Metabolomic profiles are gender, disease and time specific in the interleukin-10 gene-deficient mouse model of inflammatory bowel disease.

Metabolomic profiling can be used to study disease-induced changes in inflammatory bowel diseases (IBD). The aim of this study was to investigate the difference in the metabolomic profile of males and females as they developed IBD. Using the IL-10 gene-deficient mouse model of IBD and wild-type mice, urine at age 4, 6, 8, 12, 16, and 20 weeks was collected and analyzed by nuclear magnetic resonance (NMR) spectroscopy. Multivariate data analysis was employed to assess differences in metabolomic profiles that occurred as a consequence of IBD development and severity (at week 20). These changes were contrasted to those that occurred as a consequence of gender. Our results demonstrate that both IL-10 gene-deficient and wild-type mice exhibit gender-related changes in urinary metabolomic profile over time. Some male-female separating metabolites are common to both IL-10 gene-deficient and control wild-type mice and, therefore, appear to be related predominantly to gender maturation. In addition, we were able to identify gender-separating metabolites that are unique for IL-10 gene-deficient and wild-type mice and, therefore, may be indicative of a gender-specific involvement in the development and severity of the intestinal inflammation. The comparison of the gender-separating metabolomic profile from IL-10 gene-deficient mice and wild-type mice during the development of IBD allowed us to identify changes in profile patterns that appear to be imperative in the development of intestinal inflammation, but yet central to gender-related differences in IBD development. The knowledge of metabolomic profile differences by gender and by disease severity has potential clinical implications in the design of both biomarkers of disease as well as the development of optimal therapies

Coral reef drag coefficients – water depth dependence

Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 47 (2017): 1061-1075, doi:10.1175/JPO-D-16-0248.1.A major challenge in modeling the circulation over coral reefs is uncertainty in the drag coefficient because existing estimates span two orders of magnitude. Current and pressure measurements from five coral reefs are used to estimate drag coefficients based on depth-average flow, assuming a balance between the cross-reef pressure gradient and the bottom stress. At two sites wind stress is a significant term in the cross-reef momentum balance and is included in estimating the drag coefficient. For the five coral reef sites and a previous laboratory study, estimated drag coefficients increase as the water depth decreases consistent with open channel flow theory. For example, for a typical coral reef hydrodynamic roughness of 5 cm, observational estimates, and the theory indicate that the drag coefficient decreases from 0.4 in 20 cm of water to 0.005 in 10 m of water. Synthesis of results from the new field observations with estimates from previous field and laboratory studies indicate that coral reef drag coefficients range from 0.2 to 0.005 and hydrodynamic roughnesses generally range from 2 to 8 cm. While coral reef drag coefficients depend on factors such as physical roughness and surface waves, a substantial fraction of the scatter in estimates of coral reef drag coefficients is due to variations in water depth.The Red Sea field program was supported by Awards USA 00002 and KSA 00011 made by KAUST to S. Lentz and J. Churchill. The Palau field program was funded by NSF Award OCE-1220529

Surface gravity wave transformation across a platform coral reef in the Red Sea

Author Posting. © American Geophysical Union, 2016. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 121 (2016); 693–705, doi:10.1002/2015JC011142.The transformation of surface gravity waves across a platform reef in the Red Sea is examined using 18 months of observations and a wave transformation model developed for beaches. The platform reef is 200 m across, 700 m long, and the water depth varies from 0.3 to 1.2 m. Assuming changes in wave energy flux are due to wave breaking and bottom drag dissipation, the wave transformation model with optimal parameters characterizing the wave breaking (γm = 0.25) and bottom drag (hydrodynamic roughness zo = 0.08 m) accounts for 75%–90% of the observed wave-height variance at four sites. The observations and model indicate that wave breaking dominates the dissipation in a 20–30 m wide surf zone while bottom drag dominates the dissipation over the rest of the reef. Friction factors (drag coefficients) estimated from the observed wave energy balance range from fw = 0.5 to fw = 5 and increase as wave-orbital displacements decrease. The observed dependence on wave-orbital displacement is roughly consistent with extrapolation of an empirical relationship based on numerous laboratory studies of oscillatory flow. As a consequence of the dependence on wave-orbital displacement, wave friction factors vary temporally due to changes in water depth and incident wave heights, and spatially across the reef as the waves decay.USA Grant Number: 00002; KSA Grant Number: 00011; King Abdullah University of Science and Technology (KAUST); NSF Grant Numbers: OCE-1435665, OCE-1332646 and OCE-13572902016-07-2

The characteristics and dynamics of wave-driven flow across a platform coral reef in the Red Sea

Author Posting. © American Geophysical Union, 2016. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 121 (2016): 1360–1376, doi:10.1002/2015JC011141.Current dynamics across a platform reef in the Red Sea near Jeddah, Saudi Arabia, are examined using 18 months of current profile, pressure, surface wave, and wind observations. The platform reef is 700 m long, 200 m across with spatial and temporal variations in water depth over the reef ranging from 0.6 to 1.6 m. Surface waves breaking at the seaward edge of the reef cause a 2–10 cm setup of sea level that drives cross-reef currents of 5–20 cm s−1. Bottom stress is a significant component of the wave setup balance in the surf zone. Over the reef flat, where waves are not breaking, the cross-reef pressure gradient associated with wave setup is balanced by bottom stress. The quadratic drag coefficient for the depth-average flow decreases with increasing water depth from Cda = 0.17 in 0.4 m of water to Cda = 0.03 in 1.2 m of water. The observed dependence of the drag coefficient on water depth is consistent with open-channel flow theory and a hydrodynamic roughness of zo = 0.06 m. A simple one-dimensional model driven by incident surface waves and wind stress accurately reproduces the observed depth-averaged cross-reef currents and a portion of the weaker along-reef currents over the focus reef and two other Red Sea platform reefs. The model indicates the cross-reef current is wave forced and the along-reef current is partially wind forced.This research is based on work supported by awards USA 00002 and KSA 00011 KAUST. K. Davis was supported by a WHOI Postdoctoral Fellowship. T. Farrar was partly supported by NSF grant OCE-1435665. S. Lentz was partly supported by NSF grants OCE-1332646 and OCE-1357290.2016-08-1

Decellularization reduces the immune response to aortic valve allografts in the rat

ObjectivesCryopreserved valve allografts used in congenital cardiac surgery are associated with a significant cellular and humoral immune response. This might be reduced by removal of antigenic cellular elements (decellularization). The aim of this study was to determine the immunologic effect of decellularization in a rat allograft valve model.MethodsBrown Norway and Lewis rat aortic valves were decellularized with a series of hypotonic and hypertonic buffers, protease inhibitors, gentle detergents (Triton X-100), and phosphate-buffered saline. Valves were implanted into Lewis rats in syngeneic and allogeneic combinations. Cellular (CD3 and CD8) infiltrates were assessed with morphometric analysis, and the humoral response was assessed with flow cytometry.ResultsMorphometric analysis identified a significant reduction in CD3+ cell infiltrates (cells per square millimeter of leaflet tissue) in decellularized allografts compared with that seen in nondecellularized allografts at 1 (79 ± 29 vs 3310 ± 223, P < .001), 2 (26 ± 11 vs 109 ± 20, P = .004), and 4 weeks (283 ± 122 vs 984 ± 145, P < .001). Anti-CD8 staining confirmed the majority of infiltrates were cytotoxic T cells. Flow cytometric mean channel fluorescence intensity identified a negative shift (abrogated antibody formation) for decellularized allografts compared with nondecellularized allografts at 2 (19 ± 1 vs 27 ± 3, P = .033), 4 (35 ± 2 vs 133 ± 29, P = .001), and 16 weeks (28 ± 2 vs 166 ± 54, P = .017).ConclusionsDecellularization significantly reduces the cellular and humoral immune response to allograft tissue. This could prolong the durability of valve allografts and might prevent immunologic sensitization of allograft recipients

Transcriptional activation by mitochondrial transcription factor A involves preferential distortion of promoter DNA

Mitochondrial transcription factor A (mtTFA/TFAM) is a nucleus-encoded, high-mobility-group-box (HMG-box) protein that regulates transcription of the mitochondrial genome by specifically recognizing light-strand and heavy-strand promoters (LSP, HSP1). TFAM also binds mitochondrial DNA in a non-sequence specific (NSS) fashion and facilitates its packaging into nucleoid structures. However, the requirement and contribution of DNA-bending for these two different binding modes has not been addressed in detail, which prompted this comparison of binding and bending properties of TFAM on promoter and non-promoter DNA. Promoter DNA increased the stability of TFAM to a greater degree than non-promoter DNA. However, the thermodynamic properties of DNA binding for TFAM with promoter and non-specific (NS) DNA were similar to each other and to other NSS HMG-box proteins. Fluorescence resonance energy transfer assays showed that TFAM bends promoter DNA to a greater degree than NS DNA. In contrast, TFAM lacking the C-terminal tail distorted both promoter and non-promoter DNA to a significantly reduced degree, corresponding with markedly decreased transcriptional activation capacity at LSP and HSP1 in vitro. Thus, the enhanced bending of promoter DNA imparted by the C-terminal tail is a critical component of the ability of TFAM to activate promoter-specific initiation by the core mitochondrial transcription machinery

School-based interventions to prevent anxiety, depression and conduct disorders in children and young people:a systematic review, network meta-analysis and economic evaluation

Background: Schools in the UK increasingly have to respond to anxiety, depression and conduct disorder as key causes of morbidity in children and young people. Objective: The objective was to assess the comparative effectiveness of educational setting-based interventions for the prevention of anxiety, depression and conduct disorder in children and young people. Design: This study comprised a systematic review, a network meta-analysis and an economic evaluation. Data sources: The databases MEDLINE, EMBASE™ (Elsevier, Amsterdam, the Netherlands), PsycInfo® (American Psychological Association, Washington, DC, USA) and Cochrane Central Register of Controlled Trials (CENTRAL) were searched to 4 April 2018, and the NHS Economic Evaluation Database (NHS EED) was searched on 22 May 2019 for economic evaluations. No language or date filters were applied. Main outcomes: The main outcomes were post-intervention self-reported anxiety, depression or conduct disorder symptoms. Review methods: Randomised/quasi-randomised trials of universal or targeted interventions for the prevention of anxiety, depression or conduct disorder in children and young people aged 4–18 years were included. Screening was conducted independently by two reviewers. Data extraction was conducted by one reviewer and checked by a second. Intervention- and component-level network meta-analyses were conducted in OpenBUGS. A review of the economic literature and a cost–consequence analysis were conducted. Results: A total of 142 studies were included in the review, and 109 contributed to the network meta-analysis. Of the 109 studies, 57 were rated as having an unclear risk of bias for random sequence generation and allocation concealment. Heterogeneity was moderate. In universal secondary school settings, mindfulness/relaxation interventions [standardised mean difference (SMD) –0.65, 95% credible interval (CrI) –1.14 to –0.19] and cognitive–behavioural interventions (SMD –0.15, 95% CrI –0.34 to 0.04) may be effective for anxiety. Cognitive–behavioural interventions incorporating a psychoeducation component may be effective (SMD –0.30, 95% CrI –0.59 to –0.01) at preventing anxiety immediately post intervention. There was evidence that exercise was effective in preventing anxiety in targeted secondary school settings (SMD –0.47, 95% CrI –0.86 to –0.09). There was weak evidence that cognitive–behavioural interventions may prevent anxiety in universal (SMD –0.07, 95% CrI –0.23 to 0.05) and targeted (SMD –0.38, 95% CrI –0.84 to 0.07) primary school settings. There was weak evidence that cognitive–behavioural (SMD –0.04, 95% CrI –0.16 to 0.07) and cognitive–behavioural + interpersonal therapy (SMD –0.18, 95% CrI –0.46 to 0.08) may be effective in preventing depression in universal secondary school settings. Third-wave (SMD –0.35, 95% CrI –0.70 to 0.00) and cognitive–behavioural interventions (SMD –0.11, 95% CrI –0.28 to 0.05) incorporating a psychoeducation component may be effective at preventing depression immediately post intervention. There was no evidence of intervention effectiveness in targeted secondary, targeted primary or universal primary school settings post intervention. The results for university settings were unreliable because of inconsistency in the network meta-analysis. A narrative summary was reported for five conduct disorder prevention studies, all in primary school settings. None reported the primary outcome at the primary post-intervention time point. The economic evidence review reported heterogeneous findings from six studies. Taking the perspective of a single school budget and based on cognitive–behavioural therapy intervention costs in universal secondary school settings, the cost–consequence analysis estimated an intervention cost of £43 per student. Limitations: The emphasis on disorder-specific prevention excluded broader mental health interventions and restricted the number of eligible conduct disorder prevention studies. Restricting the study to interventions delivered in the educational setting may have limited the number of eligible university-level interventions. Conclusions: There was weak evidence of the effectiveness of school-based, disorder-specific prevention interventions, although effects were modest and the evidence not robust. Cognitive–behavioural therapy-based interventions may be more effective if they include a psychoeducation component. Future work: Future trials for prevention of anxiety and depression should evaluate cognitive–behavioural interventions with and without a psychoeducation component, and include mindfulness/relaxation or exercise comparators, with sufficient follow-up. Cost implications must be adequately measured. Study registration: This study is registered as PROSPERO CRD42016048184. Funding: This project was funded by the National Institute for Health Research (NIHR) Public Health Research programme and will be published in full in Public Health Research; Vol. 9, No. 8. See the NIHR Journals Library website for further project information

Acupuncture, or non-directive counselling versus usual care for the treatment of depression: a pilot study

<p>Abstract</p> <p>Background</p> <p>Depression is one of the most common reasons for consulting in primary care. Acupuncture is a popular complementary therapy choice for depression but its evidence base is poor with more robust high quality trials being required. More than half of depressed patients experience painful symptoms, with severe pain being associated with poor response to antidepressants. Acupuncture may have much to offer as an intervention for depression that also helps alleviate pain. Non-directive counselling is the most widely used psychological approach for depression in NHS settings, and provides a useful pragmatic comparison for acupuncture that would, according to our pre-trial qualitative research, be of high interest to doctors and patients.</p> <p>Methods and design</p> <p>The pilot study uses five arms and involves a pragmatic design. All patients will continue to receive usual care. Four groups of patients will be allocated to acupuncture, or non-directive counselling, in addition to usual GP care. The acupuncture and counselling arms will be further split into two groups to explore different treatment regimens. The primary outcome measure is the BDI II. Potentially eligible patients will be screened for depression using the PHQ-9, which is also a secondary outcome measure. Other secondary measures include the SF 36 bodily pain subscale, the CORE OM, the WBQ-12 and the EQ5D. Health economic data will be collected and measures of therapeutic engagement will be used to compare patient's views of therapists and GPs. The study will employ a fully randomised preference design with collection of data on patient preferences and prior expectations.</p> <p>Discussion</p> <p>This study has been implemented, and data are currently being analysed to inform the design of a full scale trial. Two practical operational issues that impacted on study implementation are discussed. Firstly, the challenge of recruiting depressed patients via GP consultation. Secondly, the problem of poor uptake and high attrition for counselling and acupuncture, which appeared to be associated with poor questionnaire return, and resulted in missing data. These problems may be relevant to other researchers working in the area of depression, or similar illnesses, where patients may lack motivation and energy to engage in research, or attend for treatment.</p> <p>Trial Registration</p> <p>Current Controlled Trials (ISRCTN 59267538)</p

Tamm Review: Management of mixed-severity fire regime forests in Oregon, Washington, and Northern California

Increasingly, objectives for forests with moderate- or mixed-severity fire regimes are to restore successionally diverse landscapes that are resistant and resilient to current and future stressors. Maintaining native species and characteristic processes requires this successional diversity, but methods to achieve it are poorly explained in the literature. In the Inland Pacific US, large, old, early seral trees were a key historical feature of many young and old forest successional patches, especially where fires frequently occurred. Large, old trees are naturally fire-tolerant, but today are often threatened by dense understory cohorts that create fuel ladders that alter likely post-fire successional pathways. Reducing these understories can contribute to resistance by creating conditions where canopy trees will survive disturbances and climatic stressors; these survivors are important seed sources, soil protectors, and critical habitat elements. Historical timber harvesting has skewed tree size and age class distributions, created hard edges, and altered native patch sizes. Manipulating these altered forests to promote development of larger patches of older, larger, and more widely-spaced trees with diverse understories will increase landscape resistance to severe fires, and enhance wildlife habitat for underrepresented conditions. Closed-canopy, multi-layered patches that develop in hot, dry summer environments are vulnerable to droughts, and they increase landscape vulnerability to insect outbreaks and severe wildfires. These same patches provide habitat for species such as the northern spotted owl, which has benefited from increased habitat area. Regional and local planning will be critical for gauging risks, evaluating trade-offs, and restoring dynamics that can support these and other species. The goal will be to manage for heterogeneous landscapes that include variably-sized patches of (1) young, middle-aged, and old, closed canopy forests growing in upper montane, northerly aspect, and valley bottom settings, (2) a similar diversity of open-canopy, fire-tolerant patches growing on ridgetops, southerly aspects, and lower montane settings, and (3) significant montane chaparral and grassland areas. Tools to achieve this goal include managed wildfire, prescribed burning, and variable density thinning at small to large scales. Specifics on ‘‘how much and where?” will vary according to physiographic, topographic and historical templates, and regulatory requirements, and be determined by means of a socio-ecological process

Tamm Review: Management of mixed-severity fire regime forests in Oregon, Washington, and Northern California

Increasingly, objectives for forests with moderate- or mixed-severity fire regimes are to restore successionally diverse landscapes that are resistant and resilient to current and future stressors. Maintaining native species and characteristic processes requires this successional diversity, but methods to achieve it are poorly explained in the literature. In the Inland Pacific US, large, old, early seral trees were a key historical feature of many young and old forest successional patches, especially where fires frequently occurred. Large, old trees are naturally fire-tolerant, but today are often threatened by dense understory cohorts that create fuel ladders that alter likely post-fire successional pathways. Reducing these understories can contribute to resistance by creating conditions where canopy trees will survive disturbances and climatic stressors; these survivors are important seed sources, soil protectors, and critical habitat elements. Historical timber harvesting has skewed tree size and age class distributions, created hard edges, and altered native patch sizes. Manipulating these altered forests to promote development of larger patches of older, larger, and more widely-spaced trees with diverse understories will increase landscape resistance to severe fires, and enhance wildlife habitat for underrepresented conditions. Closed-canopy, multi-layered patches that develop in hot, dry summer environments are vulnerable to droughts, and they increase landscape vulnerability to insect outbreaks and severe wildfires. These same patches provide habitat for species such as the northern spotted owl, which has benefited from increased habitat area. Regional and local planning will be critical for gauging risks, evaluating trade-offs, and restoring dynamics that can support these and other species. The goal will be to manage for heterogeneous landscapes that include variably-sized patches of (1) young, middle-aged, and old, closed canopy forests growing in upper montane, northerly aspect, and valley bottom settings, (2) a similar diversity of open-canopy, fire-tolerant patches growing on ridgetops, southerly aspects, and lower montane settings, and (3) significant montane chaparral and grassland areas. Tools to achieve this goal include managed wildfire, prescribed burning, and variable density thinning at small to large scales. Specifics on ‘‘how much and where?” will vary according to physiographic, topographic and historical templates, and regulatory requirements, and be determined by means of a socio-ecological process