Extubation after breathing trials with automatic tube compensation, T-tube, or pressure support ventilation.
Automatic tube compensation (ATC) is a new option to compensate for the pressure drop across the endotracheal or tracheostomy tube (ETT), especially during ventilator-assisted spontaneous breathing. While several benefits of this mode have so far been documented, ATC has not yet been used to predict whether the ETT could be safely removed at the end of weaning, from mechanical ventilation. We undertook a systematic trial using a randomized block design. During a 2-year period, all eligible patients of a medical intensive care unit were treated with ATC, conventional pressure support ventilation (PSV, 5 cmH2O), or T-tube for 2-h. Tolerance of the breathing trial served as a basis for the decision to remove the endotracheal tube. Extubation failure was considered if reintubation was necessary or if the patient required non-invasive ventilatory assistance (both within 48 h). After the inclusion of 90 patients (30 per group) we did not observe significant differences between the modes. Twelve patients failed the initial weaning trial. However, half of the patients who appeared to fail the spontaneous breathing trial on the T-tube, PSV, or both, were successfully extubated after a succeeding trial with ATC. Extubation was thus withheld from four and three of these patients while breathing with PSV or the T-tube, respectively, but to any patient breathing with ATC. It seems that ATC can be used as an alternative mode during the final phase of weaning from mechanical ventilation. Furthermore, this study may promote a larger multicenter trial on weaning with ATC compared with standard modes.


Probiotics for preventing acute otitis media in children.
Acute otitis media (AOM), or acute middle ear infection, is one of the most frequently occurring childhood diseases, and the most common reason given for prescribing antibiotics in this age group. Guidelines often recommend antibiotics as first-line treatment for severe AOM. However, antibiotics also lead to antibiotic resistance, so preventing episodes of AOM is an urgent priority. To assess the effects of probiotics to prevent the occurrence and reduce the severity of acute otitis media in children. We searched CENTRAL, PubMed, Embase, and three other databases (October 2018), two trial registers (October 2018), and conducted a backwards and forwards citation analysis (August 2018). We did not apply any language, publication date, or publication status restrictions. Randomised controlled trials (RCTs) of children (aged up to 18 years), comparing probiotics with placebo, usual care, or no probiotic. Two review authors independently assessed the eligibility of trials for inclusion and risk of bias of the included trials, and extracted data using pre-piloted data extraction forms. We analysed dichotomous data as either risk ratio (RR) or odds ratios (OR) and continuous data as mean differences (MD). We included 17 RCTs involving 3488 children, of which 16 RCTs were included in the meta-analyses. Of the 16 RCTs that reported the mean age of children, mean age overall was 2.4 years; in 4 RCTs the mean age of children participating in the trial was less than 1 year old; in 2 RCTs the mean age was between 1 and 2 years old; and in 10 RCTs the mean age was older than 2 years. Probiotic strains evaluated by the trials varied, with 11 of the included RCTs evaluating Lactobacillus-containing probiotics, and six RCTs evaluating Streptococcus-containing probiotics.The proportion of children (i.e. the number of children in each group) experiencing one or more episodes of AOM during the treatment was lower for those taking probiotics (RR 0.77, 95% confidence interval (CI) 0.63 to 0.93; 16 trials; 2961 participants; number needed to treat for an additional beneficial outcome (NNTB) = 10; moderate-certainty evidence).Post hoc subgroup analysis found that among children not prone to otitis media, a lower proportion of children receiving probiotics experienced AOM (RR 0.64, 95% CI 0.49 to 0.84; 11 trials; 2227 participants; NNTB = 9; moderate-certainty evidence). However, among children who were otitis prone, there was no difference between probiotic and comparator groups (RR 0.97, 95% CI 0.85 to 1.11; 5 trials; 734 participants; high-certainty evidence). The test for subgroup differences was significant (P = 0.007).None of the included trials reported on the severity of AOM.The proportion of children experiencing adverse events did not differ between the probiotic and comparator groups (OR 1.54, 95% CI 0.60 to 3.94; 4 trials; 395 participants; low-certainty evidence).Probiotics decreased the proportion of children taking antibiotics for any infection (RR 0.66, 95% CI 0.51 to 0.86; 8 trials; 1768 participants; NNTB = 8; moderate-certainty evidence). Test for subgroup differences (use of antibiotic specifically for AOM, use of antibiotic for infections other than AOM) was not significant.There was no difference in the mean number of school days lost (MD -0.95, 95% CI -2.47 to 0.57; 5 trials; 1280 participants; moderate-certainty evidence). There was no difference between groups in the level of compliance in taking the intervention (RR 1.02, 95% CI 0.99 to 1.05; 5 trials; 990 participants).Probiotics decreased the proportion of children having other infections (RR 0.75, 95% CI 0.65 to 0.87; 11 trials; 3610 participants; NNTB = 12; moderate-certainty evidence). Test for subgroup differences (acute respiratory infections, gastrointestinal infections) was not significant.Probiotic strains trialled and their dose, frequency, and duration of administration varied considerably across studies, which likely contributed to the substantial levels of heterogeneity. Sensitivity testing of funnel plots did not reveal publication bias. Probiotics may prevent AOM in children not prone to AOM, but the inconsistency of the subgroup analyses suggests caution in interpreting these results. Probiotics decreased the proportion of children taking antibiotics for any infection. The proportion of children experiencing adverse events did not differ between the probiotic and comparator groups. The optimal strain, duration, frequency, and timing of probiotic administration still needs to be established.


Familial aggregation of preeclampsia and intrauterine growth restriction in a genetically isolated population in The Netherlands.
Preeclampsia and intrauterine growth restriction are related, pregnancy-specific disorders with a substantial genetic influence, which may have a joint genetic aetiology. We investigated familial aggregation, consanguinity and parent-of-origin effects for preeclampsia and IUGR. Fifty women with previous preeclampsia and 56 with previous pregnancies complicated by intrauterine growth restriction were recruited from a recent genetically isolated population in the Netherlands. Their relationships were estimated by means of a large genealogy database that contains information on more than 110 000 individuals from the isolate over 23 generations. Relationships were quantified using kinship and inbreeding coefficients. Parent-of-origin effects were evaluated by comparing parental kinships. Eighty-six women (39 preeclampsia and 47 intrauterine growth restriction) could be linked to one common ancestor within 14 generations. The proportion of related women with previous preeclampsia (95.6%) or pregnancies complicated by intrauterine growth restriction (95.1%) was significantly greater than expected by chance (P<0.001). Combined analysis of both disorders did not change the magnitude of familial aggregation. The proportion of women born from consanguineous marriages was increased in women with previous preeclampsia (81.8%) and those with intrauterine growth restriction (78%) compared to a random sample (P<0.001). Maternal and paternal kinships were not significantly different in both disorders. We demonstrate cosegregation of preeclampsia and intrauterine growth restriction, supporting a common genetic aetiology. The high proportion of parental consanguineous marriages suggests the possibility of an underlying recessive mutation. No evidence was found for a parent-of-origin effect either in preeclampsia or in intrauterine growth restriction.


Development of a Neo-Epitope Specific Assay for Serological Assessment of Type VII Collagen Turnover and Its Relevance in Fibroproliferative Disorders.
Type VII collagen is the main component of the anchoring fibrils connecting the basement membrane to the underlying interstitial matrix. Mutations in the type VII collagen gene cause dystrophic epidermolysis bullosa. Increased levels of type VII collagen in the skin have been reported in patients with systemic sclerosis (SSc), whereas reduced levels in the airways have been related to asthma. This indicates that type VII collagen plays an important part in upholding tissue integrity and that its remodeling may lead to pathological states. The aim of this study was to investigate the role of type VII collagen remodeling in fibroproliferative disorders. We produced monoclonal antibody targeting a specific fragment of type VII collagen (C7M) released to the systemic circulation and developed a neo-epitope specific competitive enzyme-linked immunosorbent assay (ELISA). Biological relevance was evaluated in serum from patients with SSc or chronic obstructive pulmonary disease (COPD). The C7M ELISA was technically robust and specific for the C7M neo-epitope. Serum C7M levels were significantly elevated in two cohorts of patients with SSc and in patients with COPD as compared with healthy individuals (P < 0.0001). The C7M ELISA enabled quantification of type VII collagen turnover in serum. Elevated serum C7M levels indicated that the turnover rate of type VII collagen was significantly increased in patients with SSc or COPD, suggesting a pathological role. Thus, the C7M ELISA may become useful in future investigations of type VII collagen turnover in fibroproliferative disorders, and it may prove a valuable tool for evaluating novel anti-fibrotic drugs.


Endoparasitic plants and fungi show evolutionary convergence across phylogenetic divisions.
Endoparasitic plants are the most reduced flowering plants, spending most of their lives as a network of filaments within the tissues of their hosts. Despite their extraordinary life form, we know little about their biology. Research into a few species has revealed unexpected insights, such as the total loss of plastome, the reduction of the vegetative phase to a proembryonic stage, and elevated information exchange between host and parasite. To consolidate our understanding, we review life history, anatomy, and molecular genetics across the four independent lineages of endoparasitic plants. We highlight convergence across these clades and a striking trans-kingdom convergence in life history among endoparasitic plants and disparate lineages of fungi at the molecular and physiological levels. We hypothesize that parasitism of woody plants preselected for the endoparasitic life history, providing parasites a stable host environment and the necessary hydraulics to enable floral gigantism and/or high reproductive output. Finally, we propose a broader view of endoparasitic plants that connects research across disciplines, for example, pollen-pistil and graft incompatibility interactions and plant associations with various fungi. We shine a light on endoparasitic plants and their hosts as under-explored ecological microcosms ripe for identifying unexpected biological processes, interactions and evolutionary convergence.


CNS lymphatic drainage and neuroinflammation are regulated by meningeal lymphatic vasculature.
Neuroinflammatory diseases, such as multiple sclerosis, are characterized by invasion of the brain by autoreactive T cells. The mechanism for how T cells acquire their encephalitogenic phenotype and trigger disease remains, however, unclear. The existence of lymphatic vessels in the meninges indicates a relevant link between the CNS and peripheral immune system, perhaps affecting autoimmunity. Here we demonstrate that meningeal lymphatics fulfill two critical criteria: they assist in the drainage of cerebrospinal fluid components and enable immune cells to enter draining lymph nodes in a CCR7-dependent manner. Unlike other tissues, meningeal lymphatic endothelial cells do not undergo expansion during inflammation, and they express a unique transcriptional signature. Notably, the ablation of meningeal lymphatics diminishes pathology and reduces the inflammatory response of brain-reactive T cells during an animal model of multiple sclerosis. Our findings demonstrate that meningeal lymphatics govern inflammatory processes and immune surveillance of the CNS and pose a valuable target for therapeutic intervention.


Best prediction of yields for long lactations.
Lactation records of any reasonable length now can be processed with the selection index method known as best prediction (BP). Previous prediction programs were limited to the 305-d standard used since 1935. Best prediction was implemented in 1998 to calculate lactation records in USDA genetic evaluations, replacing the test interval method used since 1969 to calculate lactation records. Best prediction is more complex but also more accurate, particularly when testing is less frequent. Programs were reorganized to output better graphics, give users simpler access to options, and provide additional output, such as BP of daily yields. Test-day data for 6 breeds were extracted from the national dairy database, and lactation lengths were required to be > or =500 d (Ayrshire, Milking Shorthorn) or > or =800 d (all others). Average yield and SD at any day in milk (DIM) were estimated by fitting 3-parameter Wood's curves (milk, fat, protein) and 4-parameter exponential functions (somatic cell score) to means and SD of 15- (< or =300 DIM) and 30-d (>300 DIM) intervals. Correlations among TD yields were estimated using an autoregressive matrix to account for biological changes and an identity matrix to model daily measurement error. Autoregressive parameters (r) were estimated separately for first (r = 0.998) and later parities (r = 0.995). These r values were slightly larger than previous estimates due to the inclusion of the identity matrix. Correlations between traits were modified so that correlations between somatic cell score and other traits may be nonzero. The new lactation curves and correlation functions were validated by extracting TD data from the national database, estimating 305-d yields using the original and new programs, and correlating those results. Daily BP of yield were validated using daily milk weights from on-farm meters in university research herds. Correlations ranged from 0.900 to 0.988 for 305-d milk yield. High correlations ranged from 0.844 to 0.988 for daily yields, although correlations were as low as 0.015 on d 1 of lactation, which may be due to calving-related disorders that are not accounted for by BP. Correlations between 305-d yield calculated using 50-d intervals from 50 to 250 DIM and 305-yield calculated using all TD to 500 DIM increased as TD data accumulated. Many cows can profitably produce for >305 DIM, and the revised program provides a flexible tool to model these records.


Influence of the support on stabilizing local defects in strained monolayer oxide films.
Two-dimensional materials with a honeycomb lattice, such as graphene and hexagonal boron nitride, often contain local defects in which the hexagonal elements are replaced by four-, five-, seven-, and eight-membered rings. An example is the Stone-Wales (S-W) defect, where a bond rotation causes four hexagons to be transformed into a cluster of two pentagons and two heptagons. A further series of similar defects incorporating divacancies results in larger structures of non-hexagonal elements. In this paper, we use scanning tunneling microscopy (STM) and density functional theory (DFT) modeling to investigate the structure and energetics of S-W and divacancy defects in a honeycomb (2 × 2) Ti2O3 monolayer grown on an Au(111) substrate. The epitaxial rumpled Ti2O3 monolayer is pseudomorphic and in a state of elastic compression. As a consequence, divacancy defects, which induce tension in freestanding films, relieve the compression in the epitaxial Ti2O3 monolayer and therefore have significantly lower energies when compared with their freestanding counterparts. We find that at the divacancy defect sites there is a local reduction of the charge transfer between the film and the substrate, the rumpling is reduced, and the film has an increased separation from the substrate. Our results demonstrate the capacity of the substrate to significantly influence the energetics, and hence favor vacancy-type defects, in compressively strained 2D materials. This approach could be applied more broadly, for example to tensile monolayers, where vacancy-type defects would be rare and interstitial-type defects might be favored.


Pressor response to 5-hydroxytryptamine, norepinephrine and KCi in the perfused hindquarter preparation from the spontaneously hypertensive rat.
The pressor response to 5-hydroxytryptamine (5-HT), norepinephrine (NE), and KCI was studied in the blood- and Ringer's- perfused hindquarters of the spontaneously hypertensive rat (SHR) and the Kyoto normotensive Wistar rat in two age groups: 8 to 10 weeks and 6 to 8 months. In both preparations, the response to 5-HT, NE and KCI was greater in the young and old SHRs than in the age-matched normotensive Wistar rats. The enhanced responsiveness to 5-HT in old SHRs was of greater magnitude than that to NE or KCI, whereas in young SHRs the enhanced responsiveness to the three pressor agents was of similar magnitude. This appears to be due in part to a greater reduction in responsiveness to NE and KCI than to 5-HT as the animal becomes older. Enhanced responsiveness to 5-HT also occurs in the renal hypertensive rat. However, there was no difference in responsiveness to low doses of NE or KCI in the renal hypertensive rat. The response to 5-HT in the old SHR was blocked by methysergide but was not affected by phentolamine, isoproterenol or nitroglycerin. In the old SHR made hypotensive by occlusion of the abdominal aorta for a duration of 3 to 5 weeks, the responsiveness to all three pressor agents was reduced but was most marked for 5-HT. These latter results suggest that blood pressure per se contributes to the enhanced responsiveness to NE, KCI and, to a greater extent, 5-HT.


The contribution of individual subunits to the coupling of the voltage sensor to pore opening in Shaker K channels: effect of ILT mutations in heterotetramers.
Voltage-gated ion channels couple conformational change(s) of the voltage-sensing domain to those of the opening of an intracellular gate to allow ionic conduction. Much larger positive potentials are required to couple these conformational changes to the opening of the gate of Shaker K(+) channels with the concurrent mutations V369I, I372L, and S376T (ILT) at the N-terminal end of the S4 segment. We used cut-open oocyte voltage clamp to study the biophysical and thermodynamical properties of heterotetrameric concatemerized channels with different stoichiometries of ILT mutations. The voltage-sensing domains of ILT mutant channels require smaller depolarization to activate but their intracellular gate does not immediately follow the movement of the voltage-sensing domain, requiring larger depolarization to open. Our results demonstrate that each subunit contributes equally to the rightward shift of the conductance-voltage relationship and that a single ILT-containing subunit is sufficient to induce a large enthalpic and entropic barrier, limiting opening of the intracellular gate.


Purification and partial characterization of equine infectious anemia virus reverse transcriptase.
Previously we raised a rabbit monospecific antibody (C2003) against a synthetic peptide derived from a sequence within the C-terminal portion of the reverse transcriptase (RT) of the human immunodeficiency virus type 1 (HIV-1). This sequence is found to be conserved in the predicted amino acid sequence of a related lentivirus, the equine infectious anemia virus (EIAV). It was previously determined that the C2003 antibody could cross-react with native EIAV RT and directly inhibit the DNA polymerase activity of the enzyme. We have now fractionated EIAV RT by immunoaffinity chromatography with immobilized C2003 antibody. The procedure yielded an equimolar mixture of two proteins of 66 and 51 kDa associated with both DNA polymerase and RNase H activities. When the EIAV RT proteins were examined by in situ activity gel assays, polymerase activity was found to be principally associated with the 66-kDa component. The fidelity of DNA synthesis by EIAV RT was found to be equivalent to that of HIV-1 RT and lower than that of AMV RT. These observations indicate that the RTs of EIAV and HIV-1 share similar structural and functional properties.


Cytosolic [Ca2+] regulation of InsP3-evoked puffs.
InsP3-mediated puffs are fundamental building blocks of cellular Ca2+ signalling, and arise through the concerted opening of clustered InsP3Rs (InsP3 receptors) co-ordinated via Ca2+-induced Ca2+ release. Although the Ca2+ dependency of InsP3Rs has been extensively studied at the single channel level, little is known as to how changes in basal cytosolic [Ca2+] would alter the dynamics of InsP3-evoked Ca2+ signals in intact cells. To explore this question, we expressed Ca2+-permeable channels (nicotinic acetylcholine receptors) in the plasma membrane of voltage-clamped Xenopus oocytes to regulate cytosolic [Ca2+] by changing the electrochemical gradient for extracellular Ca2+ entry, and imaged Ca2+ liberation evoked by photolysis of caged InsP3. Elevation of basal cytosolic [Ca2+] strongly increased the amplitude and shortened the latency of global Ca2+ waves. In oocytes loaded with EGTA to localize Ca2+ signals, the number of sites at which puffs were observed and the frequency and latency of puffs were strongly dependent on cytosolic [Ca2+], whereas puff amplitudes were only weakly affected. The results of the present study indicate that basal cytosolic [Ca2+] strongly affects the triggering of puffs, but has less of an effect on puffs once they have been initiated.


Do patients improve in general psychiatric outpatient care? Problem severity among patients and the effectiveness of a psychiatric outpatient unit.
This study evaluated a routine psychiatric outpatient unit that admitted a variety of diagnoses and was staffed with a multi-professional team. The aim was to describe the problem severity among patients of a routine psychiatric outpatient unit in Sweden and to evaluate the statistical and clinical effectiveness of routine care assessed at the termination of treatment. Newly admitted patients were diagnosed according to the ICD-10 and completed questionnaires at the beginning and end of their treatment regarding symptoms (Brief Symptom Inventory) and interpersonal problems (Inventory of Interpersonal Problems); 98.6% of the patients belonged to the dysfunctional group at pre-treatment, showing that there were considerable sufferings among new patients. There were significant improvements in most of the variables. The effect size regarding symptoms (Global Severity Index) was d=0.76 and 0.43 in the interpersonal total score. No difference between different diagnostic groups was found. As for the clinical significant change, the results showed that 64.5% of the patients were improved regarding symptom remission but also that a considerable number of patients (60.5%) still belonged to the dysfunctional group after the treatment. The study indicates that the effectiveness of a routine psychiatric outpatient practice seems to be similar to results obtained from speciality research clinics and randomized controlled trial studies. However, the results also show that there is a considerable amount of patients still in the dysfunctional group after the treatment, a fact that implies that further improvements of the treatment could be made.


TRIGEN INTERTAN intramedullary nail versus sliding hip screw: a prospective, randomized multicenter study on pain, function, and complications in 684 patients with an intertrochanteric or subtrochanteric fracture and one year of follow-up.
Both intramedullary nails and sliding hip screws are used with good results in the treatment of intertrochanteric and subtrochanteric fractures. The aim of our study was to assess whether use of the TRIGEN INTERTAN nail, as compared with a sliding hip screw, resulted in less postoperative pain, improved functional mobility, and reduced surgical complication rates for patients with an intertrochanteric or subtrochanteric fracture. In a prospective, randomized multicenter study, 684 elderly patients were treated with the INTERTAN nail or with a sliding hip screw with or without a trochanteric stabilizing plate. The patients were assessed during their hospital stay and at three and twelve months postoperatively. A visual analogue scale (VAS) pain score was recorded at all time points, and functional mobility was assessed with use of the timed Up & Go test. The Harris hip score (HHS) was used to assess hip function more specifically. Quality of life was measured with the EuroQol-5D (EQ-5D). Radiographic findings as well as intraoperative and postoperative complications were recorded and analyzed. Patients treated with an INTERTAN nail had slightly less pain at the time of early postoperative mobilization (VAS score, 48 versus 52; p = 0.042), although this did not influence the length of the hospital stay and there was no difference at three or twelve months. Regardless of the fracture and implant type, functional mobility, hip function, patient satisfaction, and quality-of-life assessments were comparable between the groups at three and twelve months. The numbers of patients with surgical complications were similar for the two groups (twenty-nine in the sliding-hip-screw group and thirty-two in the INTERTAN group, p = 0.67). INTERTAN nails and sliding hip screws are similar in terms of pain, function, and reoperation rates twelve months after treatment of intertrochanteric and subtrochanteric fractures.


Diet and Other Lifestyle Factors Associated with Prostate Cancer Differ Between the German and Italian Region of Switzerland.
In Switzerland, prostate cancer mortality is higher in the German than in the Italian-speaking region. We aimed at exploring the association of living in one of the two regions with lifestyle factors presumably lowering the risk of prostate cancer. We pooled data from the Swiss Health Survey, conducted every 5 years 1992 - 2012. Information on diet (meat, fish, dairy, fruits and vegetables), alcohol, smoking, physical activity and body mass index were dichotomized into "risky" and "risk-reducing" lifestyle behaviour with respect to prostate cancer. Multivariable logistic regression analyses were performed to assess associations between the German and Italian region of Switzerland and each single lifestyle factor. Living in the Italian region was associated with "risk-reducing" diet, i.e. with a higher prevalence of low dairy products and meat consumption and high fish consumption (odds ratio [OR] 1.34, 95% confidence interval [CI] 1.21 - 1.48; OR 3.31, 95% CI 2.94 - 3.72; OR 1.90, 95% CI 1.71 - 2.12, respectively). However, men in the Italian region were less likely to have low alcohol consumption and regular physical activity than men in the German region (OR 0.43, 95% CI 0.36 - 0.52 and OR 0.77, 95% CI 0.69 - 0.86, respectively). Prostate cancer risk-reducing dietary behaviour (i.e., less dairy products, less meat and more fish) was more common in the Italian region, whereas other risk-reducing lifestyle behaviours were more common in the German region.


Efficacy of Honeycomb TCP-induced Microenvironment on Bone Tissue Regeneration in Craniofacial Area.
Artificial bone materials that exhibit high biocompatibility have been developed and are being widely used for bone tissue regeneration. However, there are no biomaterials that are minimally invasive and safe. In a previous study, we succeeded in developing honeycomb β-tricalcium phosphate (β-TCP) which has through-and-through holes and is able to mimic the bone microenvironment for bone tissue regeneration. In the present study, we investigated how the difference in hole-diameter of honeycomb β-TCP (hole-diameter: 75, 300, 500, and 1600 μm) influences bone tissue regeneration histologically. Its osteoconductivity was also evaluated by implantation into zygomatic bone defects in rats. The results showed that the maximum bone formation was observed on the β-TCP with hole-diameter 300μm, included bone marrow-like tissue and the pattern of bone tissue formation similar to host bone. Therefore, the results indicated that we could control bone tissue formation by creating a bone microenvironment provided by β-TCP. Also, in zygomatic bone defect model with honeycomb β-TCP, the result showed there was osseous union and the continuity was reproduced between the both edges of resected bone and β-TCP, which indicated the zygomatic bone reproduction fully succeeded. It is thus thought that honeycomb β-TCP may serve as an excellent biomaterial for bone tissue regeneration in the head, neck and face regions, expected in clinical applications.


Mutation analysis of 24 known cancer genes in the NCI-60 cell line set.
The panel of 60 human cancer cell lines (the NCI-60) assembled by the National Cancer Institute for anticancer drug discovery is a widely used resource. The NCI-60 has been characterized pharmacologically and at the molecular level more extensively than any other set of cell lines. However, no systematic mutation analysis of genes causally implicated in oncogenesis has been reported. This study reports the sequence analysis of 24 known cancer genes in the NCI-60 and an assessment of 4 of the 24 genes for homozygous deletions. One hundred thirty-seven oncogenic mutations were identified in 14 (APC, BRAF, CDKN2, CTNNB1, HRAS, KRAS, NRAS, SMAD4, PIK3CA, PTEN, RB1, STK11, TP53, and VHL) of the 24 genes. All lines have at least one mutation among the cancer genes examined, with most lines (73%) having more than one. Identification of those cancer genes mutated in the NCI-60, in combination with pharmacologic and molecular profiles of the cells, will allow for more informed interpretation of anticancer agent screening and will enhance the use of the NCI-60 cell lines for molecularly targeted screens.


Effects of mammalian herbivore declines on plant communities: observations and experiments in an African savanna.
1. Herbivores influence the structure and composition of terrestrial plant communities. However, responses of plant communities to herbivory are variable and depend on environmental conditions, herbivore identity and herbivore abundance. As anthropogenic impacts continue to drive large declines in wild herbivores, understanding the context dependence of herbivore impacts on plant communities becomes increasingly important. 2. Exclosure experiments are frequently used to assess how ecosystems reorganize in the face of large wild herbivore defaunation. Yet in many landscapes, declines in large wildlife are often accompanied by other anthropogenic activities, especially land conversion to livestock production. In such cases, exclosure experiments may not reflect typical outcomes of human-driven extirpations of wild herbivores. 3. Here, we examine how plant community responses to changes in the identity and abundance of large herbivores interact with abiotic factors (rainfall and soil properties). We also explore how effects of wild herbivores on plant communities differ between large-scale herbivore exclosures and landscape sites where anthropogenic activity has caused wildlife declines, often accompanied by livestock increases. 4. Abiotic context modulated the responses of plant communities to herbivore declines with stronger effect sizes in lower-productivity environments. Also, shifts in plant community structure, composition and species richness following wildlife declines differed considerably between exclosure experiments and landscape sites in which wild herbivores had declined and were often replaced by livestock. Plant communities in low wildlife landscape sites were distinct in both composition and physical structure from both exclosure and control sites in experiments. The power of environmental (soil and rainfall) gradients in influencing plant response to herbivores was also greatly dampened or absent in the landscape sites. One likely explanation for these observed differences is the compensatory effect of livestock associated with the depression or extirpation of wildlife. 5.Synthesis. Our results emphasize the importance of abiotic environmental heterogeneity in modulating the effects of mammalian herbivory on plant communities and the importance of such covariation in understanding effects of wild herbivore declines. They also suggest caution when extrapolating results from exclosure experiments to predict the consequences of defaunation as it proceeds in the Anthropocene.


Self-rated health in children at risk for obesity: associations of physical activity, sedentary behaviour, and BMI.
Self-rated health (SRH) is a common indicator of health-related quality of life; however, little is known about SRH in children. This study explored the associations of physical activity (PA), sedentary behavior (SED), and BMI with SRH in children at risk for obesity. Participants were 527 children aged 8-10 years in the Quebec Adipose and Lifestyle Investigation in Youth study (inclusion criteria: ≥ 1 parent clinically obese). PA and SED were measured by accelerometer, specific SED behaviors by self-report, and height and weight measured. About 40% of children were overweight or obese; 48% reported less-than- excellent health. The odds of reporting less-than-excellent health were higher among obese girls (OR 3.0, 95% CI 1.4-5.2) and boys (OR 2.7, 95% CI 1.5-6.1) versus healthy weight children. Boys not meeting PA guidelines and boys in the lowest moderate-to-vigorous PA tertile were at 2 and 6 times higher odds of less-than-excellent SRH, respectively, versus more active boys. In girls, higher computer/video time and reading time were associated with higher and lower odds of less-than-excellent SRH, respectively. Obesity is inversely associated with SRH in boys and girls, PA is positively associated with SRH in boys, and SED behaviors are associated with SRH in girls.


Gα12 ablation exacerbates liver steatosis and obesity by suppressing USP22/SIRT1-regulated mitochondrial respiration.
Nonalcoholic fatty liver disease (NAFLD) arises from mitochondrial dysfunction under sustained imbalance between energy intake and expenditure, but the underlying mechanisms controlling mitochondrial respiration have not been entirely understood. Heterotrimeric G proteins converge with activated GPCRs to modulate cell-signaling pathways to maintain metabolic homeostasis. Here, we investigated the regulatory role of G protein α12 (Gα12) on hepatic lipid metabolism and whole-body energy expenditure in mice. Fasting increased Gα12 levels in mouse liver. Gα12 ablation markedly augmented fasting-induced hepatic fat accumulation. cDNA microarray analysis from Gna12-KO liver revealed that the Gα12-signaling pathway regulated sirtuin 1 (SIRT1) and PPARα, which are responsible for mitochondrial respiration. Defective induction of SIRT1 upon fasting was observed in the liver of Gna12-KO mice, which was reversed by lentivirus-mediated Gα12 overexpression in hepatocytes. Mechanistically, Gα12 stabilized SIRT1 protein through transcriptional induction of ubiquitin-specific peptidase 22 (USP22) via HIF-1α increase. Gα12 levels were markedly diminished in liver biopsies from NAFLD patients. Consistently, Gna12-KO mice fed a high-fat diet displayed greater susceptibility to diet-induced liver steatosis and obesity due to decrease in energy expenditure. Our results demonstrate that Gα12 regulates SIRT1-dependent mitochondrial respiration through HIF-1α-dependent USP22 induction, identifying Gα12 as an upstream molecule that contributes to the regulation of mitochondrial energy expenditure.


Unusual long-chain N-acyl homoserine lactone production by and presence of quorum quenching activity in bacterial isolates from diseased tilapia fish.
Growth-dependent cell-cell communication termed quorum sensing is a key regulatory system in bacteria for controlling gene expression including virulence factors. In this study five potential bacterial pathogens including Bacillus sp. W2.2, Klebsiella sp. W4.2, Pseudomonas sp. W3 and W3.1 and Serratia sp. W2.3 were isolated from diseased Tilapia fish in Malaysia, supplied by the leading global fish supplier. Proteolytic activity assays confirmed that with the exception of Klebsiella sp. W4.2, all isolates showed distinct proteolytic activity. Furthermore Bacillus sp. W2.2 and Pseudomonas sp. strains W3 and W3.1 also displayed haemolytic activity. By using high resolution liquid chromatography mass spectrometry, we revealed the presence of unusually long-chain N-(3-oxohexadecanoyl)-homoserine lactone (3-oxo-C16-HSL) from Pseudomonas sp. W3.1 and N-dodecanoyl-homoserine lactone (C12-HSL) from Serratia sp. W2.3, respectively. Interestingly, Pseudomonas sp. W3.1 also produced a wide range of Pseudomonas quinolone signalling (PQS) molecules. Pseudomonas sp. W3 did not show any quorum sensing properties but possessed quorum quenching activity that inactivated AHLs. This study is the first documentation that shows unusual long-chain AHLs production in Serratia sp. and Pseudomonas sp. isolated from diseased fish and the latter also produce a wide range of PQS molecules.


Paradoxical effects on force generation after efficient β1-adrenoceptor knockdown in reconstituted heart tissue.
Stimulation of myocardial β(1)-adrenoceptors (AR) is a major mechanism that increases cardiac function. We investigated the functional consequences of genetic β(1)-AR knockdown in three-dimensional engineered heart tissue (EHT). For β(1)-AR knockdown, short interfering RNA (siRNA) sequences targeting specifically the β(1)-AR (shB1) and a scrambled control (shCTR) were subcloned into a recombinant adeno-associated virus (AAV)-short hairpin RNA (shRNA) expression system. Transduction efficiency was ∼100%, and radioligand binding revealed 70% lower β(1)-AR density in AAV6-shB1-transduced EHTs. Force measurements, performed over the culture period of 14 days, showed paradoxically higher force generation in AAV6-shB1 compared with shCTR under basal (0.19 ± 0.01 versus 0.13 ± 0.01 mN) and after β-AR-stimulated conditions with isoprenaline (Δfractional shortening: 72 ± 5% versus 34 ± 4%). Large scale gene expression analysis revealed that AAV6-shCTR compared with nontransduced EHTs showed only few differentially regulated genes (<20), whereas AAV6-shB1 induced marked changes in gene expression (>250 genes), indicating that β(1)-AR knockdown itself determines the outcome. None of the regulated genes pointed to obvious off-target effects to explain higher force generation. Moreover, compensational regulation of β(2)-AR signaling or changes in prominent β(1)-AR downstream targets could be ruled out. In summary, we show paradoxically higher force generation and isoprenaline responses after efficient β(1)-AR knockdown in EHTs. Our findings 1) reveal an unexpected layer of complexity in gene regulation after specific β(1)-AR knockdown rather than unspecific dysregulations through transcriptional interference, 2) challenge classic assumptions on the role of cardiac β(1)-AR, and 3) may open up new avenues for β-AR loss-of-function research in vivo.


Control of eye orientation: where does the brain's role end and the muscle's begin?
Our understanding of how the brain controls eye movements has benefited enormously from the comparison of neuronal activity with eye movements and the quantification of these relationships with mathematical models. Although these early studies focused on horizontal and vertical eye movements, recent behavioural and modelling studies have illustrated the importance, but also the complexity, of extending previous conclusions to the problems of controlling eye and head orientation in three dimensions (3-D). An important facet in understanding 3-D eye orientation and movement has been the discovery of mobile, soft-tissue sheaths or 'pulleys' in the orbit which might influence the pulling direction of extraocular muscles. Appropriately placed pulleys could generate the eye-position-dependent tilt of the ocular rotation axes which are characteristic for eye movements which follow Listing's law. Based on such pulley models of the oculomotor plant it has recently been proposed that a simple two-dimensional (2-D) neural controller would be sufficient to generate correct 3-D eye orientation and movement. In contrast to this apparent simplification in oculomotor control, multiple behavioural observations suggest that the visuo-motor transformations, as well as the premotor circuitry for saccades, pursuit eye movements and the vestibulo-ocular reflexes, must include a neural controller which operates in 3-D, even when considering an eye plant with pulleys. This review summarizes the most recent work and ideas on this controversy. In addition, by proposing directly testable hypotheses, we point out that, in analogy to the previously successful steps towards elucidating the neural control of horizontal eye movements, we need a quantitative characterization first of motoneuron and next of premotor neuron properties in 3-D before we can succeed in gaining further insight into the neural control of 3-D motor behaviours.


Parthenolide-Induced Cytotoxicity in H9c2 Cardiomyoblasts Involves Oxidative Stress.
Cardiac cellular injury as a consequence of ischemia and reperfusion involves nuclear factor-κB (NF-κ B), amongst other factors, and NF-κ B inhibitors could substantially reduce myocardial infarct size. Parthenolide, a sesquiterpene lactone compound which could inhibit NF-κ B, has been shown to ameliorate myocardial reperfusion injury but may also produce toxic effects in cardiomyocytes at high concentrations. The aim of this study was to examine the cytotoxic effects of this drug on H9c2 cardiomyoblasts, which are precursor cells of cardiomyocytes. Cell viability and apoptosis were examined by MTT and TUNEL assay, respectively, and protein expression was analyzed by western blot. Reactive oxygen species (ROS) production was measured using DCFH-DA as dye. Cytosolic Ca(2+) concentration and mitochondrial membrane potential were measured microfluorimetrically using, respectively, fura 2 and rhodamine 123 as dyes. Parthenolide caused apoptosis at 30 μ M, as judged by TUNEL assay and Bax and cytochrome c translocation. It also caused collapse of mitochondrial membrane potential and endoplasmic reticulum stress. Parthenolide triggered ROS formation, and vitamin C (antioxidant) partially alleviated parthenolide-induced cell death. The results suggested that parthenolide at high concentrations caused cytotoxicity in cardiomyoblasts in part by inducing oxidative stress, and demonstrated the imperative for cautious and appropriate use of this agent in cardioprotection. Cardiomyoblast; Endoplasmic reticulum stress; Oxidative stress; Parthenolide; Reperfusion injury.


OppA, the substrate-binding subunit of the oligopeptide permease, is the major Ecto-ATPase of Mycoplasma hominis.
Most ATPases, involved in energy-driven processes, act in the cytoplasm. However, external membrane-bound ATPases have also been described in parasites and eukaryotic cells. In Mycoplasma hominis, a bacterium lacking a cell wall, the surface-exposed substrate-binding protein OppA of an oligopeptide permease (Opp) contains an ATP binding P-loop structure in the C-terminal region. With ATP affinity chromatography and tryptic digestion in the presence or absence of ATP, the functionality of the Mg(2+)-dependent ATP binding site is demonstrated. In addition to ATP, ADP also could bind to OppA. The presence of an ATPase activity on the surface of M. hominis is indicated by the inactivation of ATP hydrolyzing activity of intact mycoplasma cells by the impermeable ATPase inhibitor 4',4'-diisothiocyanostilbene-2',2'-disulfonic acid and influenced by the ATP analog 5'-fluorosulfonyl-benzoyladenosine. Comparing equimolar amounts of OppA in intact mycoplasma cells and in the purified form indicated that more than 80% of the surface-localized ATPase activity is derived from OppA, implying that OppA is the main ATPase on the surface of mycoplasma cells. Together, these data present the first evidence that the cytoadhesive substrate binding protein OppA of the oligopeptide permease also functions as an ecto-ATPase in Mycoplasma hominis.


Clinical prediction rule for atrial fibrillation after coronary artery bypass grafting.
This study was designed to devise and validate a practical prediction rule for atrial fibrillation/atrial flutter (AF) after coronary artery bypass grafting (CABG) using easily available clinical and standard electrocardiographic (ECG) criteria. Reported prediction rules for postoperative AF have suffered from inconsistent results and controversy surrounding the added predictive value of a prolonged P-wave duration. In 1,851 consecutive patients undergoing CABG with cardiopulmonary bypass, preoperative clinical characteristics and standard 12-lead ECG data were examined. Patients were continuously monitored for the occurrence of sustained postoperative AF while hospitalized. Multiple logistic regression was used to determine significant predictors of AF and to develop a prediction rule that was evaluated through jackknifing. Atrial fibrillation occurred in 508 of 1,553 patients (33%). Multivariate analysis showed that greater age (odds ratio [OR] 1.1 per year [95% confidence intervals (CI) 1.0 to 1.1], p < 0.0001), prior history of AF (OR 3.7 [95% CI 2.3 to 6.0], p < 0.0001), P-wave duration >110 ms (OR 1.3 [95% CI 1.1 to 1.7], p = 0.02), and postoperative low cardiac output (OR 3.0 [95% CI 1.7 to 5.2], p = 0.0001) were independently associated with AF risk. Using the prediction rule we defined three risk categories for AF: <60 points, 61 of 446 (14%); 60 to 79 points, 330 of 908 (36%); and >or=80 points, 117 of 199 (59%). The area under the receiver-operator characteristic curve for the model was 0.69. These data show that post-CABG AF can be predicted with moderate accuracy using easily available patient characteristics and may prove useful in prognostic and risk stratification of patients after CABG. The presence of intraatrial conduction delay on ECG contributed least to the prediction model.


Polymorphisms in C2, CFB and C3 are associated with progression to advanced age related macular degeneration associated with visual loss.
Age related macular degeneration (AMD) is a leading cause of blindness. AMD is a complex disorder caused by genetic and environmental factors in which single nucleotide polymorphisms (SNPs) in the genes CFH and LOC387715/HTRA1/ARMS2 have prognostic importance for progression to advanced AMD (with visual loss). CFH may also have a pharmacogenetic role by affecting treatment response to widely used nutritional supplements. This paper examines other AMD susceptibility genes to determine if these genotypes influenced disease progression and treatment response. Three cohorts, totalling 3137 individuals, were genotyped for SNPs in 13 genes previously published to be associated with advanced AMD (other than CFH and LOC387715/ARMS2/HTRA1). Those genes found associated were then evaluated for their involvement in disease progression. Interactions between the genes and with AREDS (Age-Related Eye Disease Study) nutritional supplements were investigated. Positive independent associations were noted in SNPs in the genes C2 (p = 0.0001, odds ratio (OR) 0.35, 95% confidence interval (CI) 0.2 to 0.6), CFB (p = 0.0001, OR 0.35, 95% CI 0.2 to 0.6), C3 (p = 0.0001, OR 3.91, 95% CI 1.94 to 7.88), APOE (epsilon4, p = 0.01, OR 0.50, 95% CI 0.29 to 0.86) and VEGFA (p = 0.01, OR 2.23, 95% CI 1.06 to 4.68). C2/CFB and C3 were independently related to progression from early/intermediate to advanced AMD with OR 0.32 (95% CI 0.14 to 0.73) and 3.32 (95% CI 1.46 to 7.59), respectively. Gene-gene and pharmacogenetic interactions were not observed. No preferential associations were observed with geographic atrophy or choroidal neovascularisation. This study provides insights into the genetic pathogenesis of AMD. Five genes have now been shown to be independently involved in progression from intermediate disease (before vision loss has occurred) to advanced disease in which blindness is frequent.


Comparison of 3 assessment modes of acupuncture effect on patients with chronic prostatitis/chronic pelvic pain syndrome: A study protocol for a randomized controlled trial.
Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a common disorder. Some studies have indicated that acupuncture may ameliorate the symptoms of CP/CPPS. However, results are varied and range widely, perhaps due to different modes of assessment including timepoints, places of assessment, and especially subjective scales. We propose to determine the efficacy of acupuncture relative to sham acupuncture for patients with CP/CPPS, and compare different modes of assessment regarding the therapeutic effects of acupuncture. Sixty patients with CP/CPPS will be randomly assigned to receive either acupuncture or sham-acupuncture (30 patients, each). Treatment will be conducted 3 times/week, for 4 weeks. The coprimary outcomes will each be the change from baseline of the total NIH (National Institutes of Health) CPSI (Chronic Prostatitis Symptom Index) score associated with 3 modes of assessment: Mode 1, the scale recorded at the hospital within 10 minutes after the last session of 4 weeks of acupuncture treatment, in the company of the outcome assessors; Mode 2, the scale recorded the same day, but not at the hospital; and Mode 3, the scale recorded at the hospital 1 to 3 days after the last acupuncture session. The 3 key secondary outcomes include will be the 3 modes assessment of the changes from baseline of the NIH-CPSI total scores in the acupuncture group at week 4 after treatment. Analysis was by intention-to-treat, and multiplicity was controlled for with a step-down closed-testing procedure. To our knowledge, previous studies did not include the details of assessment scales when determining the efficacy of acupuncture in CP/CPPS. Furthermore, it is not clear which mode was used to assess the effect. The answers provided by the proposed study may improve the reproducibility of acupuncture research and the reliability of results.


Factors associated with disability among middle-aged and older African American women with osteoarthritis.
Middle-aged and older African American women experience disproportionate rates of functional limitations and disability from osteoarthritis (OA) compared to other racial ethnic groups; however, little is known about what factors contribute to this disparity within African American women. To examine factors associated with physical function and disability among African American women ages 50-80 with OA using the disablement process model. This descriptive study included 120 African American women with OA from the Southwestern region of the United States. Regression techniques were used to model the correlates of physical function and disability and to test a mediation model. BMI and pain severity were significantly related to functional limitations. Depressive symptoms mediated the relationship between racial discrimination and disability. Biological, intra-individual, and extra-individual factors are related to disablement outcomes in this sample of African American women, which is consistent with theory suggesting the need for treatment coupled with environmental modifications. This study can inform the development of future bio-behavioral interventions.


Modelling the relationship between obesity and mental health in children and adolescents: findings from the Health Survey for England 2007.
A number of studies have reported significant associations between obesity and poor psychological wellbeing in children but findings have been inconsistent. This study utilised data from 3,898 children aged 5-16 years obtained from the Health Survey for England 2007. Information was available on Body Mass Index (BMI), parental ratings of child emotional and behavioural health (Strengths and Difficulties Questionnaire), self-reported physical activity levels and sociodemographic variables. A multilevel modelling approach was used to allow for the clustering of children within households. Curvilinear relationships between both internalising (emotional) and externalising (behavioural) symptoms and adjusted BMI were observed. After adjusting for potential confounders the relationships between obesity and psychological adjustment (reported externalising and internalising symptoms) remained statistically significant. Being overweight, rather than obese, had no impact on overall reported mental health. 17% of children with obesity were above the suggested screening threshold for emotional problems, compared to 9% of non-obese children. Allowing for clustering and potential confounding variables children classified as obese had an odds ratio (OR) of 2.13 (95% CI 1.39 to 3.26) for being above the screening threshold for an emotional disorder compared to non-obese young people. No cross-level interactions between household income and the relationships between obesity and internalising or externalising symptoms were observed. In this large, representative, UK-based community sample a curvilinear association with emotional wellbeing was observed for adjusted BMI suggesting the possibility of a threshold effect. Further research could focus on exploring causal relationships and developing targeted interventions.


Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides.
Calotropis gigantea produces specialized secondary metabolites known as cardenolides, which have anticancer and antimalarial properties. Although transcriptomic studies have been conducted in other cardenolide-producing species, no nuclear genome assembly for an Asterid cardenolide-producing species has been reported to date. A high-quality de novo assembly was generated for C. gigantea, representing 157,284,427 bp with an N50 scaffold size of 805,959 bp, for which quality assessments indicated a near complete representation of the genic space. Transcriptome data in the form of RNA-sequencing libraries from a developmental tissue series was generated to aid the annotation and construction of a gene expression atlas. Using an ab initio and evidence-driven gene annotation pipeline, 18,197 high-confidence genes were annotated. Homologous and syntenic relationships between C. gigantea and other species within the Apocynaceae family confirmed previously identified evolutionary relationships, and suggest the emergence or loss of the specialized cardenolide metabolites after the divergence of the Apocynaceae subfamilies. The C. gigantea genome assembly, annotation, and RNA-sequencing data provide a novel resource to study the cardenolide biosynthesis pathway, especially for understanding the evolutionary origin of cardenolides and the engineering of cardenolide production in heterologous organisms for existing and novel pharmaceutical applications.


In Vitro Susceptibility of Mycobacterium tuberculosis to Amikacin, Kanamycin, and Capreomycin.
Amikacin, kanamycin, and capreomycin are among the most important second-line drugs for multidrug-resistant tuberculosis. Although amikacin and kanamycin are administered at the same dose and show the same pharmacokinetics, they have different WHO breakpoints, suggesting that the two drugs have different MICs. The aim of this study was to investigate possible differences in MICs between the aminoglycosides and capreomycin. Using the direct concentration method, a range of concentrations of amikacin, kanamycin, and capreomycin (0.25, 0.50, 1.0, 2.0, 4.0, 8.0, 16.0, 32.0, and 64.0 mg/liter) were tested against 57 clinical Mycobacterium tuberculosis strains. The 7H10 agar plates were examined for mycobacterial growth after 14 days. At 2 mg/liter, 48 strains (84%) were inhibited by amikacin and only 5 strains (9%) were inhibited by kanamycin (P < 0.05, Wilcoxon signed-rank test). The median MICs of amikacin, kanamycin, and capreomycin were 2, 4, and 8 mg/liter, respectively. No difference in amikacin, kanamycin, and capreomycin MIC distributions was observed between multidrug-resistant strains and fully susceptible strains. The results indicate that amikacin is more active than kanamycin and capreomycin against M. tuberculosis with the absolute concentration method. Determination of the impact of this difference on clinical outcomes in daily practice requires a prospective study, including pharmacokinetic and pharmacodynamic evaluations.


Care After Chemotherapy: Peripheral Neuropathy, Cannabis for Symptom Control, and Mindfulness.
As cancer therapies improve, patients are living longer. With these improvements in therapy comes a responsibility to optimize patients' quality of life during cancer therapy and beyond. This report reviews three timely and important topics. The first section reviews the mechanism underlying chemotherapy-induced peripheral neuropathy and evaluates the evidence for interventions to prevent and treat peripheral neuropathy. It also provides a framework for approaching the diagnosis and management of this common and bothersome side effect. The second section addresses the controversial but effective use of cannabinoids for cancer and chemotherapy symptoms. Although clinical trials are difficult to conduct because of the political and social stigma of this class of drugs, this review provides evidence of the efficacy of cannabinoids for treatment of pain and nausea. The last section addresses the mind-body connection, with a focus on the negative emotions patients with cancer often experience. This section assesses the literature regarding mindfulness-based programs to improve cancer-related stress. These three topics may appear unrelated, but all address one common goal: treating the body and the mind to optimize quality of life during and after cancer therapy.


AQUa: an adaptive framework for compression of sequencing quality scores with random access functionality.
The past decade has seen the introduction of new technologies that significantly lowered the cost of genome sequencing. As a result, the amount of genomic data that must be stored and transmitted is increasing exponentially. To mitigate storage and transmission issues, we introduce a framework for lossless compression of quality scores. This article proposes AQUa, an adaptive framework for lossless compression of quality scores. To compress these quality scores, AQUa makes use of a configurable set of coding tools, extended with a Context-Adaptive Binary Arithmetic Coding scheme. When benchmarking AQUa against generic single-pass compressors, file sizes are reduced by up to 38.49% when comparing with GNU Gzip and by up to 6.48% when comparing with 7-Zip at the Ultra Setting, while still providing support for random access. When comparing AQUa with the purpose-built, single-pass, and state-of-the-art compressor SCALCE, which does not support random access, file sizes are reduced by up to 21.14%. When comparing AQUa with the purpose-built, dual-pass, and state-of-the-art compressor QVZ, which does not support random access, file sizes are larger by 6.42-33.47%. However, for one test file, the file size is 0.38% smaller, illustrating the strength of our single-pass compression framework. This work has been spurred by the current activity on genomic information representation (MPEG-G) within the ISO/IEC SC29/WG11 technical committee. The software is available on Github: https://github.com/tparidae/AQUa. firstname.lastname@example.com.


Residual anxiety may be associated with depressive relapse during continuation therapy of bipolar II depression.
Anxiety symptoms are common in bipolar disorder. We explored the effect of anxiety on the outcome of acute and continuation pharmacotherapy of bipolar II depression. Data were derived from a randomized double-blind 12-week acute (N = 129) and 6-month continuation (N = 55) comparison of venlafaxine versus lithium monotherapy in bipolar II depression in adults. We distinguished between the items of the Hamilton Rating Scale for Depression (HRSD) that capture depression vs. anxiety (i.e., psychomotor agitation, psychic anxiety, somatic anxiety, hypochondriasis, and obsessive-compulsive concerns) and examined the effect of treatment on depression and anxiety. Additionally, we explored whether baseline anxiety or depression predicted changes over time in depression and anxiety ratings or moderated treatment outcomes. We also explored whether residual depressive and anxious symptoms predicted relapse during continuation therapy. Venlafaxine was superior to lithium in reducing both depression and anxiety, though its effects on anxiety were more modest than those on depression. Baseline anxiety predicted change over time in anxiety, but not depression. By contrast, baseline depression did not predict change over time in depression or anxiety. Residual anxiety, specifically uncontrollable worry, was a stronger predictor of relapse than residual depression. Successful treatment of symptoms of anxiety in bipolar depression may protect against depressive relapse.


The importance of strigolactone transport regulation for symbiotic signaling and shoot branching.
This review presents the role of strigolactone transport in regulating plant root and shoot architecture, plant-fungal symbiosis and the crosstalk with several phytohormone pathways. The authors, based on their data and recently published results, suggest that long-distance, as well local strigolactone transport might occur in a cell-to-cell manner rather than via the xylem stream. Strigolactones (SLs) are recently characterized carotenoid-derived phytohormones. They play multiple roles in plant architecture and, once exuded from roots to soil, in plant-rhizosphere interactions. Above ground SLs regulate plant developmental processes, such as lateral bud outgrowth, internode elongation and stem secondary growth. Below ground, SLs are involved in lateral root initiation, main root elongation and the establishment of the plant-fungal symbiosis known as mycorrhiza. Much has been discovered on players and patterns of SL biosynthesis and signaling and shown to be largely conserved among different plant species, however little is known about SL distribution in plants and its transport from the root to the soil. At present, the only characterized SL transporters are the ABCG protein PLEIOTROPIC DRUG RESISTANCE 1 from Petunia axillaris (PDR1) and, in less detail, its close homologue from Nicotiana tabacum PLEIOTROPIC DRUG RESISTANCE 6 (PDR6). PDR1 is a plasma membrane-localized SL cellular exporter, expressed in root cortex and shoot axils. Its expression level is regulated by its own substrate, but also by the phytohormone auxin, soil nutrient conditions (mainly phosphate availability) and mycorrhization levels. Hence, PDR1 integrates information from nutrient availability and hormonal signaling, thus synchronizing plant growth with nutrient uptake. In this review we discuss the effects of PDR1 de-regulation on plant development and mycorrhization, the possible cross-talk between SLs and other phytohormone transporters and finally the need for SL transporters in different plant species.


Exploring constructive cascade networks.
Constructive algorithms have proved to be powerful methods for training feedforward neural networks. An important property of these algorithms is generalization. A series of empirical studies were performed to examine the effect of regularization on generalization in constructive cascade algorithms. It was found that the combination of early stopping and regularization resulted in better generalization than the use of early stopping alone. A cubic penalty term that greatly penalizes large weights was shown to be beneficial for generalization in cascade networks. An adaptive method of setting the regularization magnitude in constructive algorithms was introduced and shown to produce generalization results similar to those obtained with a fixed, user-optimized regularization setting. This adaptive method also resulted in the construction of smaller networks for more complex problems. The acasper algorithm, which incorporates the insights obtained from the empirical studies, was shown to have good generalization and network construction properties. This algorithm was compared to the cascade correlation algorithm on the Proben 1 and additional regression data sets.


Alcoholic Liver Disease: Pathogenesis and Current Management.
Excessive alcohol consumption is a global healthcare problem. The liver sustains the greatest degree of tissue injury by heavy drinking because it is the primary site of ethanol metabolism. Chronic and excessive alcohol consumption produces a wide spectrum of hepatic lesions, the most characteristic of which are steatosis, hepatitis, and fibrosis/cirrhosis. Steatosis is the earliest response to heavy drinking and is characterized by the deposition of fat in hepatocytes. Steatosis can progress to steatohepatitis, which is a more severe, inflammatory type of liver injury. This stage of liver disease can lead to the development of fibrosis, during which there is excessive deposition of extracellular matrix proteins. The fibrotic response begins with active pericellular fibrosis, which may progress to cirrhosis, characterized by excessive liver scarring, vascular alterations, and eventual liver failure. Among problem drinkers, about 35 percent develop advanced liver disease because a number of disease modifiers exacerbate, slow, or prevent alcoholic liver disease progression. There are still no FDA-approved pharmacological or nutritional therapies for treating patients with alcoholic liver disease. Cessation of drinking (i.e., abstinence) is an integral part of therapy. Liver transplantation remains the life-saving strategy for patients with end-stage alcoholic liver disease.


Exploring oligomeric state of the serotonin1A receptor utilizing photobleaching image correlation spectroscopy: implications for receptor function.
The oligomerization of G protein-coupled receptors (GPCRs) represents an important process in GPCR function and drug discovery. We have addressed cholesterol-dependent oligomerization state of the serotonin1A receptor, a representative GPCR and an important drug target, utilizing photobleaching image correlation spectroscopy (pbICS). pbICS allows determination of oligomeric state of membrane receptors since change in cluster density upon photobleaching is dependent on the oligomeric state. Our results show that oligomeric state of the serotonin1A receptor is modulated by cell membrane cholesterol and a trimeric population of the receptor prevails in control (normal) cholesterol conditions. Interestingly, upon lowering membrane cholesterol, the predominant oligomeric population of the receptor changes to dimers. This is associated with an increase in specific ligand binding activity of the receptor, thereby implying a crucial role of receptor dimers in ligand binding activity. Upon cholesterol replenishment, the distribution of receptor oligomers is further changed such that the trimers become the major population, with a concomitant restoration of ligand binding activity to the control level. These results demonstrate the utility of pbICS in monitoring oligomeric states of membrane receptors in general, and the cholesterol-dependent oligomeric state of the serotonin1A receptor in particular. We envision that functional correlates of oligomeric states of GPCRs could provide better understanding of GPCR function in health and disease, and help design better therapeutic strategies.


Fishing gear-related injury in California marine wildlife.
We reviewed medical records from select wildlife rehabilitation facilities in California to determine the prevalence of injury in California Brown Pelicans (Pelecanus occidentalis), gulls (Larus spp.), and pinniped species (Zalophus californianus, Mirounga angustirostris, and Phoca vitulina) due to fishing gear entanglement and ingestion from 2001 to 2006. Of 9,668 Brown Pelican, gull, and pinniped cases described during the 6-yr study period (2001-06), 1,090 (11.3%) were fishing gear-related. Pelican injuries caused by fishing gear were most common in the Monterey Bay region, where 59.6% of the pelicans rescued in this area and admitted to a rehabilitation center were injured by fishing gear over the 6-yr period. The highest prevalence of fishing gear-related injury in gulls was documented in the Los Angeles/Orange County region (16.1%), whereas the highest prevalences in pinnipeds were seen in the San Diego region (3.7%). Despite these higher prevalences of gull and pinniped fishing gear-related injuries in these specific regions, there was no statistical significance in these trends. Juvenile gulls and pinnipeds were more commonly injured by fishing gear than adults (gulls: P = 0.03, odds ratio = 1.29; pinnipeds: P = 0.01, odds ratio = 2.07). Male pinnipeds were twice as likely to be injured by fishing gear as females (P < 0.01, odds ratio = 2.19). The proportion of fishing gear-related injury cases that were successfully rehabilitated and released (percentage of cases successfully rehabilitated to the point of release out of the total number of fishing gear-related injury cases) was high in all three species groups (pelicans: 63%; gulls: 54%; pinnipeds: 70%). Fishing gear-related injuries in Brown Pelicans and gulls were highest in the fall, but there was only a significant difference between seasons for fishing gear-related injuries in pelicans. Fishing gear-related injuries in pinnipeds most commonly occurred in summer; however, a statistical difference was not detected between seasons for pinnipeds. Derelict fishing gear-lost, abandoned or discarded sport and commercial line, nets, traps, etc.-in the marine environment is a significant cause of injury in California coastal marine wildlife. We evaluated data for stranded animals only; our results may underestimate the true number of coastal marine animals injured by lost or discarded fishing gear in California.


Specific loss of histone H3 lysine 9 trimethylation and HP1gamma/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD).
Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant muscular dystrophy in which no mutation of pathogenic gene(s) has been identified. Instead, the disease is, in most cases, genetically linked to a contraction in the number of 3.3 kb D4Z4 repeats on chromosome 4q. How contraction of the 4qter D4Z4 repeats causes muscular dystrophy is not understood. In addition, a smaller group of FSHD cases are not associated with D4Z4 repeat contraction (termed "phenotypic" FSHD), and their etiology remains undefined. We carried out chromatin immunoprecipitation analysis using D4Z4-specific PCR primers to examine the D4Z4 chromatin structure in normal and patient cells as well as in small interfering RNA (siRNA)-treated cells. We found that SUV39H1-mediated H3K9 trimethylation at D4Z4 seen in normal cells is lost in FSHD. Furthermore, the loss of this histone modification occurs not only at the contracted 4q D4Z4 allele, but also at the genetically intact D4Z4 alleles on both chromosomes 4q and 10q, providing the first evidence that the genetic change (contraction) of one 4qD4Z4 allele spreads its effect to other genomic regions. Importantly, this epigenetic change was also observed in the phenotypic FSHD cases with no D4Z4 contraction, but not in other types of muscular dystrophies tested. We found that HP1gamma and cohesin are co-recruited to D4Z4 in an H3K9me3-dependent and cell type-specific manner, which is disrupted in FSHD. The results indicate that cohesin plays an active role in HP1 recruitment and is involved in cell type-specific D4Z4 chromatin regulation. Taken together, we identified the loss of both histone H3K9 trimethylation and HP1gamma/cohesin binding at D4Z4 to be a faithful marker for the FSHD phenotype. Based on these results, we propose a new model in which the epigenetic change initiated at 4q D4Z4 spreads its effect to other genomic regions, which compromises muscle-specific gene regulation leading to FSHD pathogenesis.


Effect of endogenous and synthetic antioxidants on hydrogen peroxide-induced guinea-pig colon contraction.
The effects of the endogenous antioxidant alpha-lipoic acid on guinea pig colon smooth muscle contraction (Gpcc) induced by hydrogen peroxide were examined. Having previously shown that the histone deacetylase (HDAC) benzamide inhibitor MGCD0103 inhibits guinea-pig smooth muscle contraction, as do various sulfur-containing antioxidants, we asked whether hybrid compounds possessing both alpha-lipoic acid-derived antioxidant properties and HDAC inhibitory activity could inhibit Gpcc. Guinea pig colon (Gpc) was incubated at 37 degrees C with Krebs buffer; the four stimulants-hydrogen peroxide, carbachol, histamine, and sodium fluoride-were added independently. The response to each stimulant alone was compared with that in the presence of each of the test compounds: MGCD0103, alpha-lipoic acid, and two of their hybrids, UCL M084 and UCL M109. NaF (10 mM), carbachol (0.05 microM), histamine (0.1 microM), and hydrogen peroxide (1 microM) produced Gpcc of about 50-60% above basal level. With the exception of MGCD0103 against hydrogen peroxide, all four test compounds at 1 microM-MGCD0103, alpha-lipoic acid, UCL M084, and UCL M109-produced a significant inhibition of 35-60% of Gpcc induced by hydrogen peroxide, NaF, and carbachol, although none reduced histamine or ovalbumin-induced Gpcc. Benzalkonium chloride (Bcl), a G-protein inhibitor, reduced the hydrogen peroxide-induced Gpcc by 35%. Contraction by stimulants used to induce Gpcc is known to involve G-proteins. All four test compounds-MGCD0103, alpha-lipoic acid and two of their hybrids, UCL M084 and UCL M109-reduced Gpcc induced by NaF and carbachol, suggesting that G-protein pathway involvement is relevant to the action of the test compounds, as is also indicated by the Bcl-induced inhibition of hydrogen peroxide-induced contractions. Additionally, alpha-lipoic acid and the two hybrids showed >30% inhibition of hydrogen peroxide-induced contractions, consistent with the antioxidant properties of the 1,2-dithiolane ring.


Effect of antipsychotic-induced hyperprolactinemia on anthropometric measures, insulin sensitivity and lipid profile in patients with schizophrenia or related psychoses.
This study consisting of two subprojects was undertaken to evaluate the effects of hyperprolactinemia on cardiovascular disease (CVD) risk parameters such as anthropometric measures, insulin sensitivity and blood lipids in patients with schizophrenia or related psychoses on long term treatment with antipsychotics. In subproject Ι, 45 patients receiving the 2nd generation antipsychotics risperidone, clozapine or olanzapine were compared regarding prolactin (PRL), body mass index (BMI), insulin, homeostasis model assessment of insulin resistance (HOMA-IR) and blood lipids. In subproject Π, 24 patients receiving 1st or 2nd generation antipsychotics were investigated with diurnal profile of PRL and oral glucose tolerance test (OGTT). Elevated PRL levels were found in about 45% of the patients and occurred more often in patients receiving risperidone or haloperidol, compared to patients receiving clozapine or olanzapine. In contrast, in subproject Ι, insulin and HOMA-IR were higher and high density lipoprotein cholesterol was lower in patients receiving clozapine or olanzapine, compared with patients receiving risperidone. However, PRL levels did not correlate to BMI, insulin, HOMA-IR or lipids in any of these three treatment groups. In subproject Π, OGTT showed impaired glucose tolerance in 25% and new-onset diabetes in 4% of the 24 patients investigated. Additionally, the PRL (median 24 h) levels correlated positively to the 2 h glucose level at OGTT (rs=0.42, p=0.04). Our findings point to that hyperprolactinemia due to 1st and 2nd generation antipsychotics may decrease insulin sensitivity, whereas other mechanisms probably underlie insulin resistance induced by PRL-sparing antipsychotics such as clozapine and olanzapine.


Use of a novel mobilizable vector to inactivate the scrA gene of Streptococcus sobrinus by allelic replacement.
The virulence factors of the cariogenic bacterium Streptococcus sobrinus have been difficult to assess because of a lack of tools for the genetic manipulation of this organism. The construction of an Escherichia coli-Streptococcus shuttle vector, pDL289, that can be mobilized into S. sobrinus by the conjugative plasmid pAM beta 1 was described in a previous report. The vector contains pVA380-1 for replication and mobilization in streptococci, the pSC101 replicon for maintenance in E. coli, a kanamycin resistance marker that functions in both hosts, and the multiple cloning site and lacZ from pGEM7Zf(-). pDL289 is stable with or without selection in several species of Streptococcus. In this study, a derivative with a deletion in the minus origin of the pVA380-1 component of pDL289 was constructed. This derivative, pDL289 delta 202, was less stable than pDL289 in Streptococcus gordonii Challis, Streptococcus mutans, and S. sobrinus. Both pDL289 and pDL289 delta 202 were mobilizable by pAM beta 1 into S. sobrinus, with frequencies of 3 x 10(-6) and 1 x 10(-7) transconjugants per recipient CFU, respectively. The cloned scrA gene of S. sobrinus 6715-10 coding for the EIISuc of the sucrose-specific phosphoenolpyruvate phosphotransferase system was interrupted by the insertion of a streptococcal spectinomycin resistance gene active in E. coli and streptococci. The interrupted scrA gene was subcloned into both pDL289 and pDL289 delta 202. Each recombinant plasmid was introduced into the DL1 strain of S. gordonii Challis, which was then used as a recipient for the conjugative transfer of pAM beta 1. The latter plasmid was used to mobilize each recombinant plasmid from S. gordonii Challis DL1 to S. sobrinus 6715-10RF. Subsequently, recombinants derived from a double-crossover event were isolated on the basis of resistance to spectinomycin and susceptibility to kanamycin. Recombinational events were confirmed by Southern hybridization, and the inactivation of the EII Suc in double crossovers was confirmed by phosphotransferase system assays. This is the first report of allelic replacement in S. sobrinus.


Nephrogenic systemic fibrosis in advanced chronic kidney disease: a single hospital's experience in Taiwan.
Nephrogenic systemic fibrosis (NSF) or nephrogenic fibrosing dermopathy (NFD) clinically resembles scleromyxedema which develops in the setting of advanced chronic kidney diseases. Limited data exist about its epidemiology in Asian countries. A total of 153 magnetic resonance imaging (MRI) examinations, including 81 contrast-enhancement, were identified in 127 patients with advanced chronic kidney disease at stage five undergoing MRI or angiography examination between January 2005 and July 2007, in our hospital. The diagnosis of NFD/NSF was established based on clinical manifestation and histopathology. NFD/NSF was diagnosed in none of the 105 patients on haemodialysis but in one of the 22 patients on peritoneal dialysis. This 24-year-old woman was a case of systemic lupus erythematosus since age 15 and who developed skin lesions two months before the initiation of peritoneal dialysis but nine months after four exposures to gadodiamide during MRI study. The skin condition had significantly improved within three months under a combination regimen of systemic pentoxifylline and topical clobetasol propionate ointment, with further amelioration during subsequent treatment with colchicine. Our results lend support to the predisposition of gadolinium-containing contrast agents to the development of NFD/NSF in patients with advanced renal failure, even before the initiation of dialysis. The cause of a lower incidence rate in our series remains to be determined.


Casein kinase 2 binds to the C terminus of Na+/H+ exchanger 3 (NHE3) and stimulates NHE3 basal activity by phosphorylating a separate site in NHE3.
Na(+)/H(+) exchanger 3 (NHE3) is the epithelial-brush border isoform responsible for most intestinal and renal Na(+) absorption. Its activity is both up- and down-regulated under normal physiological conditions, and it is inhibited in most diarrheal diseases. NHE3 is phosphorylated under basal conditions and Ser/Thr phosphatase inhibitors stimulate basal exchange activity; however, the kinases involved are unknown. To identify kinases that regulate NHE3 under basal conditions, NHE3 was immunoprecipitated; LC-MS/MS of trypsinized NHE3 identified a novel phosphorylation site at S(719) of the C terminus, which was predicted to be a casein kinase 2 (CK2) phosphorylation site. This was confirmed by an in vitro kinase assay. The NHE3-S719A mutant but not NHE3-S719D had reduced NHE3 activity due to less plasma membrane NHE3. This was due to reduced exocytosis plus decreased plasma membrane delivery of newly synthesized NHE3. Also, NHE3 activity was inhibited by the CK2 inhibitor 2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole DMAT when wild-type NHE3 was expressed in fibroblasts and Caco-2 cells, but the NHE3-S(719) mutant was fully resistant to DMAT. CK2 bound to the NHE3 C-terminal domain, between amino acids 590 and 667, a site different from the site it phosphorylates. CK2 binds to the NHE3 C terminus and stimulates basal NHE3 activity by phosphorylating a separate single site on the NHE3 C terminus (S(719)), which affects NHE3 trafficking.


Developing a structured education programme for clients with COPD.
This article describes the development of a Structured Education Pulmonary Rehabilitation Programme (SEPRP), for the PRINCE (Pulmonary Rehabilitation In Nurse-led Community Environments) study. This process involved a literature review of existing PR programmes, a content analysis of national and international PR programmes and a concept analysis of empowerment. Secondly, two small descriptive qualitative studies were undertaken to further inform programme content exploring the views of health professionals and clients on programme content, as well as their perceptions of living with COPD. The findings of these two stages led to the development of the eight-week PRINCE SEPRP, based on a philosophy of empowerment and the SEPRP was underpinned by the Transtheoretical model (TTM) of behaviour change. Programme content included managing medications and managing breathlessness, knowing and managing symptoms, recognizing and managing acute exacerbations as well as an individualized exercise programme. Participants' experiences of self management following participation in the SEPRP were also examined. The findings indicate that nurses working in primary care have an important role in informing the development of SEPRP as well as having a key role in their delivery. They have the potential to work in empowering ways with COPD clients and the PRINCE SEPRP is just one example of how this can be put into practice.


The genetics of spondyloarthropathies.
The spondyloarthropathies constitute a group of inflammatory joint diseases linked by shared characteristics that include a strong common genetic background. Genetic factors include major histocompatibility complex (MHC) genes, among which HLA-B27 contributes 30% of the overall genetic susceptibility to spondyloarthropathies, and non-MHC genes, none of which have been identified to date. Genome screens have identified regions that may contain susceptibility genes for spondyloarthropathies. In particular, a locus on the long arm of chromosome 9 (9q31-34) was identified by two groups working independently from each other. Studies using the candidate gene approach ruled out a role for most of the tested genes, including CARD15/NOD2. However, several independent groups have reported significant associations between ankylosing spondylitis and the IL-1 gene cluster on the long arm of chromosome 2.


Heterozygous huntingtin promotes cadmium neurotoxicity and neurodegeneration in striatal cells via altered metal transport and protein kinase C delta dependent oxidative stress and apoptosis signaling mechanisms.
Huntington's disease (HD) is functionally linked to environmental factors including cigarette use and dyshomeostasis in the levels of metals. Interestingly, one of the most abundant heavy metals in cigarettes is cadmium (Cd), which also accumulates in the striatum and causes neurotoxicity upon exposure. Thus, we hypothesized that heterozygous huntingtin (HTT), responsible for the majority of cases of HD in patients, in combination with Cd exposure would cause neurotoxicity and neurodegeneration via increased intracellular accumulation of Cd and activation of oxidative stress signaling mechanisms in a mouse striatal cell line model of HD. We report that heterozygous HTT striatal cells are significantly more susceptible to Cd-induced cytotoxicity as compared to wild-type HTT cells upon exposure for 48 h. The heterozygous HTT and Cd-induced cytotoxicity led to a NADPH oxidase (NOX) mediated oxidative stress that was attenuated by exogenous antioxidants and a NOX inhibitor, apocynin. Heterozygous HTT coupled with Cd exposure caused increased expression of protein kinase C δ (PKCδ) and other key oxidative stress proteins levels, enhanced the activation of caspase-9 and caspase-3 mediated apoptosis, and blocked the overexpression of extracellular signal-regulated kinase (ERK). We observed significantly greater intracellular accumulation of Cd and reduced expression of divalent metal transporter 1 (DMT1) protein in the heterozygous HTT striatal cells upon Cd exposure. Treatment with zinc, manganese, and iron as well as exogenous antioxidants significantly attenuated the Cd-induced cytotoxicity. Collectively, these results demonstrate that heterozygous HTT exhibits greater neurotoxic properties when coupled with Cd exposure to cause cell death via caspase mediated apoptosis, altered metal transport, and modulation of ERK and PKCδ dependent oxidative signaling mechanisms.


Nature-based supportive care opportunities: a conceptual framework.
Given preliminary evidence for positive health outcomes related to contact with nature for cancer populations, research is warranted to ascertain possible strategies for incorporating nature-based care opportunities into oncology contexts as additional strategies for addressing multidimensional aspects of cancer patients' health and recovery needs. The objective of this study was to consolidate existing research related to nature-based supportive care opportunities and generate a conceptual framework for discerning relevant applications in the supportive care setting. Drawing on research investigating nature-based engagement in oncology contexts, a two-step analytic process was used to construct a conceptual framework for guiding nature-based supportive care design and future research. Concept analysis methodology generated new representations of understanding by extracting and synthesising salient concepts. Newly formulated concepts were transposed to findings from related research about patient-reported and healthcare expert-developed recommendations for nature-based supportive care in oncology. Five theoretical concepts (themes) were formulated describing patients' reasons for engaging with nature and the underlying needs these interactions address. These included: connecting with what is genuinely valued, distancing from the cancer experience, meaning-making and reframing the cancer experience, finding comfort and safety, and vital nurturance. Eight shared patient and expert recommendations were compiled, which address the identified needs through nature-based initiatives. Eleven additional patient-reported recommendations attend to beneficial and adverse experiential qualities of patients' nature-based engagement and complete the framework. The framework outlines salient findings about helpful nature-based supportive care opportunities for ready access by healthcare practitioners, designers, researchers and patients themselves.


Systemic hematogenous maintenance of memory inflation by MCMV infection.
Several low-grade persistent viral infections induce and sustain very large numbers of virus-specific effector T cells. This was first described as a response to cytomegalovirus (CMV), a herpesvirus that establishes a life-long persistent/latent infection, and sustains the largest known effector T cell populations in healthy people. These T cells remain functional and traffic systemically, which has led to the recent exploration of CMV as a persistent vaccine vector. However, the maintenance of this remarkable response is not understood. Current models propose that reservoirs of viral antigen and/or latently infected cells in lymph nodes stimulate T cell proliferation and effector differentiation, followed by migration of progeny to non-lymphoid tissues where they control CMV reactivation. We tested this model using murine CMV (MCMV), a natural mouse pathogen and homologue of human CMV (HCMV). While T cells within draining lymph nodes divided at a higher rate than cells elsewhere, antigen-dependent proliferation of MCMV-specific effector T cells was observed systemically. Strikingly, inhibition of T cell egress from lymph nodes failed to eliminate systemic T cell division, and did not prevent the maintenance of the inflationary populations. In fact, we found that the vast majority of inflationary cells, including most cells undergoing antigen-driven division, had not migrated into the parenchyma of non-lymphoid tissues but were instead exposed to the blood supply. Indeed, the immunodominance and effector phenotype of inflationary cells, both of which are primary hallmarks of memory inflation, were largely confined to blood-localized T cells. Together these results support a new model of MCMV-driven memory inflation in which most immune surveillance occurs in circulation, and in which most inflationary effector T cells are produced in response to viral antigen presented by cells that are accessible to the blood supply.


Periodontal infection profiles in type 1 diabetes.
We investigated the levels of subgingival plaque bacteria and serum IgG responses in patients with type 1 diabetes and non-diabetic controls of comparable periodontal status. Fifty type 1 diabetes patients (mean duration 20.3 years, range 6-41) were age-and gender-matched with 50 non-diabetic individuals with similar levels of periodontal disease. Full-mouth clinical periodontal status was recorded, and eight plaque samples/person were collected and analysed by checkerboard hybridization with respect to 12 species. Homologous serum IgG titres were assessed by checkerboard immunoblotting. In a sub-sample of pairs, serum cytokines and selected markers of cardiovascular risk were assessed using multiplex technology. Among the investigated species, only levels of Eubacterium nodatum were found to be higher in diabetic patients, while none of the IgG titres differed between the groups, both before and after adjustments for microbial load. Patients with diabetes had significantly higher serum levels of soluble E-selectin (p=0.04), vascular cell adhesion molecule-1 (VCAM-1; p=0.0008), adiponectin (p=0.01) and lower levels of plasminogen activator inhibitor-1 (PAI-1; p=0.02). After controlling for the severity of periodontal disease, patients with type 1 diabetes and non-diabetic controls showed comparable subgingival infection patterns and serum antibody responses.


Liver-specific deletion of the Plpp3 gene alters plasma lipid composition and worsens atherosclerosis in apoE-/- mice.
The PLPP3 gene encodes for a ubiquitous enzyme that dephosphorylates several lipid substrates. Genome-wide association studies identified PLPP3 as a gene that plays a role in coronary artery disease susceptibility. The aim of the study was to investigate the effect of Plpp3 deletion on atherosclerosis development in mice. Because the constitutive deletion of Plpp3 in mice is lethal, conditional Plpp3 hepatocyte-specific null mice were generated by crossing floxed Plpp3 mice with animals expressing Cre recombinase under control of the albumin promoter. The mice were crossed onto the athero-prone apoE-/- background to obtain Plpp3f/fapoE-/-Alb-Cre+ and Plpp3f/fapoE-/-Alb-Cre- offspring, the latter of which were used as controls. The mice were fed chow or a Western diet for 32 or 12 weeks, respectively. On the Western diet, Alb-Cre+ mice developed more atherosclerosis than Alb-Cre- mice, both at the aortic sinus and aorta. Lipidomic analysis showed that hepatic Plpp3 deletion significantly modified the levels of several plasma lipids involved in atherosclerosis, including lactosylceramides, lysophosphatidic acids, and lysophosphatidylinositols. In conclusion, Plpp3 ablation in mice worsened atherosclerosis development. Lipidomic analysis suggested that the hepatic Plpp3 deletion may promote atherosclerosis by increasing plasma levels of several low-abundant pro-atherogenic lipids, thus providing a molecular basis for the observed results.


Phosphatase inhibitors activate normal and defective CFTR chloride channels.
The cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel is regulated by phosphorylation and dephosphorylation at multiple sites. Although activation by protein kinases has been studied in some detail, the dephosphorylation step has received little attention. This report examines the mechanisms responsible for the dephosphorylation and spontaneous deactivation ("rundown") of CFTR chloride channels excised from transfected Chinese hamster ovary (CHO) and human airway epithelial cells. We report that the alkaline phosphatase inhibitors bromotetramisole, 3-isobutyl-1-methylxanthine, theophylline, and vanadate slow the rundown of CFTR channel activity in excised membrane patches and reduce dephosphorylation of CFTR protein in isolated membranes. It was also found that in unstimulated cells, CFTR channels can be activated by exposure to phosphatase inhibitors alone. Most importantly, exposure of mammalian cells to phosphatase inhibitors alone activates CFTR channels that have disease-causing mutations, provided the mutant channels are present in the plasma membrane (R117H, G551D, and delta F508 after cooling). These results suggest that CFTR dephosphorylation is dynamic and that membrane-associated phosphatase activity may be a potential therapeutic target for the treatment of cystic fibrosis.


Challenges in the development of bio-based solvents: a case study on methyl(2,2-dimethyl-1,3-dioxolan-4-yl)methyl carbonate as an alternative aprotic solvent.
Many traditional solvents have drawbacks including sustainability and toxicity issues. Legislation, such as REACH, is driving the move towards less hazardous chemicals and production processes. Therefore, safer bio-based solvents need to be developed. Herein, a 10 step method has been proposed for the development of new bio-based solvents, which utilises a combination of in silico modelling of Hansen solubility parameters (HSPs), experimental Kamlet-Abboud-Taft parameters, a selection of green synthetic routes followed by application testing and toxicity measurements. The challenges that the chemical industry face in the development of new bio-based solvents are highlighted through a case study on methyl(2,2-dimethyl-1,3-dioxolan-4-yl)methyl carbonate (MMC), which can be synthesised from glycerol. Although MMC is an attractive candidate as a replacement solvent, simply being bio-derived is not enough for a molecule to be regarded as green. The methodology of solvent development described here is a broadly applicable protocol that will indicate if a new bio-based solvent is functionally proficient, and will also highlight the importance of early stage Kamlet-Abboud-Taft parameters determination and toxicity testing in the development of a green solvent.


Anatomical coupling among distributed cortical regions in youth varies as a function of individual differences in vocabulary abilities.
Patient lesion and functional magnetic resonance imaging (fMRI) studies have provided convincing evidence that a distributed brain network subserves word knowledge. However, little is known about the structural correlates of this network within the context of typical development and whether anatomical coupling in linguistically relevant regions of cortex varies as a function of vocabulary skill. Here we investigate the association between vocabulary and anatomical coupling in 235 typically developing youth (ages 6-19 years) using structural MRI. The study's primary aim was to evaluate whether higher vocabulary performance was associated with greater vertex-level cortical thickness covariation in distributed regions of cortex known to be associated with word knowledge. Results indicate that better vocabulary skills are associated with greater anatomical coupling in several linguistically relevant regions of cortex, including the left inferior parietal (temporal-parietal junction), inferior temporal, middle frontal, and superior frontal gyri and the right inferior frontal and precentral gyri. Furthermore, in high vocabulary scorers, stronger coupling is found among these regions. Thus, complementing patient and fMRI studies, this is the first investigation to highlight the relevance of anatomical covariance within the cortex to vocabulary skills in typically developing youth, further elucidating the distributed nature of neural systems subserving word knowledge.