint, which leads to an overdetermined system. For the variational method with mass conservation constraint, only the conventional meteorological observational data are taken into account. Data collected in the Yellow River Source Region Climate and Environment Observation and Research Station at Maqu, China, during 11–25 August 2010 are used to test this new scheme. Results indicate that this scheme is more reliable and accurate than both the flux-profile method and the variational method without mass conservation constraint. In addition, the effect of the weights in the cost function is examined. Sensitivity tests show that the fluxes estimated by the proposed scheme are insensitive to the stability functions explored in the cost function and measurement errors.
Comments on “Preconditioning Deep Convection with Cumulus Congestus”
Authors: Schultz David M. 
Published: August 2013

Abstract
The hypothesis that cumulus congestus clouds in the tropics moisten dry layers above the boundary layer and promote the formation of deep moist convection was tested by Hohenegger and Stevens. This comment asks whether their hypothesis is also true for cumulus congestus clouds and deep moist convection in the midlatitudes. This comment also requests clarification on how their expression for moisture convergence is calculated and used in their article, especially in light of previous studies showing that moisture flux convergence is a less-than-adequate diagnostic for convection initiation and that deep moist convection requires sufficient lift and instability, in addition to sufficient moisture.
Altered brain metabolism in vestibular migraine: Comparison of interictal and ictal findings
Authors: Shin Jung H , Kim Yu K , Kim Hyo-Jung , Kim Ji-Soo 
Published: August 2013

Background Vestibular symptoms/signs frequently coexist with migraine, but the mechanisms of migraine-related vestibular dysfunction remain to be elucidated. This study aimed to determine altered brain metabolism in vestibular migraine. Methods Two patients with vestibular migraine underwent 18F-fluorodeoxy glucose (FDG) positron-emission tomography (PET) during and between attacks of vestibular migraine in addition to detailed neurotological evaluation. We analyzed the regional brain metabolism of the patients in comparison with that of age-matched healthy controls in each patient. We also compared ictal with interictal FDG PET using a subtraction method. Results During the attacks, both patients showed an activation of the bilateral cerebellum and frontal cortices, and deactivation of the bilateral posterior parietal and occipitotemporal areas. One patient also showed hypermetabolism in the dorsal pons and midbrain, right posterior insula, and right temporal cortex while the other patient had an additional activation of the left temporal cortex. Compared with interictal images, ictal PET showed increased metabolism in the bilateral cerebellum, frontal cortices, temporal cortex, posterior insula, and thalami. Conclusion During the attacks of vestibular migraine, the increased metabolism in the temporo-parieto-insular areas and bilateral thalami indicates activation of the vestibulo-thalamo-cortical pathway, and decreased metabolism in the occipital cortex may represent reciprocal inhibition between the visual and vestibular systems.
Supramolecular ferric porphyrins and a cyclodextrin dimer as antidotes for cyanide poisoning
Authors: Yamagiwa T , Kawaguchi AT , Saito T , Inoue S , Morita S , Watanabe K , Kitagishi H , Koji K , Inokuchi S 
Published: August 2013

Objectives: This study aimed to evaluate the antidotal effect of a newly developed supramolecular complex, ferric porphyrins and a cyclodextrin dimer (FeIIIPIm3CD), that possess a higher binding constant and quicker binding rate to cyanide ions than those of hydroxocobalamin (OHCbl) in the presence of serum protein. Methods: First, in vitro cytochrome activity and cell viability were evaluated in murine fibroblast cells cultured with various doses of FeIIIPIm3CD and potassium cyanide (KCN). Next, BALB/c mice were pretreated with intravenous OHCbl (0.23 mmol/kg), FeIIIPIm3CD (0.23 mmol/kg), or saline and then received KCN (lethal dose 100% (LD100): 0.23 mmol/kg) through a stomach tube. Finally, as a resuscitation model, KCN-induced apnea was treated with a bolus injection of an equimolar dose of antidotes followed by a slow infusion of the same reagent. Results: FeIIIPIm3CD showed dose-dependent antidotal effects in vitro. Pretreatment with FeIII PIm3CD prevented KCN-induced apnea significantly better than OHCbl. Resuscitation with FeIIIPIm3CD resulted in an earlier resumption of respiration than that seen with OHCbl. However, 24-h survival was similar among the treatments (FeIIIPIm3CD, nine of nine mice; OHCbl, eight of nine mice). Conclusion: FeIIIPIm3CD exerted significant antidotal effects on cyanide toxicity in vitro and in vivo, with a potency equal in the mortality of cyanide-poisoned mice or superior in the respiratory status during an acute phase to those of OHCbl.
Self-Reported Preconception Care of HIV-Positive Women of Reproductive Potential
Authors: Loutfy Mona R. , Blitz Sandra , Zhang Yimeng , Hart Trevor A. , Walmsley Sharon L. , Smaill Fiona M. , Rachlis Anita R. , Yudin Mark H. , Angel Jonathan B. , Ralph Edward D. , Tharao Wangari , Raboud Janet M. ,   for the Ontario HIV Fertility Research Team
Published: August 2013

Objectives: We determined the proportion and correlates of self-reported pregnancy planning discussions (that is preconception counseling) that HIV-positive women reported to their family physicians (FPs), HIV specialists, and obstetrician/gynecologists (OB/Gyns). Methods: In a cross-sectional substudy, HIV-positive women of reproductive potential were asked whether their care providers discussed pregnancy planning. Logistic regression was used to calculate odds ratios for the correlates of preconception counseling. Results: A total of 431 eligible participants (median age 38, interquartile range = 32-43) reported having discussion with a physician (92% FP, 96% HIV specialists, and 45% OB/Gyns). In all, 34%, 41%, and 38% had their pregnancy planning discussion with FP, HIV specialist, and Ob/Gyns, respectively; 51% overall. In the multivariable model, significant correlates of preconception counseling were age ( P = .02), marital status ( P < .01), number of years living in Canada ( P < .001), and age of youngest child ( P < .01). Conclusions: Preconception care in our cohort was suboptimal. We recommend that counseling on healthy preconception should be part of routine HIV care.
Horizontally transferred genes in the genome of Pacific white shrimp, Litopenaeus vannamei
Authors: Yuan Jian-Bo , Zhang Xiao-Jun , Liu Cheng-Zhang , Wei Jian-Kai , Li Fu-Hua , Xiang Jian-Hai 
Published: August 2013

AbstractBackgroundIn recent years, as the development of next-generation sequencing technology, a growing number of genes have been reported as being horizontally transferred from prokaryotes to eukaryotes, most of them involving arthropods. As a member of the phylum Arthropoda, the Pacific white shrimpLitopenaeus vannameihas to adapt to the complex water environments with various symbiotic or parasitic microorganisms, which provide a platform for horizontal gene transfer (HGT).ResultsIn this study, we analyzed the genome-wide HGT events inL. vannamei. Through homology search and phylogenetic analysis, followed by experimental PCR confirmation, 14 genes with HGT event were identified: 12 of them were transferred from bacteria and two from fungi. Structure analysis of these genes showed that the introns of the two fungi-originated genes were substituted by shrimp DNA fragment, two genes transferred from bacteria had shrimp specific introns inserted in them. Furthermore, around other three bacteria-originated genes, there were three large DNA segments inserted into the shrimp genome. One segment was a transposon that fully transferred, and the other two segments contained only coding regions of bacteria. Functional prediction of these 14 genes showed that 6 of them might be related to energy metabolism, and 4 others related to defense of the organism.ConclusionsHGT events from bacteria or fungi were happened in the genome ofL. vannamei, and these horizontally transferred genes can be transcribed in shrimp. This is the first time to report the existence of horizontally transferred genes in shrimp. Importantly, most of these genes are exposed to a negative selection pressure and appeared to be functional.
Evidence for inflammation-mediated memory dysfunction in gastropods: putative PLA2and COX inhibitors abolish long-term memory failure induced by systemic immune challenges
Authors: Hermann Petra M , Park Deborah , Beaulieu Emily , Wildering Willem C 
Published: August 2013

Abstract

Background
Previous studies associate lipid peroxidation with long-term memory (LTM) failure in a gastropod model (Lymnaea stagnalis) of associative learning and memory. This process involves activation of Phospholipase A2 (PLA2), an enzyme mediating the release of fatty acids such as arachidonic acid that form the precursor for a variety of pro-inflammatory lipid metabolites. This study investigated the effect of biologically realistic challenges of L. stagnalis host defense response system on LTM function and potential involvement of PLA2, COX and LOX therein.

Results
Systemic immune challenges by means of β-glucan laminarin injections induced elevated H2O2 release from L. stagnalis circulatory immune cells within 3 hrs of treatment. This effect dissipated within 24 hrs after treatment. Laminarin exposure has no direct effect on neuronal activity. Laminarin injections disrupted LTM formation if training followed within 1 hr after injection but had no behavioural impact if training started 24 hrs after treatment. Intermediate term memory was not affected by laminarin injection. Chemosensory and motor functions underpinning the feeding response involved in this learning model were not affected by laminarin injection. Laminarin’s suppression of LTM induction was reversed by treatment with aristolochic acid, a PLA2 inhibitor, or indomethacin, a putative COX inhibitor, but not by treatment with nordihydro-guaiaretic acid, a putative LOX inhibitor.

Conclusions
A systemic immune challenge administered shortly before behavioural training impairs associative LTM function in our model that can be countered with putative inhibitors of PLA2 and COX, but not LOX. As such, this study establishes a mechanistic link between the state of activity of this gastropod’s innate immune system and higher order nervous system function. Our findings underwrite the rapidly expanding view of neuroinflammatory processes as a fundamental, evolutionary conserved cause of cognitive and other nervous system disorders.
Assessing the bioconfinement potential of a Nicotianahybrid platform for use in plant molecular farming applications
Authors: Rice J Hollis , Mundell Richard E , Millwood Reginald J , Chambers Orlando D , Stewart C Neal , Davies H Maelor 
Published: August 2013

Abstract

Background
The introduction of pharmaceutical traits in tobacco for commercial production could benefit from the utilization of a transgene bioconfinement system. It has been observed that interspecific F1
Nicotiana hybrids (Nicotiana tabacum × Nicotiana glauca) are sterile and thus proposed that hybrids could be suitable bioconfined hosts for biomanufacturing. We genetically tagged hybrids with green fluorescent protein (GFP), which was used as a visual marker to enable gene flow tracking and quantification for field and greenhouse studies. GFP was used as a useful proxy for pharmaceutical transgenes.

Results
Analysis of DNA content revealed significant genomic downsizing of the hybrid relative to that of N. tabacum. Hybrid pollen was capable of germination in vitro, albeit with a very low frequency and with significant differences between plants. In two field experiments, one each in Tennessee and Kentucky, we detected outcrossing at only one location (Tennessee) at 1.4%. Additionally, from 50 hybrid plants at each field site, formation of 84 and 16 seed was observed, respectively. Similar conclusions about hybrid fertility were drawn from greenhouse crosses. In terms of above-ground biomass, the hybrid yield was not significantly different than that of N. tabacum in the field.

Conclusion

N. tabacum × N. glauca hybrids show potential to contribute to a bioconfinement- and biomanufacturing host system. Hybrids exhibit extremely low fertility with no difference of green biomass yields relative to N. tabacum. In addition, hybrids are morphologically distinguishable from tobacco allowing for identity preservation. This hybrid system for biomanufacturing would optimally be used where N. glauca is not present and in physical isolation of N. tabacum production to provide total bioconfinement.