The Minimum Information Required for a Glycomics Experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data

MIRAGE (Minimum Information Required for A Glycomics Experiment) is an initiative that was created by experts in the fields of glycobiology, glycoanalytics, and glycoinformatics to produce guidelines for reporting results from the diverse types of experiments and analyses used in structural and functional studies of glycans in the scientific literature. As a sequel to the guidelines for sample preparation (Struwe et al. 2016, Glycobiology, 26, 907-910) and mass spectrometry (MS) data (Kolarich et al. 2013, Mol. Cell Proteomics. 12, 991-995), here we present the first version of guidelines intended to improve the standards for reporting data from glycan microarray analyses. For each of eight areas in the workflow of a glycan microarray experiment, we provide guidelines for the minimal information that should be provided in reporting results. We hope that the MIRAGE glycan microarray guidelines proposed here will gain broad acceptance by the community, and will facilitate interpretation and reproducibility of the glycan microarray results with implications in comparison of data from different laboratories and eventual deposition of glycan microarray data in international databases

Salvage radiotherapy for patients with PSA relapse after radical prostatectomy: a single institution experience

<p>Abstract</p> <p>Background</p> <p>To assess the efficacy of salvage radiotherapy (RT) for persistent or rising PSA after radical prostatectomy and to determine prognostic factors identifying patients who may benefit from salvage RT.</p> <p>Methods</p> <p>Between 1990 and 2003, 59 patients underwent RT for PSA recurrence after radical prostatectomy. Patients received a median of 66 Gy to the prostate bed with 3D or 2D RT. The main end point was biochemical failure after salvage RT, defined as an increase of the serum PSA value >0.2 ng/ml confirmed by a second elevation.</p> <p>Results</p> <p>Median follow-up was 38 months. The 3-year and 5-year bDFS rates were 56.1% and 41.2% respectively. According to multivariate analysis, only preRT PSA ≥1 ng/ml was associated with biochemical relapse.</p> <p>Conclusion</p> <p>When delivered early, RT is an effective treatment after radical prostatectomy. Only preRT PSA ≥1 ng/ml predicted relapse.</p

A prebiotic intervention study in children with autism spectrum disorders (ASDs)

Different dietary approaches, such as gluten and casein free diets, or the use of probiotics and prebiotics have been suggested in autistic spectrum disorders in order to reduce gastrointestinal (GI) disturbances. GI symptoms are of particular interest in this population due to prevalence and correlation with the severity of behavioural traits. Nowadays, there is lack of strong evidence about the effect of dietary interventions on these problems, particularly prebiotics. Therefore, we assessed the impact of exclusion diets and a 6-week Bimuno® galactooligosaccharide (B-GOS®) prebiotic intervention in 30 autistic children. RESULTS: The results showed that children on exclusion diets reported significantly lower scores of abdominal pain and bowel movement, as well as lower abundance of Bifidobacterium spp. and Veillonellaceae family, but higher presence of Faecalibacterium prausnitzii and Bacteroides spp. In addition, significant correlations were found between bacterial populations and faecal amino acids in this group, compared to children following an unrestricted diet. Following B-GOS® intervention, we observed improvements in anti-social behaviour, significant increase of Lachnospiraceae family, and significant changes in faecal and urine metabolites. CONCLUSIONS: To our knowledge, this is the first study where the effect of exclusion diets and prebiotics has been evaluated in autism, showing potential beneficial effects. A combined dietary approach resulted in significant changes in gut microbiota composition and metabolism suggesting that multiple interventions might be more relevant for the improvement of these aspects as well as psychological traits

Chronic dialysis in the infant less than 1 year of age

Dialysis in the infant carries a mortality rate of 16%. Institution of dialysis may be the result of adequate nutritional intake, but avoidance of nutritional intake should never be seen as a way to prevent dialysis. Increased caloric intake, usually via enteral feeding tubes, is needed for optimal growth in the infant with end-stage renal disease (ESRD) in order to attain adequate nutrition with resulting good growth. “Renal” formulae may be constituted as dilute (as in the polyuric infant) or concentrated (as in the anuric infant) to fit the infants needs. Peritoneal dialysis (PD) is the usual mode of renal replacement therapy (97%), with access via a surgically placed cuffed catheter with attention to the placement of the exit site in order to avoid fecal or urinary contamination. PD volumes of 30–40 ml/kg per pass or 800–1,200 ml/m 2 per pass usually result in dialysis adequacy. Additional dietary sodium (3–5 mEq/kg per day) and protein (3–4 g/kg per day) are needed, due to sodium and protein losses in the dialysate. Protein losses are associated with significant infectious morbidity and nonresponsiveness to routine immunizations. Hemodialysis (HD) can be performed either as single- or dual-needle access that have minimal dead space (less then 2 ml) and recirculation rate (less then 5%). Attnetion to extracorporeal blood volume (<10% of intravascular volume), blood flow rates (3–5 ml/kg per min), heparinization (activated clotting times), ultrafiltration (ultrafiltration monitor), and temperature control is imperative during each treatment. Because infants' nutrition is mostly fluid, HD may be needed 4–6 days/week (especially in the oligoanuric infant) to avoid excessive volume overload between treatments. At the end of the treatment a slow blood return with minimal saline rinse is needed to avoid hemodynamic compromise. Infant dialysis, although technically challenging with a significant morbidity and mortality rate, can be safely carried out in the infant with ESRD but requires infant-specific equipment and trained personnel.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47836/1/467_2004_Article_BF00867678.pd

SMC complexes differentially compact mitotic chromosomes according to genomic context

Structural maintenance of chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply conserved SMC complexes, organize chromosomes in the budding yeast Saccharomyces cerevisiae. The canonical role of cohesin is to co-align sister chromatids, while condensin generally compacts mitotic chromosomes. We find strikingly different roles for the two complexes in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosome arms, independently of sister chromatid cohesion. Polymer simulations demonstrate that this role can be fully accounted for through cis-looping of chromatin. Second, condensin is generally dispensable for compaction along chromosome arms. Instead, it plays a targeted role compacting the rDNA proximal regions and promoting resolution of peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that distinct SMC-dependent looping activities are selectively deployed to appropriately compact chromosomes

Nothing Lasts Forever: Environmental Discourses on the Collapse of Past Societies

The study of the collapse of past societies raises many questions for the theory and practice of archaeology. Interest in collapse extends as well into the natural sciences and environmental and sustainability policy. Despite a range of approaches to collapse, the predominant paradigm is environmental collapse, which I argue obscures recognition of the dynamic role of social processes that lie at the heart of human communities. These environmental discourses, together with confusion over terminology and the concepts of collapse, have created widespread aporia about collapse and resulted in the creation of mixed messages about complex historical and social processes

Controversies in the management of advanced prostate cancer

For advanced prostate cancer, the main hormone treatment against which other treatments are assessed is surgical castration. It is simple, safe and effective, however it is not acceptable to all patients. Medical castration by means of luteinizing hormone-releasing hormone (LH-RH) analogues such as goserelin acetate provides an alternative to surgical castration. Diethylstilboestrol, previously the only non-surgical alternative to orchidectomy, is no longer routinely used. Castration reduces serum testosterone by around 90%, but does not affect androgen biosynthesis in the adrenal glands. Addition of an anti-androgen to medical or surgical castration blocks the effect of remaining testosterone on prostate cells and is termed combined androgen blockade (CAB). CAB has now been compared with castration alone (medical and surgical) in numerous clinical trials. Some trials show advantage of CAB over castration, whereas others report no significant difference. The author favours the view that CAB has an advantage over castration. No study has reported that CAB is less effective than castration. Of the anti-androgens which are available for use in CAB, bicalutamide may be associated with a lower incidence of side-effects compared with the other non-steroidal anti-androgens and, in common with nilutamide, has the advantage of once-daily dosing. Only one study has compared anti-androgens within CAB: bicalutamide plus LH-RH analogue and flutamide plus LH-RH analogue. At 160-week follow-up, the groups were equivalent in terms of survival and time to progression. However, bicalutamide caused significantly less diarrhoea than flutamide. Withdrawal and intermittent therapy with anti-androgens extend the range of treatment options. © 1999 Cancer Research Campaig

The disruption of proteostasis in neurodegenerative diseases

Cells count on surveillance systems to monitor and protect the cellular proteome which, besides being highly heterogeneous, is constantly being challenged by intrinsic and environmental factors. In this context, the proteostasis network (PN) is essential to achieve a stable and functional proteome. Disruption of the PN is associated with aging and can lead to and/or potentiate the occurrence of many neurodegenerative diseases (ND). This not only emphasizes the importance of the PN in health span and aging but also how its modulation can be a potential target for intervention and treatment of human diseases.info:eu-repo/semantics/publishedVersio

Identifying and assessing the benefits of interventions for postnatal depression: a systematic review of economic evaluations

Abstract Background Economic evaluations of interventions for postnatal depression (PND) are essential to ensure optimal healthcare decision-making. Due to the wide-ranging effects of PND on the mother, baby and whole family, there is a need to include outcomes for all those affected and to include health and non-health outcomes for accurate estimates of cost-effectiveness. This study aimed to identify interventions to prevent or treat PND for which an economic evaluation had been conducted and to evaluate the health and non-health outcomes included. Methods A systematic review was conducted applying a comprehensive search strategy across eight electronic databases and other sources. Full or partial economic evaluations of interventions involving preventive strategies (including screening), and any treatments for women with or at-risk of PND, conducted in OECD countries were included. We excluded epidemiological studies and those focussing on costs only. The included studies underwent a quality appraisal to inform the analysis. Results Seventeen economic evaluations met the inclusion criteria, the majority focused on psychological /psychosocial interventions. The interventions ranged from additional support from health professionals, peer support, to combined screening and treatment strategies. Maternal health outcomes were measured in all studies; however child health outcomes were included in only four of them. Across studies, the maternal health outcomes included were quality-adjusted-life-years gained, improvement in depressive symptoms, PND cases detected or recovered, whereas the child health outcomes included were cognitive functioning, depression, sleep and temperament. Non-health outcomes such as couples’ relationships and parent-infant interaction were rarely included. Other methodological issues such as limitations in the time horizon and perspective(s) adopted were identified, that were likely to result in imprecise estimates of benefits. Conclusions The exclusion of relevant health and non-health outcomes may mean that only a partial assessment of cost-effectiveness is undertaken, leading to sub-optimal resource allocation decisions. Future research should seek ways to expand the evaluative space of economic evaluations and explore approaches to integrate health and non-health outcomes for all individuals affected by this condition. There is a need to ensure that the time horizon adopted in studies is appropriate to allow true estimation of the long-term benefits and costs of PND interventions