Association of ultra-processed food intake with risk of inflammatory bowel disease: Prospective cohort study

Objective: To evaluate the relation between intake of ultra-processed food and risk of inflammatory bowel disease (IBD).Design: Prospective cohort study.Setting: 21 low, middle, and high income countries across seven geographical regions (Europe and North America, South America, Africa, Middle East, south Asia, South East Asia, and China).Participants: 116 087 adults aged 35-70 years with at least one cycle of follow-up and complete baseline food frequency questionnaire (FFQ) data (country specific validated FFQs were used to document baseline dietary intake). Participants were followed prospectively at least every three years.Main outcome measures: The main outcome was development of IBD, including Crohn\u27s disease or ulcerative colitis. Associations between ultra-processed food intake and risk of IBD were assessed using Cox proportional hazard multivariable models. Results are presented as hazard ratios with 95% confidence intervals.Results: Participants were enrolled in the study between 2003 and 2016. During the median follow-up of 9.7 years (interquartile range 8.9-11.2 years), 467 participants developed incident IBD (90 with Crohn\u27s disease and 377 with ulcerative colitis). After adjustment for potential confounding factors, higher intake of ultra-processed food was associated with a higher risk of incident IBD (hazard ratio 1.82, 95% confidence interval 1.22 to 2.72 for ≥5 servings/day and 1.67, 1.18 to 2.37 for 1-4 servings/day compared with \u3c1 serving/day, P=0.006 for trend). Different subgroups of ultra-processed food, including soft drinks, refined sweetened foods, salty snacks, and processed meat, each were associated with higher hazard ratios for IBD. Results were consistent for Crohn\u27s disease and ulcerative colitis with low heterogeneity. Intakes of white meat, red meat, dairy, starch, and fruit, vegetables, and legumes were not associated with incident IBD.Conclusions: Higher intake of ultra-processed food was positively associated with risk of IBD. Further studies are needed to identify the contributory factors within ultra-processed foods.Study registration: ClinicalTrials.gov NCT03225586

P(I) Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5).

mRNA export from the nucleus depends on the ATPase activity of the DEAD-box protein Dbp5/DDX19. Although Dbp5 has measurable ATPase activity alone, several regulatory factors (e.g., RNA, nucleoporin proteins, and the endogenous small molecule InsP6) modulate catalytic activity in vitro and in vivo to facilitate mRNA export. An analysis of the intrinsic and regulator-activated Dbp5 ATPase cycle is necessary to define how these factors control Dbp5 and mRNA export. Here, we report a kinetic and equilibrium analysis of the Saccharomyces cerevisiae Dbp5 ATPase cycle, including the influence of RNA on Dbp5 activity. These data show that ATP binds Dbp5 weakly in rapid equilibrium with a binding affinity (KT~4 mM) comparable to the KM for steady-state cycling, while ADP binds an order of magnitude more tightly (KD~0.4 mM). The overall intrinsic steady-state cycling rate constant (kcat) is limited by slow, near-irreversible ATP hydrolysis and even slower subsequent phosphate release. RNA increases kcat and rate-limiting Pi release 20-fold, although Pi release continues to limit steady-state cycling in the presence of RNA, in conjunction with RNA binding. Together, this work identifies RNA binding and Pi release as important biochemical transitions within the Dbp5 ATPase cycle and provides a framework for investigating the means by which Dbp5 and mRNA export is modulated by regulatory factors.E.V.W. is supported by National Science Foundation Graduate Research Fellowship No. DGE-1122492 and J.V. is supported by an Alberta Innovates Health Solutions Postdoctoral Fellowship. M.M. and Y.M. were supported by a Senior Research Fellowship from the Wellcome Trust (101908/Z/13/Z) and by National Institutes of Health grant R01 GM102869. Research support for B.M. was provided by the Natural Sciences and Engineering Research Council of Canada (RGPIN 435380), Canada Foundation for Innovation (31271), Government of Alberta Research Capacity Program, and Canada Research Chairs program.This is the final version of the article. It first appeared from Elsevier via https://doi.org/10.1016/j.jmb.2015.12.01

Berkeley Supernova Ia Program I: Observations, Data Reduction, and Spectroscopic Sample of 582 Low-Redshift Type Ia Supernovae

In this first paper in a series we present 1298 low-redshift (z\leq0.2) optical spectra of 582 Type Ia supernovae (SNe Ia) observed from 1989 through 2008 as part of the Berkeley SN Ia Program (BSNIP). 584 spectra of 199 SNe Ia have well-calibrated light curves with measured distance moduli, and many of the spectra have been corrected for host-galaxy contamination. Most of the data were obtained using the Kast double spectrograph mounted on the Shane 3 m telescope at Lick Observatory and have a typical wavelength range of 3300-10,400 Ang., roughly twice as wide as spectra from most previously published datasets. We present our observing and reduction procedures, and we describe the resulting SN Database (SNDB), which will be an online, public, searchable database containing all of our fully reduced spectra and companion photometry. In addition, we discuss our spectral classification scheme (using the SuperNova IDentification code, SNID; Blondin & Tonry 2007), utilising our newly constructed set of SNID spectral templates. These templates allow us to accurately classify our entire dataset, and by doing so we are able to reclassify a handful of objects as bona fide SNe Ia and a few other objects as members of some of the peculiar SN Ia subtypes. In fact, our dataset includes spectra of nearly 90 spectroscopically peculiar SNe Ia. We also present spectroscopic host-galaxy redshifts of some SNe Ia where these values were previously unknown. [Abridged]Comment: 34 pages, 11 figures, 11 tables, revised version, re-submitted to MNRAS. Spectra will be released in January 2013. The SN Database homepage (http://hercules.berkeley.edu/database/index_public.html) contains the full tables, plots of all spectra, and our new SNID template

Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants

Background: Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification. Results: We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. First, sequences of four chromosomes in the 22 Mb Micromonas pusilla (CCMP1545) genome were finished. Comparison with the finished 21 Mb genome of Micromonas commoda (RCC299; named herein) shows they share ≤8,141 of ~10,000 protein-encoding genes, depending on the analysis method. Unlike RCC299 and other sequenced eukaryotes, CCMP1545 has two abundant repetitive intron types and a high percent (26 %) GC splice donors. Micromonas has more genus-specific protein families (19 %) than other genome sequenced prasinophytes (11 %). Comparative analyses using predicted proteomes from other prasinophytes reveal proteins likely related to scale formation and ancestral photosynthesis. Our studies also indicate that peptidoglycan (PG) biosynthesis enzymes have been lost in multiple independent events in select prasinophytes and plants. However, CCMP1545, polar Micromonas CCMP2099 and prasinophytes from other classes retain the entire PG pathway, like moss and glaucophyte algae. Surprisingly, multiple vascular plants also have the PG pathway, except the Penicillin-Binding Protein, and share a unique bi-domain protein potentially associated with the pathway. Alongside Micromonas experiments using antibiotics that halt bacterial PG biosynthesis, the findings highlight unrecognized phylogenetic complexity in PG-pathway retention and implicate a role in chloroplast structure or division in several extant Viridiplantae lineages. Conclusions: Extensive differences in gene loss and architecture between related prasinophytes underscore their divergence. PG biosynthesis genes from the cyanobacterial endosymbiont that became the plastid, have been selectively retained in multiple plants and algae, implying a biological function. Our studies provide robust genomic resources for emerging model algae, advancing knowledge of marine phytoplankton and plant evolution

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution

Effect Modification of the Association between Short-term Meteorological Factors and Mortality by Urban Heat Islands in Hong Kong

Background Prior studies from around the world have indicated that very high temperatures tend to increase summertime mortality. However possible effect modification by urban micro heat islands has only been examined by a few studies in North America and Europe. This study examined whether daily mortality in micro heat island areas of Hong Kong was more sensitive to short term changes in meteorological conditions than in other areas. Method An urban heat island index (UHII) was calculated for each of Hong Kong’s 248 geographical tertiary planning units (TPU). Daily counts of all natural deaths among Hong Kong residents were stratified according to whether the place of residence of the decedent was in a TPU with high (above the median) or low UHII. Poisson Generalized Additive Models (GAMs) were used to estimate the association between meteorological variables and mortality while adjusting for trend, seasonality, pollutants and flu epidemics. Analyses were restricted to the hot season (June-September). Results Mean temperatures (lags 0–4) above 29°C and low mean wind speeds (lags 0–4) were significantly associated with higher daily mortality and these associations were stronger in areas with high UHII. A 1°C rise above 29°C was associated with a 4.1% (95% confidence interval (CI): 0.7%, 7.6%) increase in natural mortality in areas with high UHII but only a 0.7% (95% CI: −2.4%, 3.9%) increase in low UHII areas. Lower mean wind speeds (5th percentile vs. 95th percentile) were associated with a 5.7% (95% CI: 2.7, 8.9) mortality increase in high UHII areas vs. a −0.3% (95% CI: −3.2%, 2.6%) change in low UHII areas. Conclusion The results suggest that urban micro heat islands exacerbate the negative health consequences of high temperatures and low wind speeds. Urban planning measures designed to mitigate heat island effects may lessen the health effects of unfavorable summertime meteorological conditions

Developing an online learning community for mental health professionals and service users: a discursive analysis

<p>Abstract</p> <p>Background</p> <p>There is increasing interest in online collaborative learning tools in health education, to reduce costs, and to offer alternative communication opportunities. Patients and students often have extensive experience of using the Internet for health information and support, and many health organisations are increasingly trying out online tools, while many healthcare professionals are unused to, and have reservations about, online interaction.</p> <p>Methods</p> <p>We ran three week-long collaborative learning courses, in which 19 mental health professionals (MHPs) and 12 mental health service users (MHSUs) participated. Data were analysed using a discursive approach to consider the ways in which participants interacted, and how this contributed to the goal of online learning about using Internet technologies for mental health practice.</p> <p>Results</p> <p>MHSUs and MHPs were able to discuss issues together, listening to the views of the other stakeholders. Discussions on synchronous format encouraged participation by service users while the MHPs showed a preference for an asynchronous format with longer, reasoned postings. Although participants regularly drew on their MHP or MHSU status in discussions, and participants typically drew on either a medical expert discourse or a "lived experience" discourse, there was a blurred boundary as participants shifted between these positions.</p> <p>Conclusions</p> <p>The anonymous format was successful in that it produced a "co-constructed asymmetry" which permitted the MHPs and MHSUs to discuss issues online, listening to the views of other stakeholders. Although anonymity was essential for this course to 'work' at all, the recourse to expert or lay discourses demonstrates that it did not eliminate the hierarchies between teacher and learner, or MHP and MHSU. The mix of synchronous and asynchronous formats helped MHSUs to contribute. Moderators might best facilitate service user experience by responding within an experiential discourse rather than an academic one.</p

A Subset of Latency-Reversing Agents Expose HIV-Infected Resting CD4⁺ T-Cells to Recognition by Cytotoxic T-Lymphocytes

Resting CD4⁺ T-cells harboring inducible HIV proviruses are a critical reservoir in antiretroviral therapy (ART)-treated subjects. These cells express little to no viral protein, and thus neither die by viral cytopathic effects, nor are efficiently cleared by immune effectors. Elimination of this reservoir is theoretically possible by combining latency-reversing agents (LRAs) with immune effectors, such as CD8⁺ T-cells. However, the relative efficacy of different LRAs in sensitizing latently-infected cells for recognition by HIV-specific CD8⁺ T-cells has not been determined. To address this, we developed an assay that utilizes HIV-specific CD8⁺ T-cell clones as biosensors for HIV antigen expression. By testing multiple CD8⁺ T-cell clones against a primary cell model of HIV latency, we identified several single agents that primed latently-infected cells for CD8⁺ T-cell recognition, including IL-2, IL-15, two IL-15 superagonists (IL-15SA and ALT-803), prostratin, and the TLR-2 ligand Pam₃CSK₄. In contrast, we did not observe CD8⁺ T-cell recognition of target cells following treatment with histone deacetylase inhibitors or with hexamethylene bisacetamide (HMBA). In further experiments we demonstrate that a clinically achievable concentration of the IL-15 superagonist ‘ALT-803’, an agent presently in clinical trials for solid and hematological tumors, primes the natural ex vivo reservoir for CD8⁺ T-cell recognition. Thus, our results establish a novel experimental approach for comparative evaluation of LRAs, and highlight ALT-803 as an LRA with the potential to synergize with CD8⁺ T-cells in HIV eradication strategies.United States. National Institutes of Health (AI111860

Summarizing activity limitations in children with chronic illnesses living in the community: a measurement study of scales using supplemented interRAI items

<p>Abstract</p> <p>Background</p> <p>To test the validity and reliability of scales intended to measure activity limitations faced by children with chronic illnesses living in the community. The scales were based on information provided by caregivers to service program personnel almost exclusively trained as social workers. The items used to measure activity limitations were interRAI items supplemented so that they were more applicable to activity limitations in children with chronic illnesses. In addition, these analyses may shed light on the possibility of gathering functional information that can span the life course as well as spanning different care settings.</p> <p>Methods</p> <p>Analyses included testing the internal consistency, predictive, concurrent, discriminant and construct validity of two activity limitation scales. The scales were developed using assessment data gathered in the United States of America (USA) from over 2,700 assessments of children aged 4 to 20 receiving Medicaid Early and Periodic Screening, Diagnostic and Treatment (EPSDT) services, specifically Personal Care Services to assist children in overcoming activity limitations. The Medicaid program in the USA pays for health care services provided to children in low-income households. Data were collected in a single, large state in the southwestern USA in late 2008 and early 2009. A similar sample of children was assessed in 2010, and the analyses were replicated using this sample.</p> <p>Results</p> <p>The two scales exhibited excellent internal consistency. Evidence on the concurrent, predictive, discriminant, and construct validity of the proposed scales was strong. Quite importantly, scale scores were not correlated with (confounded with) a child's developmental stage or age. The results for these scales and items were consistent across the two independent samples.</p> <p>Conclusions</p> <p>Unpaid caregivers, usually parents, can provide assessors lacking either medical or nursing training with reliable and valid information on the activity limitations of children. One can summarize these data in scales that are both internally consistent and valid. Researchers and clinicians can use supplemented interRAI items to provide guidance for professionals and programs serving children, as well as older persons. This research emphasizes the importance of developing medical information systems that allow one to integrate information not only across care settings but also across an individual's life course.</p