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We assessed how diatom metrics were related to different ranges of agricultural land use. Diatom assemblage composition, nutrients, and landscape characteristics were determined at 232 sites in eight agriculturally dominated study areas of the continental United States. Two regional groups based on differences in diatom relations to human disturbance were determined. Changes in diatom species composition were related to nutrients, pH, and conductivity in the eastern study areas (due to more wetlands) and more exclusively to nutrients in the west-central study areas. Homogenization of diatom flora among streams was related to high agricultural disturbance at this transcontinental scale. Species traits were developed separately for the east and west-central study groups and calculated two ways: indicator species analysis for taxa in low and high TN or TP conditions and weighted average partial least squares models of TN and TP concentration. These diatom metrics were significantly related to many indicators of agricultural land use in watersheds, especially percent row crops. Further analysis was conducted on only the west-central region due to its larger sample size. Overall, diatom metrics using species responses to N gradients were better related to agricultural land use than were species responses to P gradients. Most nutrient-based diatom metrics changed greatly in response to low ranges of percent row crops, but only a few high N diatom metrics responded to high row crop conditions. The greater response of diatoms to changes in low agriculture conditions may be due to past diatom evolution occurring when most waters had low nutrient conditions.

Stable isotope probing is a combined molecular and isotopic technique used to probe the identity and function of uncultivated microorganisms within environmental samples. Employing stable isotopes of common elements such as carbon and nitrogen, RNA-SIP exploits an increase in the buoyant density of RNA caused by the active metabolism and incorporation of heavier mass isotopes into the RNA after cellular utilization of labeled substrates pulsed into the community. Labeled RNAs are subsequently separated from unlabeled RNAs by density gradient centrifugation followed by identification of the RNAs by sequencing. Therefore, RNA stable isotope probing is a culture-independent technique that provides simultaneous information about microbiome community, composition and function. This chapter presents the detailed protocol for performing an RNA-SIP experiment, including the formation, ultracentrifugation, and fractional analyses of stable isotope-labeled RNAs extracted from environmental samples.

Background: Evidence suggests that elective cardiac patients are at risk of functional and psychological deterioration in the time preceding surgery. This poses a risk to successful post-operative rehabilitation. This prospective one-group pre-test, post-test evaluation was designed to assess a clinical Pre-operative Rehabilitation (PREHAB) home-based exercise programme, to optimise pre-operative physical function and frailty in patients awaiting elective Coronary Artery By-Pass Graft (CABG) or Valve Surgery., Method: Consenting patients awaiting cardiac surgery, with wait time ≥ 6 weeks were referred to a Senior Physiotherapist for baseline assessment. Patients were offered PREHAB in the form of functional home-based exercise that was prescribed from baseline physical outcomes. All patients were followed up via telephone to ensure progression of exercise and any problems associated with it. This continued weekly until the patient attended Surgical Pre-assessment clinic, where all outcome measures were re-assessed., Results: Twenty two patients, out of a total number of 36 patients seen in the surgical clinic between March 2016 and August 2016, participated in the prehab clinical evaluation. Twenty patients completed their prescribed exercises on a weekly basis prior to surgery. No adverse events or cardiac symptoms were reported as a result of the home exercise intervention. Paired t-Test analyses revealed a significant mean difference in clinical frailty score (CFS) of -0.53 ± 0.51 (95% CI [-0.774, -0.279], P = 0.0003). Significant mean difference in six-minute walk test (6MWT) distance of 42.5 ± 27.8 m (95% CI [23.840, 61.251], P = 0.0005), 6MWT walking speed of 0.5 ± 0.4kmh (95% CI, [0.2433, 0.7567], P = 0.001), and short physical performance battery (SPPB) total score of 2.2 ± 1.7, (95% CI [3.066, 1.200], P = 0.0002) were also observed. The change in 6MWT distance was shown to be significantly associated with hospital length of stay (LOS) (r = 0.7; P = 0.03)., Conclusion: This small exploratory evaluation suggests that providing a home-based PREHAB programme for frail patients undergoing CABG or Valve surgery may be able to improve functional ability and reduce hospital length of stay for those patients undergoing cardiac surgery. A frailty score with greater sensitivity may be required to elucidate the influence frailty could have in reducing length of stay. A large randomised controlled study is required to reveal the potential beneficial effects of PREHAB in this patient population.

Acid stimulated accumulation of insoluble phosphorus within microbial cells is highly beneficial to wastewater treatment but remains largely unexplored. Using single cell analyses and next generation sequencing, the response of active polyphosphate accumulating microbial communities under conditions of enhanced phosphorus uptake under both acidic and aerobic conditions was characterised. Phosphorus accumulation activities were highest under acidic conditions (pH 5.5>8.5), where a significant positive effect on bioaccumulation was observed at pH 5.5 when compared to pH 8.5. In contrast to the Betaproteobacteria and Actinobacteria dominated enhanced biological phosphorus removal process, the functionally active polyP accumulators at pH 5.5 belonged to the Gammaproteobacteria, with key accumulators identified as members of the families Aeromonadaceae and Enterobacteriaceae. This study demonstrated a significant enrichment of key polyphosphate kinase and exopolyphosphatase genes within the community metagenome after acidification, concomitant with an increase in P accumulation kinetics., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

We investigated occurrence, transport pathways, and effects of polybrominated diphenyl ether (PBDE) flame retardants and other endocrine disrupting chemicals (EDCs) in aquatic media and the foodweb in the lower Columbia River. In 2009 and 2010, foodweb sampling at three sites along a gradient of contaminant exposure near Skamania (Washington), Columbia City (Oregon) and Longview (Washington) included water (via passive samplers), bed sediment, invertebrate biomass residing in sediment, a resident fish species (largescale suckers [Catostomus macrocheilus]), and eggs from osprey (Pandion haliaetus). This paper primarily reports fish tissue concentrations. In 2009, composites of fish brain, fillet, liver, stomach, and gonad tissues revealed that overall contaminant concentrations were highest in livers, followed by brain, stomach, gonad, and fillet. Concentrations of halogenated compounds in tissue samples from all three sites ranged from <1 to 400nanograms per gram of wet tissue. Several chemical classes, including PBDEs, organochlorine pesticides, and polychlorinated biphenyls (PCBs), were detected at all sites and in nearly all fish tissues sampled. In 2010, only fish livers were sampled and inter-site concentration differences were not as pronounced as in 2009. Chemical concentrations in sediments, fish tissues, and osprey eggs increased moving downstream from Skamania to the urbanized sites near Columbia City and Longview. Numerous organochlorine (OC) pesticides, both banned and currently used, and PBDEs, were present at each site in multiple media and concentrations exceeded environmental quality benchmarks in some cases. Frequently detected OC compounds included hexachlorobenzene, pentachloroanisole, dichlorodiphenyltrichloroethane (DDT) and its degradates, chlorpyrifos, and oxyfluorofen. Biomagnification of BDE47, 100, 153, and 154 occurred in largescale suckers and osprey eggs. Results support the hypothesis that contaminants in the environment lead to bioaccumulation and potential negative effects in multiple levels of the foodweb., (Published by Elsevier B.V.)

Here we demonstrate a cost effective and scalable microbial ecology sequencing platform using the Ion Torrent Personal Genome Machine (PGM). We assessed both PCR amplified 16S rRNA and shotgun metagenomic approaches and generated 100,000+ to 1,000,000+ reads using 'post-light' based sequencing technology within different sized semi-conductor chips. Further development of Golay barcoded Ion Tags allowed multiplex analyses of microbial communities with substantially reduced costs compared with platforms such as 454/GS-FLX. Using these protocols we assessed the bacterial and archaeal dynamics within covered anaerobic digesters used to treat piggery wastes. Analysis of these sequence data showed that these novel methanogenic waste treatment systems are dominated by bacterial taxa, in particular Clostridium, Synergistia and Bacteroides that were maintained as a stable community over extended time periods. Archaeal community dynamics were more stochastic with the key methanogenic taxa more difficult to resolve, principally due to the poor congruence seen between community structures generated either by nested PCR or metagenomic approaches for archaeal analyses. Our results show that for microbial community structure and function analyses, the PGM platform provides a low cost, scalable and high throughput solution for both Tag sequencing and metagenomic analyses., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Background: The aims of the present study were to determine the tracheal intubating conditions, onset time, duration of action, and hemodynamic responses following the administration of cisatracurium 0.15 mg x kg(-1) to infants and children., Methods: One hundred and eighty-one infants and children aged 1 month to 12 years were randomized to two groups to receive anesthesia with nitrous oxide-oxygen-halothane (group H) or nitrous oxide-oxygen-thiopental-fentanyl (group TF). Intubation conditions were assessed 120 s after cisatracurium administration using a 4-part scale. Neuromuscular transmission was monitored by recording the evoked compound electromyogram of the adductor pollicis., Results: The proportion of patients with excellent or good intubating conditions was similar in both groups (88 of 90, 98% in group H; 85 of 90, 94% in group TF). However, there was a significantly greater proportion of excellent intubating conditions in group H (79 of 90, 88%) compared with group TF (65 of 90, 72%) (P = 0.01) and recovery time was significantly longer in group H compared with group TF (P < 0.001). There was also a higher proportion of excellent intubating conditions in infants compared with older subjects (P = 0.02) and a shorter onset time (P < 0.001) and longer recovery time (P < 0.001) in younger compared with older patients. Changes in heart rate and arterial pressure were negligible 1 min following the cisatracurium administration., Conclusions: Cisatracurium 0.15 mg x kg(-1) produces acceptable intubating conditions at 120 s in the great majority of infants and children. Anesthesia background and age have significant effects on intubating conditions and duration of action of cisatracurium.

Androgens are essential for normal prostate physiology and have a permissive role in the development and progression of prostate cancer. Using the mRNA differential display technique, ornithine decarboxylase (ODC) was identified to be up-regulated by androgens in human prostatic LNCaP cells. On Northern analysis, the induction of ODC expression by 10 nM androgen was rapid and continued up to 48 h exposure with a maximum 6.3-fold up-regulation. The anti-androgen Casodex inhibited the androgen-induced up-regulation of ODC, whereas the protein synthesis inhibitor cycloheximide did not. Together these data suggest that regulation is mediated through the androgen receptor protein and does require secondary protein synthesis, respectively. The kinetics of induction of ODC were almost identical to those of prostate specific antigen. Taken together these data suggest that ODC is directly regulated by androgens in LNCaP cells.

This clinical trial investigated the influence of short-term ibuprofen therapy on the early phase of the treatment of adult chronic periodontitis. The subjects were 17 patients in good general health referred for specialist periodontal treatment, having moderate chronic adult periodontitis. A series of assessments were made every 2 weeks over an 8-week period, including evaluations of oral hygiene, gingival inflammation and probing pocket depths. All participants received oral hygiene instruction, and following baseline examinations, had half the dentition, chosen at random, treated by scaling and root planing. The patients were randomly distributed into 2 groups, a test group receiving a 14-day course of 800 mg ibuprofen daily, in 4 divided doses, and a control group who did not receive any drug regime. At the 2-week assessment following the drug regime, significantly greater reduction in gingival bleeding, colour and pocketing was detected in the test compared with the control group. The beneficial effects were less evident thereafter. Although clinical application of the regime used in this study would not be justified by these results, further research into anti-inflammatory agents as an adjunct in the treatment of periodontal diseases could be considered, in the light of the beneficial effect on gingivitis in the early phase of periodontal treatment reported.

The aim of this controlled clinical study was to utilize computer-assisted densitometric analysis of radiographs to assess the effectiveness of treating periodontal osseous defects with a sintered hydroxyapatite implant material. It was found that over the 2-year period of the study for the osseous defects treated by the implant material, there was a gain in the height of the hard tissue relative to the cemento-enamel junction; this gain was statistically significant compared with the results for the control sites.

This study compared clinical measurements using a manual periodontal probe and an electronic pressure probe using a 0.25 N force, and related them to measurement of the bone levels at the time of surgery. All measurements were taken from the cemento-enamel junction at specified sites. It was found that neither probing technique provided a means for accurately measuring bone level. In the presence of healed tissue, little difference was found between the two instruments; whereas the manual probe more closely approximated the actual level of bone in the presence of inflammation. It was therefore concluded that under the conditions of present study the manual probe depth measurements were the more applicable for routine clinical use.

Patients with severe periodontitis and who had one or more teeth with infrabony pockets were treated by periodontal surgery with implantation of hydroxyapatite particles into the bone defects at the time of surgery. Subsequently, in three patients it was found necessary to extract a tooth for reasons not related to the previous periodontal treatment. Specimens that included the local soft tissues and crestal bone attached to the teeth were obtained at 22, 40 and 80 weeks after placement of the implant. They were decalcified and stained with haematoxylin and eosin and examined under light microscopy. The healing response was found to vary between specimens, and between sites within the same specimen. The early stage of healing showed the implant particles surrounded by collagen. Subsequently, varying degrees of resorption of the periphery of the particles was seen, and at some sites bone deposition was observed. These different healing responses were found to be progressing concurrently at sites in close proximity. Further work is needed to confirm the histological findings described in the paper.

The treatment of periodontitis by scaling and oral hygiene instruction was compared with the same regime augmented by conventional gingivectomy. The procedures were allocated randomly to contralateral sides of the maxillary arches of 28 patients. Following both regimes there was significant reduction in Plaque Index, Gingival Index, crevicular fluid and depths of pockets. There was slight gain in attachment on the non-surgical sides, and a minor loss of attachment on the surgical sides. Comparing the two regimes, over the second half of the study there was no significant difference in Plaque Index or crevicular fluid; however, on the surgical sides there was significantly greater reduction in Gingival Index and depths of pockets. Residual pockets after either technique were associated with more inflammation than where sulcus depths were less than 2 mm. Retrospective comparisons of the initial depths of pockets with the final gingival status indicated that, when initial depths of pockets had been 3 mm or over, surgical treatment was more effective than non-surgical in reducing the final values of both depths of pockets and inflammation; this finding was statistically significant for some, but not all of the parameters. Treatment of shallow pockets by either technique was more effective than the treatment of deep pockets. Final Plaque Index values of zero were associated with significantly less inflammation and pocketing than where plaque deposits could be detected.