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181.
Estimating larval retention at individual reefs by local scale three-dimensional flows is a significant problem for understanding,
and predicting, larval dispersal. Determining larval dispersal commonly involves the use of computationally demanding and
expensively calibrated/validated hydrodynamic models that resolve reef wake eddies. This study models variation in larval
retention times for a range of reef shapes and circulation regimes, using a reef-scale three-dimensional hydrodynamic model.
It also explores how well larval retention time can be estimated based on the “Island Wake Parameter”, a measure of the degree
of flow turbulence in the wake of reefs that is a simple function of flow speed, reef dimension, and vertical diffusion. The
mean residence times found in the present study (0.48–5.64 days) indicate substantial potential for self-recruitment of species
whose larvae are passive, or weak swimmers, for the first several days after release. Results also reveal strong and significant
relationships between the Island Wake Parameter and mean residence time, explaining 81–92% of the variability in retention
among reefs across a range of unidirectional flow speeds and tidal regimes. These findings suggest that good estimates of
larval retention may be obtained from relatively coarse-scale characteristics of the flow, and basic features of reef geomorphology.
Such approximations may be a valuable tool for modeling connectivity and meta-population dynamics over large spatial scales,
where explicitly characterizing fine-scale flows around reef requires a prohibitive amount of computation and extensive model
calibration. 相似文献
182.
Richard Whitlock Jeff S. Healey Stuart J. Connolly Julie Wang Matthew R. Danter Jack V. Tu Richard Novick Stephen Fremes Kevin Teoh Vikas Khera Salim Yusuf 《CMAJ》2014,186(12):905-911
Background:
Much is known about the short-term risks of stroke following cardiac surgery. We examined the rate and predictors of long-term stroke in a cohort of patients who underwent cardiac surgery.Methods:
We obtained linked data for patients who underwent cardiac surgery in the province of Ontario between 1996 and 2006. We analyzed the incidence of stroke and death up to 2 years postoperatively.Results:
Of 108 711 patients, 1.8% (95% confidence interval [CI] 1.7%–1.9%) had a stroke perioperatively, and 3.6% (95% CI 3.5%–3.7%) had a stroke within the ensuing 2 years. The strongest predictors of both early and late stroke were advanced age (≥ 65 year; adjusted hazard ratio [HR] for all stroke 1.9, 95% CI 1.8–2.0), a history of stroke or transient ischemic attack (adjusted HR 2.1, 95% CI 1.9–2.3), peripheral vascular disease (adjusted HR 1.6, 95% CI 1.5–1.7), combined coronary bypass grafting and valve surgery (adjusted HR 1.7, 95% CI 1.5–1.8) and valve surgery alone (adjusted HR 1.4, 95% CI 1.2–1.5). Preoperative need for dialysis (adjusted odds ratio [OR] 2.1, 95% CI 1.6–2.8) and new-onset postoperative atrial fibrillation (adjusted OR 1.5, 95% CI 1.3–1.6) were predictors of only early stroke. A CHADS2 score of 2 or higher was associated with an increased risk of stroke or death compared with a score of 0 or 1 (19.9% v. 9.3% among patients with a history of atrial fibrillation, 16.8% v. 7.8% among those with new-onset postoperative atrial fibrillation and 14.8% v. 5.8% among those without this condition).Interpretation:
Patients who had cardiac surgery were at highest risk of stroke in the early postoperative period and had continued risk over the ensuing 2 years, with similar risk factors over these periods. New-onset postoperative atrial fibrillation was a predictor of only early stroke. The CHADS2 score predicted stroke risk among patients with and without atrial fibrillation.Stroke remains a devastating complication following cardiac surgery, with substantial functional and economic impact.1–3 Stroke research in cardiac surgery has focused on the immediate postoperative period;4–9 however, most patients undergoing cardiac surgery have conditions such as hypertension, diabetes and atrial fibrillation, which place them at long-term risk of stroke.Early and late outcomes among patients undergoing cardiac surgery could be improved if the risk of postoperative stroke was defined and predictors of stroke identified. With this information, clinicians could optimize medical therapy for stroke risk factors such as hypertension,10,11 improve the evidence-based use of oral anticoagulation in patients with atrial fibrillation and evaluate intraoperative surgical strategies (e.g., removal of the left atrial appendage12) in patients whose clinical characteristics predict an increased risk of stroke. We examined the rate and predictors of long-term stroke within 2 years after cardiac surgery. 相似文献183.
Brett Burdo John Gray Mary P. Goetting‐Minesky Bettina Wittler Matthew Hunt Tai Li David Velliquette Julie Thomas Irene Gentzel Michael dos Santos Brito Maria Katherine Mejía‐Guerra Layne N. Connolly Dalya Qaisi Wei Li Maria I. Casas Andrea I. Doseff Erich Grotewold 《The Plant journal : for cell and molecular biology》2014,80(2):356-366
184.
Stanislaw K. Jozwiakowski Brian J. Keith Louise Gilroy Aidan J. Doherty Bernard A. Connolly 《Nucleic acids research》2014,42(15):9949-9963
A mutant of the high fidelity family-B DNA polymerase from the archaeon Thermococcus gorgonarius (Tgo-Pol), able to replicate past DNA lesions, is described. Gain of function requires replacement of the three amino acid loop region in the fingers domain of Tgo-Pol with a longer version, found naturally in eukaryotic Pol ζ (a family-B translesion synthesis polymerase). Inactivation of the 3′–5′ proof-reading exonuclease activity is also necessary. The resulting Tgo-Pol Z1 variant is proficient at initiating replication from base mismatches and can read through damaged bases, such as abasic sites and thymine photo-dimers. Tgo-Pol Z1 is also proficient at extending from primers that terminate opposite aberrant bases. The fidelity of Tgo-Pol Z1 is reduced, with a marked tendency to make changes at G:C base pairs. Together, these results suggest that the loop region of the fingers domain may play a critical role in determining whether a family-B enzyme falls into the accurate genome-replicating category or is an error-prone translesion synthesis polymerase. Tgo-Pol Z1 may also be useful for amplification of damaged DNA. 相似文献
185.
Seascape-scale trophic links for fish on inshore coral reefs 总被引:2,自引:0,他引:2
Jean P. Davis Kylie A. Pitt Brian Fry Andrew D. Olds Rod M. Connolly 《Coral reefs (Online)》2014,33(4):897-907
It is increasingly accepted that coastal habitats such as inshore coral reefs do not function in isolation but rather as part of a larger habitat network. In the Caribbean, trophic subsidies from habitats adjacent to coral reefs support the diet of reef fishes, but it is not known whether similar trophic links occur on reefs in the Indo-Pacific. Here, we test whether reef fishes in inshore coral, mangrove, and seagrass habitats are supported by trophic links. We used carbon stable isotopes and mathematical mixing models to determine the minimum proportion of resources from mangrove or seagrass habitats in the diet of five fish species from coral reefs at varying distances (0–2,200 m) from these habitats in Moreton Bay, Queensland, eastern Australia. Of the fish species that are more abundant on reefs near to mangroves, Lutjanus russelli and Acanthopagrus australis showed no minimum use of diet sources from mangrove habitat. Siganus fuscescens utilized a minimum of 25–44 % mangrove sources and this contribution increased with the proximity of reefs to mangroves (R 2 = 0.91). Seagrass or reef flat sources contributed a minimum of 14–78 % to the diet of Diagramma labiosum, a species found in higher abundance on reefs near seagrass beds, but variation in diet among reefs was unrelated to seascape structure. Seagrass or reef flat sources also contributed a minimum of 8–55 % to a fish species found only on reefs (Pseudolabrus guentheri), indicating that detrital subsidies from these habitats may subsidize fish diet on reefs. These results suggest that carbon sources from multiple habitats contribute to the functioning of inshore coral reef ecosystems and that trophic connectivity between reefs and mangroves may enhance production of a functionally important herbivore. 相似文献
186.
Jatin G. Burniston Joanne Connolly Heikki Kainulainen Steven L. Britton Lauren G. Koch 《Proteomics》2014,14(20):2339-2344
We report automated and time‐efficient (2 h per sample) profiling of muscle using ultra‐performance LC coupled directly with high‐definition MS (HDMSE). Soluble proteins extracted from rat gastrocnemius (n = 10) were digested with trypsin and analyzed in duplicate using a 90 min RPLC gradient. Protein identification and label‐free quantitation were performed from HDMSE spectra analyzed using Progenesis QI for Proteomics software. In total 1514 proteins were identified. Of these, 811 had at least three unique peptides and were subsequently used to assess the dynamic range and precision of LC‐HDMSE label‐free profiling. Proteins analyzed by LC‐HDMSE encompass the entire complement of glycolytic, β‐oxidation, and tricarboxylic acid enzymes. In addition, numerous components of the electron transport chain and protein kinases involved in skeletal muscle regulation were detected. The dynamic range of protein abundances spanned four orders of magnitude. The correlation between technical replicates of the ten biological samples was R2 = 0.9961 ± 0.0036 (95% CI = 0.9940 – 0.9992) and the technical CV averaged 7.3 ± 6.7% (95% CI = 6.87 – 7.79%). This represents the most sophisticated label‐free profiling of skeletal muscle to date. 相似文献
187.
Monica E. Calkins Tyler M. Moore Kathleen R. Merikangas Marcy Burstein Theodore D. Satterthwaite Warren B. Bilker Kosha Ruparel Rosetta Chiavacci Daniel H. Wolf Frank Mentch Haijun Qiu John J. Connolly Patrick A. Sleiman Hakon Hakonarson Ruben C. Gur Raquel E. Gur 《World psychiatry》2014,13(3):296-305
Little is known about the occurrence and predictors of the psychosis spectrum in large non‐clinical community samples of U.S. youths. We aimed to bridge this gap through assessment of psychosis spectrum symptoms in the Philadelphia Neurodevelopmental Cohort, a collaborative investigation of clinical and neurobehavioral phenotypes in a prospectively accrued cohort of youths, funded by the National Institute of Mental Health. Youths (age 11‐21; N=7,054) and collateral informants (caregiver/legal guardian) were recruited through the Children's Hospital of Philadelphia and administered structured screens of psychosis spectrum symptoms, other major psychopathology domains, and substance use. Youths were also administered a computerized neurocognitive battery assessing five neurobehavioral domains. Predictors of psychosis spectrum status in physically healthy participants (N=4,848) were examined using logistic regression. Among medically healthy youths, 3.7% reported threshold psychotic symptoms (delusions and/or hallucinations). An additional 12.3% reported significant sub‐psychotic positive symptoms, with odd/unusual thoughts and auditory perceptions, followed by reality confusion, being the most discriminating and widely endorsed attenuated symptoms. A minority of youths (2.3%) endorsed subclinical negative/disorganized symptoms in the absence of positive symptoms. Caregivers reported lower symptom levels than their children. Male gender, younger age, and non‐European American ethnicity were significant predictors of spectrum status. Youths with spectrum symptoms had reduced accuracy across neurocognitive domains, reduced global functioning, and increased odds of depression, anxiety, behavioral disorders, substance use and suicidal ideation. These findings have public health relevance for prevention and early intervention. 相似文献
188.
Determining the quality and complexity of next-generation sequencing data without a reference genome
Seyed Yahya Anvar Lusine Khachatryan Martijn Vermaat Michiel van Galen Irina Pulyakhina Yavuz Ariyurek Ken Kraaijeveld Johan T den Dunnen Peter de Knijff Peter AC ’t Hoen Jeroen FJ Laros 《Genome biology》2014,15(12)
We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users. 相似文献189.
190.
Colm G. Connolly Amanda Bischoff-Grethe Stephan J. Jordan Steven Paul Woods Ronald J. Ellis Martin P. Paulus Igor Grant for The Translational Methamphetamine AIDS Research Center Group 《PloS one》2014,9(10)