Natural and Accelerated Bioremediation Research (NABIR) Field Research Center (FRC), Oak Ridge Tennessee

The Field Research Center (FRC) in Oak Ridge (Fig. 1), Tennessee supports the U.S. Department of Energy's (DOE's) Environmental Remediation Sciences Program (ERSP) goal of understanding the complex physical, chemical, and biological properties of contaminated sites for new solutions to environmental remediation and long-term stewardship. In particular, the FRC provides the opportunity for researchers to conduct studies that promote the understanding of the processes that influence the transport and fate of subsurface contaminants, the effectiveness and long-term consequences of existing remediation options, and the development of improved remediation strategies. It offers a series of contaminated sites around the former S-3 Waste Disposal Ponds and uncontaminated sites in which investigators and students conduct field research or collect samples for laboratory analysis. FRC research also spurs the development of new and improved characterization and monitoring tools. Site specific knowledge gained from research conducted at the FRC also provides the DOE-Oak Ridge Office of Environmental Management (EM) the critical scientific knowledge needed to make cleanup decisions for the S-3 Ponds and other sites on the Oak Ridge Reservation (ORR)

Nonrigid Registration of Brain Tumor Resection MR Images Based on Joint Saliency Map and Keypoint Clustering

This paper proposes a novel global-to-local nonrigid brain MR image registration to compensate for the brain shift and the unmatchable outliers caused by the tumor resection. The mutual information between the corresponding salient structures, which are enhanced by the joint saliency map (JSM), is maximized to achieve a global rigid registration of the two images. Being detected and clustered at the paired contiguous matching areas in the globally registered images, the paired pools of DoG keypoints in combination with the JSM provide a useful cluster-to-cluster correspondence to guide the local control-point correspondence detection and the outlier keypoint rejection. Lastly, a quasi-inverse consistent deformation is smoothly approximated to locally register brain images through the mapping the clustered control points by compact support radial basis functions. The 2D implementation of the method can model the brain shift in brain tumor resection MR images, though the theory holds for the 3D case

Computational analysis of mechanical stress–strain interaction of a bioresorbable scaffold with blood vessel

This paper was accepted for publication in the journal Journal of Biomechanics and the definitive published version is available at http://dx.doi.org/10.1016/j.jbiomech.2016.05.035Crimping and deployment of bioresorbable polymeric scaffold, Absorb, were modelled using finite element method, in direct comparison with Co-Cr alloy drug eluting stent, Xience V. Absorb scaffold has an expansion rate lower than Xience V stent, with a less outer diameter achieved after balloon deflation. Due to the difference in design and material properties, Absorb also shows a higher recoiling than Xience V, which suggests that additional post-dilatation is required to achieve effective treatment for patients with calcified plaques and stiff vessels. However, Absorb scaffold induces significantly lower stresses on the artery-plaque system, which can be clinically beneficial. Eccentric plaque causes complications to stent deployment, especially non-uniform vessel expansion. Also the stress levels in the media and adventitia layers are considerably higher for the plaque with high eccentricity, for which the choice of stents, in terms of materials and designs, will be of paramount importance. Our results imply that the benefits of Absorb scaffolds are amplified in these cases

A multi-targeted approach to suppress tumor-promoting inflammation

Cancers harbor significant genetic heterogeneity and patterns of relapse following many therapies are due to evolved resistance to treatment. While efforts have been made to combine targeted therapies, significant levels of toxicity have stymied efforts to effectively treat cancer with multi-drug combinations using currently approved therapeutics. We discuss the relationship between tumor-promoting inflammation and cancer as part of a larger effort to develop a broad-spectrum therapeutic approach aimed at a wide range of targets to address this heterogeneity. Specifically, macrophage migration inhibitory factor, cyclooxygenase-2, transcription factor nuclear factor-κB, tumor necrosis factor alpha, inducible nitric oxide synthase, protein kinase B, and CXC chemokines are reviewed as important antiinflammatory targets while curcumin, resveratrol, epigallocatechin gallate, genistein, lycopene, and anthocyanins are reviewed as low-cost, low toxicity means by which these targets might all be reached simultaneously. Future translational work will need to assess the resulting synergies of rationally designed antiinflammatory mixtures (employing low-toxicity constituents), and then combine this with similar approaches targeting the most important pathways across the range of cancer hallmark phenotypes

Identification and verification of potential biomarkers in gastric cancer by integrated bioinformatic analysis

Background: Gastric cancer (GC) is a common cancer with high mortality. This study aimed to identify its differentially expressed genes (DEGs) using bioinformatics methods.Methods: DEGs were screened from four GEO (Gene Expression Omnibus) gene expression profiles. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. A protein–protein interaction (PPI) network was constructed. Expression and prognosis were assessed. Meta-analysis was conducted to further validate prognosis. The receiver operating characteristic curve (ROC) was analyzed to identify diagnostic markers, and a nomogram was developed. Exploration of drugs and immune cell infiltration analysis were conducted.Results: Nine up-regulated and three down-regulated hub genes were identified, with close relations to gastric functions, extracellular activities, and structures. Overexpressed Collagen Type VIII Alpha 1 Chain (COL8A1), Collagen Type X Alpha 1 Chain (COL10A1), Collagen Triple Helix Repeat Containing 1 (CTHRC1), and Fibroblast Activation Protein (FAP) correlated with poor prognosis. The area under the curve (AUC) of ADAM Metallopeptidase With Thrombospondin Type 1 Motif 2 (ADAMTS2), COL10A1, Collagen Type XI Alpha 1 Chain (COL11A1), and CTHRC1 was >0.9. A nomogram model based on CTHRC1 was developed. Infiltration of macrophages, neutrophils, and dendritic cells positively correlated with COL8A1, COL10A1, CTHRC1, and FAP. Meta-analysis confirmed poor prognosis of overexpressed CTHRC1.Conclusion: ADAMTS2, COL10A1, COL11A1, and CTHRC1 have diagnostic values in GC. COL8A1, COL10A1, CTHRC1, and FAP correlated with worse prognosis, showing prognostic and therapeutic values. The immune cell infiltration needs further investigations

Cigarette Smoking and Erectile Dysfunction: Focus on NO Bioavailability and ROS Generation

Introduction.  Thirty million men in the United States suffer from erectile dysfunction (ED) and this number is expected to double by 2025. Considered a major public health problem, which seriously affects the quality of life of patients and their partners, ED becomes increasingly prevalent with age and chronic smoking is a major risk factor in the development of ED. Aim.  To review available evidence concerning the effects of cigarette smoking on vascular changes associated with decreased nitric oxide (NO) bioavailability and increased reactive oxygen species (ROS) generation. Methods.  We examined epidemiological and clinical data linking cigarette smoking and ED, and the effects of smoking on vascular NO bioavailability and ROS generation. Main Outcome Measures.  There are strong parallels between smoking and ED and considerable evidence supporting the concept that smoking-related ED is associated with reduced bioavailability of NO because of increased ROS. Results.  Cigarette smoking-induced ED in human and animal models is associated with impaired arterial flow to the penis or acute vasospasm of the penile arteries. Long-term smoking produces detrimental effects on the vascular endothelium and peripheral nerves and also causes ultrastructural damage to the corporal tissue, all considered to play a role in chronic smoking-induced ED. Clinical and basic science studies provide strong indirect evidence that smoking may affect penile erection by the impairment of endothelium-dependent smooth muscle relaxation or more specifically by affecting NO production via increased ROS generation. Whether nicotine or other products of cigarette smoke mediate all effects related to vascular damage is still unknown. Conclusions.  Smoking prevention represents an important approach for reducing the risk of ED. The characterization of the components of cigarette smoke leading to ED and the mechanisms by which these components alter signaling pathways activated in erectile responses are necessary for a complete comprehension of cigarette smoking-associated ED. Tostes RS, Carneiro FS, Lee AJ, Giachini FRC, Leite R, Osawa Y, and Clinton Webb R. Cigarette smoking and erectile dysfunction: Focus on NO bioavailability and ROS generation. J Sex Med 2008;5:1284–1295.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75024/1/j.1743-6109.2008.00804.x.pd

Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol

Biostimulation is widely used to enhance reductive dechlorination of chlorinated ethenes in contaminated aquifers. However, the knowledge on corresponding biogeochemical responses is limited. In this study glycerol was injected in an aquifer contaminated with cis-dichloroethene (cDCE), and geochemical and microbial shifts were followed for 265 days. Consistent with anoxic conditions and sulfate reduction after biostimulation, MiSeq 16S rRNA gene sequencing revealed temporarily increased relative abundance of Firmicutes, Bacteriodetes and sulfate reducing Deltaproteobacteria. In line with 13C cDCE enrichment and increased Dehalococcoides mccartyi (Dcm) numbers, dechlorination was observed towards the end of the field experiment, albeit being incomplete with accumulation of vinyl chloride. This was concurrent with i) decreased concentrations of dissolved organic carbon (DOC), reduced relative abundances of fermenting and sulfate reducing bacteria that have been suggested to promote Dcm growth by providing electron donor (H2) and essential corrinoid cofactors, ii) increased sulfate concentration and increased relative abundance of Epsilonproteobacteria and Deferribacteres as putative oxidizers of reduced sulfur compounds. Strong correlations of DOC, relative abundance of fermenters and sulfate reducers, and dechlorination imply the importance of syntrophic interactions to sustain robust dechlorination. Tracking microbial and environmental parameters that promote/preclude enhanced reductive dechlorination should aid development of sustainable bioremediation strategies. This article is protected by copyright. All rights reserved.This study was supported by a VITO/KU Leuven PhD scholarship (EU FP7 project AQUAREHAB, grant 226565) to S Atashgahi. Furthermore, S Atashgahi and H Smidt received support bya grant ofBE-Basic-FES funds from theDutch Ministry of Economic Affairs and D Springael by the InterUniversity Attraction Pole (IUAP) “m-manager” of the Belgian Science Policy (BELSPO, P7/25). We thankRichard Lookman for his assistance in the field experiment and acknowledge the China Scholarship Council for the support to Y Lu and Y Zheng.info:eu-repo/semantics/publishedVersio

Nociceptive Afferents to the Premotor Neurons That Send Axons Simultaneously to the Facial and Hypoglossal Motoneurons by Means of Axon Collaterals

It is well known that the brainstem premotor neurons of the facial nucleus and hypoglossal nucleus coordinate orofacial nociceptive reflex (ONR) responses. However, whether the brainstem PNs receive the nociceptive projection directly from the caudal spinal trigeminal nucleus is still kept unclear. Our present study focuses on the distribution of premotor neurons in the ONR pathways of rats and the collateral projection of the premotor neurons which are involved in the brainstem local pathways of the orofacial nociceptive reflexes of rat. Retrograde tracer Fluoro-gold (FG) or FG/tetramethylrhodamine-dextran amine (TMR-DA) were injected into the VII or/and XII, and anterograde tracer biotinylated dextran amine (BDA) was injected into the caudal spinal trigeminal nucleus (Vc). The tracing studies indicated that FG-labeled neurons receiving BDA-labeled fibers from the Vc were mainly distributed bilaterally in the parvicellular reticular formation (PCRt), dorsal and ventral medullary reticular formation (MdD, MdV), supratrigeminal nucleus (Vsup) and parabrachial nucleus (PBN) with an ipsilateral dominance. Some FG/TMR-DA double-labeled premotor neurons, which were observed bilaterally in the PCRt, MdD, dorsal part of the MdV, peri-motor nucleus regions, contacted with BDA-labeled axonal terminals and expressed c-fos protein-like immunoreactivity which induced by subcutaneous injection of formalin into the lip. After retrograde tracer wheat germ agglutinated horseradish peroxidase (WGA-HRP) was injected into VII or XII and BDA into Vc, electron microscopic study revealed that some BDA-labeled axonal terminals made mainly asymmetric synapses on the dendritic and somatic profiles of WGA-HRP-labeled premotor neurons. These data indicate that some premotor neurons could integrate the orofacial nociceptive input from the Vc and transfer these signals simultaneously to different brainstem motonuclei by axonal collaterals

Recent progress in genetics of aging, senescence and longevity: focusing on cancer-related genes

It is widely believed that aging results from the accumulation of molecular damage, including damage of DNA and mitochondria and accumulation of molecular garbage both inside and outside of the cell. Recently, this paradigm is being replaced by the “hyperfunction theory�, which postulates that aging is caused by activation of signal transduction pathways such as TOR (Target of Rapamycin). These pathways consist of different enzymes, mostly kinases, but also phosphatases, deacetylases, GTPases, and some other molecules that cause overactivation of normal cellular functions. Overactivation of these sensory signal transduction pathways can cause cellular senescence, age-related diseases, including cancer, and shorten life span. Here we review some of the numerous very recent publications on the role of signal transduction molecules in aging and age-related diseases. As was emphasized by the author of the “hyperfunction model�, many (or actually all) of them also play roles in cancer. So these “participants� in pro-aging signaling pathways are actually very well acquainted to cancer researchers. A cancer-related journal such as Oncotarget is the perfect place for publication of such experimental studies, reviews and perspectives, as it can bridge the gap between cancer and aging researchers