A critical analysis of regulated river ecosystem responses to managed environmental flows from reservoirs

Summary 1.The flow regime of a river is fundamental in determining its ecological characteristics. Impoundment of rivers has been documented to severely impact the natural flow regime, resulting in abiotic and biotic changes in downstream ecosystems. Contemporary water legislation is driving increasing concern among environmentalists and water resource managers with respect to how these impacts can be mitigated. This has stimulated research aimed at assessing the relationship between reservoir outflow modification (i.e. managed environmental flows) and downstream ecosystem responses. 2.We carried out a critical review and synthesis of the global literature concerning post-impoundment reservoir outflow modification and associated downstream biotic and abiotic responses. Seventy-six studies published between 1981 and 2012 were analysed. In contrast to previous studies of this subject, we systematically assessed the methodological quality of research to identify strengths and weaknesses of the approaches. We also undertook a novel quantification of ecosystem responses to flow modification, thus enabling identification of priorities for future research. 3.We identified that: (i) there was a research bias towards North American and Western European studies; (ii) the majority of studies reported changes in flow magnitude (e.g. artificial floods) and primarily focused on traditionally monitored ecological groups (e.g. fish); (iii) relationships between flow, biota (e.g. macroinvertebrates) and water quality (e.g. electrical conductivity and suspended solids concentration) were evident, demonstrating the potential for managed environmental flows to manipulate river ecosystems; (iv) site-specific factors (e.g. location, climate) are likely to be important as some ecosystem responses were inconsistent between studies (e.g. fish movement in response to increases in flow magnitude); and (v) quality of study design, methodological and analytical techniques varied, and these factors may have contributed to the reported variability of ecosystem response. 4.To advance scientific understanding and guide future management of regulated flow regimes, we highlight a pressing need for: (i) diversification of study locations as well as flow modification and ecosystem response types assessed; (ii) a focus on understanding flow–ecosystem response relationships at regional scales; (iii) further quantitative studies to enable robust statistical analyses in future meta-analyses; and (iv) robust monitoring of flow experiments and the use of contemporary statistical techniques to extract maximum knowledge from ecological response data

Live to cheat another day: bacterial dormancy facilitates the social exploitation of beta-lactamases

The breakdown of antibiotics by β-lactamases may be cooperative, since resistant cells can detoxify their environment and facilitate the growth of susceptible neighbours. However, previous studies of this phenomenon have used artificial bacterial vectors or engineered bacteria to increase the secretion of β-lactamases from cells. Here, we investigated whether a broad-spectrum β-lactamase gene carried by a naturally occurring plasmid (pCT) is cooperative under a range of conditions. In ordinary batch culture on solid media, there was little or no evidence that resistant bacteria could protect susceptible cells from ampicillin, although resistant colonies could locally detoxify this growth medium. However, when susceptible cells were inoculated at high densities, late-appearing phenotypically susceptible bacteria grew in the vicinity of resistant colonies. We infer that persisters, cells that have survived antibiotics by undergoing a period of dormancy, founded these satellite colonies. The number of persister colonies was positively correlated with the density of resistant colonies and increased as antibiotic concentrations decreased. We argue that detoxification can be cooperative under a limited range of conditions: if the toxins are bacteriostatic rather than bacteridical; or if susceptible cells invade communities after resistant bacteria; or if dormancy allows susceptible cells to avoid bactericides. Resistance and tolerance were previously thought to be independent solutions for surviving antibiotics. Here, we show that these are interacting strategies: the presence of bacteria adopting one solution can have substantial effects on the fitness of their neighbours

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems

Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational modifications. Rule-based modeling overcomes this problem by representing molecules as structured objects and encoding their interactions as pattern-based rules. This greatly simplifies the process of model specification, avoiding the tedious and error prone task of manually enumerating all species and reactions that can potentially exist in a system. From a simulation perspective, rule-based models can be expanded algorithmically into fully-enumerated reaction networks and simulated using a variety of network-based simulation methods, such as ordinary differential equations or Gillespie's algorithm, provided that the network is not exceedingly large. Alternatively, rule-based models can be simulated directly using particle-based kinetic Monte Carlo methods. This "network-free" approach produces exact stochastic trajectories with a computational cost that is independent of network size. However, memory and run time costs increase with the number of particles, limiting the size of system that can be feasibly simulated. Here, we present a hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches. The method takes as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles. The model is then transformed by a process of "partial network expansion" into a dynamically equivalent form that can be simulated using a population-adapted network-free simulator. The transformation method has been implemented within the open-source rule-based modeling platform BioNetGen, and resulting hybrid models can be simulated using the particle-based simulator NFsim. Performance tests show that significant memory savings can be achieved using the new approach and a monetary cost analysis provides a practical measure of its utility. © 2014 Hogg et al

Swallowing, nutrition and patient-rated functional outcomes at 6 months following two non-surgical treatments for T1-T3 oropharyngeal cancer

Altered fractionation radiotherapy with concomitant boost (AFRT-CB) may be considered an alternative treatment for patients not appropriate for chemoradiation (CRT). As functional outcomes following AFRT-CB have been minimally reported, this exploratory paper describes the outcomes of patients managed with AFRT-CB or CRT at 6 months post-treatment

Cheating on the Edge

We present the results of an individual agent-based model of antibiotic resistance in bacteria. Our model examines antibiotic resistance when two strategies exist: “producers”–who secrete a substance that breaks down antibiotics–and nonproducers (“cheats”) who do not secrete, or carry the machinery associated with secretion. The model allows for populations of up to 10,000, in which bacteria are affected by their nearest neighbors, and we assume cheaters die when there are no producers in their neighborhood. Each of 10,000 slots on our grid (a torus) could be occupied by a producer or a nonproducer, or could (temporarily) be unoccupied. The most surprising and dramatic result we uncovered is that when producers and nonproducers coexist at equilibrium, nonproducers are almost always found on the edges of clusters of producers

Syndromic (phenotypic) diarrhea in early infancy

Syndromic diarrhea (SD), also known as phenotypic diarrhea (PD) or tricho-hepato-enteric syndrome (THE), is a congenital enteropathy presenting with early-onset of severe diarrhea requiring parenteral nutrition (PN). To date, no epidemiological data are available. The estimated prevalence is approximately 1/300,000–400,000 live births in Western Europe. Ethnic origin does not appear to be associated with SD. Infants are born small for gestational age and present with facial dysmorphism including prominent forehead and cheeks, broad nasal root and hypertelorism. Hairs are woolly, easily removed and poorly pigmented. Severe and persistent diarrhea starts within the first 6 months of life (≤ 1 month in most cases) and is accompanied by severe malabsorption leading to early and relentless protein energy malnutrition with failure to thrive. Liver disease affects about half of patients with extensive fibrosis or cirrhosis. There is currently no specific biochemical profile, though a functional T-cell immune deficiency with defective antibody production was reported. Microscopic analysis of the hair show twisted hair (pili torti), aniso- and poilkilotrichosis, and trichorrhexis nodosa. Histopathological analysis of small intestine biopsy shows non-specific villous atrophy with low or no mononuclear cell infiltration of the lamina propria, and no specific histological abnormalities involving the epithelium. The etiology remains unknown. The frequent association of the disorder with parental consanguinity and/or affected siblings suggests a genetic origin with an autosomal recessive mode of transmission. Early management consists of total PN. Some infants have a rather milder phenotype with partial PN dependency or require only enteral feeding. Prognosis of this syndrome is poor, but most patients now survive, and about half of the patients may be weaned from PN at adolescence, but experience failure to thrive and final short stature

Phylogenetic Beta Diversity Metrics, Trait Evolution and Inferring the Functional Beta Diversity of Communities

The beta diversity of communities along gradients has fascinated ecologists for decades. Traditionally such studies have focused on the species composition of communities, but researchers are becoming increasingly interested in analyzing the phylogenetic composition in the hope of achieving mechanistic insights into community structure. To date many metrics of phylogenetic beta diversity have been published, but few empirical studies have been published. Further inferences made from such phylogenetic studies critically rely on the pattern of trait evolution. The present work provides a study of the phylogenetic dissimilarity of 96 tree communities in India. The work compares and contrasts eight metrics of phylogenetic dissimilarity, considers the role of phylogenetic signal in trait data and shows that environmental distance rather than spatial distance is the best correlate of phylogenetic dissimilarity in the study system

Does the timed up and go test predict future falls among British community-dwelling older people? Prospective cohort study nested within a randomised controlled trial

Background Falling is common among older people. The Timed-Up-and-Go Test (TUG) is recommended as a screening tool for falls but its predictive value has been challenged. The objectives of this study were to examine the ability of TUG to predict future falls and to estimate the optimal cut-off point to identify those with higher risk for future falls. Methods This is a prospective cohort study nested within a randomised controlled trial including 259 British community-dwelling older people ≥65 years undergoing usual care. TUG was measured at baseline. Prospective diaries captured falls over 24 weeks. A Receiver Operating Characteristic curve analysis determined the optimal cut-off point to classify future falls risk with sensitivity, specificity, and predictive values of TUG times. Logistic regression models examined future falls risk by TUG time. Results Sixty participants (23%) fell during the 24 weeks. The area under the curve was 0.58 (95% confidence interval (95% CI) = 0.49-0.67, p = 0.06), suggesting limited predictive value. The optimal cut-off point was 12.6 seconds and the corresponding sensitivity, specificity, and positive and negative predictive values were 30.5%, 89.5%, 46.2%, and 81.4%. Logistic regression models showed each second increase in TUG time (adjusted for age, gender, comorbidities, medications and past history of two falls) was significantly associated with future falls (adjusted odds ratio (OR) = 1.09, 95% CI = 1.00-1.19, p = 0.05). A TUG time ≥12.6 seconds (adjusted OR = 3.94, 95% CI = 1.69-9.21, p = 0.002) was significantly associated with future falls, after the same adjustments. Conclusions TUG times were significantly and independently associated with future falls. The ability of TUG to predict future falls was limited but with high specificity and negative predictive value. TUG may be most useful in ruling in those with a high risk of falling rather than as a primary measure in the ascertainment of risk

Changes in the Policy Environment For Infant and Young Child feeding in Vietnam, Bangladesh, and Ethiopia, and the Role of Targeted Advocacy

There is limited literature examining shifts in policy environments for nutrition and infant and young child feeding (IYCF) over time, and on the potential contribution of targeted advocacy to improved policy environments in low- and middle-income countries. This study tracked changes in the policy environment over a four-year period in three countries, and examined the role of targeted nutrition and IYCF advocacy strategies by a global initiative