Vegetation Establishment Following Floodplain Restoration in Mediterranean-climate California

Although herbaceous communities are important components of floodplain ecosystems, the factors constraining their restoration and post-restoration dynamics are poorly understood. Over the decade following restoration of a 3.2 km reach of the Merced River and floodplain in California, we tracked herbaceous community composition to distinguish floodplain habitats and utilized perturbations from revegetation treatments and post-restoration flooding to generate community assembly rule hypotheses regarding treatment effectiveness and persistence, with a particular interest in native perennials capable of suppressing non-natives over time if undisturbed. Revegetation treatments comprised combinations of sowing a sterile cover crop, sowing native species, and inoculating mycorrhizae. Most surveyed floodplain areas comprised a low terrace characterized by exceptionally droughty soils, relatively deep groundwater, and occasional flooding lasting into summer. Few species could tolerate both flood and drought to this extent, and the flood year community was generally distinct from that in non-flood years. Both communities were dominated by ruderals capable of avoiding stress and re-establishing following disturbance, including many non-native annual grassland species. Only Artemisia douglasiana responded to the treatments, as most seeded native species failed to establish, including those native perennial grasses expected to suppress non-native annuals, while other seeded native species either established adequately from natural dispersal or failed to persist through moderate flooding. Neither the cover crop nor mycorrhizal inoculation had any meaningful effect. Restoration efforts in naturally ruderal-dominated habitats may be better spent allowing natural regeneration, addressing particularly noxious invasives, and identifying or constructing habitats supporting long-lived native perennials.Although originally developed for population sizes and population growth rates, modern capture-recapture models can estimate demographic rates in complex situations: multistate models for multiple study sites and stage-structured populations, superpopulation entry probability models for recruitment, and multievent models when state assessments are uncertain. However, combinations of these complications, such as recruitment studies with uncertain state assessments, are common, yet no single model has explicitly incorporated all of these elements. Ultimately, these models estimate the same fundamental population process with the same general approach, and we combine them in a generalized hidden process model based upon a simple discrete state and transition population model with Poisson recruitment that can estimate how recruitment and survivorship rates vary with respect to measured covariates from uncertain state assessments for a stage-structured population at multiple sites. Although closely related to the motivating models, the generalized model relaxes the Markov assumption. While we provide the distributions necessary to implement Bayesian data augmentation methods, we also provide an efficient analytical likelihood with a compact parameter space that is applicable in the absence of density-dependent mortality. As a demonstration, we estimate the influence of several covariates on recruitment and survivorship rates from uncertain observations of Salix gooddingii seedlings at different locations along a riparian gradient, and we use simulations to examine variation in the precision of estimated parameters.In Mediterranean climates, cottonwoods and willows often exhibit high germination and seedling mortality rates, with recruitment occurring primarily in the occasional year when favorable spring floods improve survivorship. However, along the Robinson Reach of the Merced River, both germination and mortality rates appeared to be atypically low. To understand why these rates were so low along this recently restored flow-regulated, gravel-bedded stream, we surveyed Populus fremontii, Salix exigua, and Salix gooddingii, estimated germination and survivorship rates, and examined their correlations with factors expected to constrain recruitment, namely seed release, seed arrival, moist germination beds, light levels, groundwater depth, groundwater recession rates, and shear stress. Germination/initial establishment rates were low due in part to low seed arrival rates. Only Salix gooddingii was abundant enough to model in detail, and while moist germination surfaces increased germination/initial establishment, rates were low overall. Survivorship rates for Salix gooddingii seedlings and for small individuals were not correlated with any examined covariates. Seedlings tolerated moderate competition, and the absence of major scouring, even during 6 year flows, enabled survival at sites with sufficiently shallow groundwater that seedlings were unaffected by groundwater recession rates

Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set

We report a measurement of the bottom-strange meson mixing phase \beta_s using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of \beta_s and the B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2, -1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +- 0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +- 0.009 (syst) ps, which are consistent and competitive with determinations by other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Vegetation Establishment Following Floodplain Restoration in Mediterranean-climate California

Although herbaceous communities are important components of floodplain ecosystems, the factors constraining their restoration and post-restoration dynamics are poorly understood. Over the decade following restoration of a 3.2 km reach of the Merced River and floodplain in California, we tracked herbaceous community composition to distinguish floodplain habitats and utilized perturbations from revegetation treatments and post-restoration flooding to generate community assembly rule hypotheses regarding treatment effectiveness and persistence, with a particular interest in native perennials capable of suppressing non-natives over time if undisturbed. Revegetation treatments comprised combinations of sowing a sterile cover crop, sowing native species, and inoculating mycorrhizae. Most surveyed floodplain areas comprised a low terrace characterized by exceptionally droughty soils, relatively deep groundwater, and occasional flooding lasting into summer. Few species could tolerate both flood and drought to this extent, and the flood year community was generally distinct from that in non-flood years. Both communities were dominated by ruderals capable of avoiding stress and re-establishing following disturbance, including many non-native annual grassland species. Only Artemisia douglasiana responded to the treatments, as most seeded native species failed to establish, including those native perennial grasses expected to suppress non-native annuals, while other seeded native species either established adequately from natural dispersal or failed to persist through moderate flooding. Neither the cover crop nor mycorrhizal inoculation had any meaningful effect. Restoration efforts in naturally ruderal-dominated habitats may be better spent allowing natural regeneration, addressing particularly noxious invasives, and identifying or constructing habitats supporting long-lived native perennials. Although originally developed for population sizes and population growth rates, modern capture-recapture models can estimate demographic rates in complex situations: multistate models for multiple study sites and stage-structured populations, superpopulation entry probability models for recruitment, and multievent models when state assessments are uncertain. However, combinations of these complications, such as recruitment studies with uncertain state assessments, are common, yet no single model has explicitly incorporated all of these elements. Ultimately, these models estimate the same fundamental population process with the same general approach, and we combine them in a generalized hidden process model based upon a simple discrete state and transition population model with Poisson recruitment that can estimate how recruitment and survivorship rates vary with respect to measured covariates from uncertain state assessments for a stage-structured population at multiple sites. Although closely related to the motivating models, the generalized model relaxes the Markov assumption. While we provide the distributions necessary to implement Bayesian data augmentation methods, we also provide an efficient analytical likelihood with a compact parameter space that is applicable in the absence of density-dependent mortality. As a demonstration, we estimate the influence of several covariates on recruitment and survivorship rates from uncertain observations of Salix gooddingii seedlings at different locations along a riparian gradient, and we use simulations to examine variation in the precision of estimated parameters. In Mediterranean climates, cottonwoods and willows often exhibit high germination and seedling mortality rates, with recruitment occurring primarily in the occasional year when favorable spring floods improve survivorship. However, along the Robinson Reach of the Merced River, both germination and mortality rates appeared to be atypically low. To understand why these rates were so low along this recently restored flow-regulated, gravel-bedded stream, we surveyed Populus fremontii, Salix exigua, and Salix gooddingii, estimated germination and survivorship rates, and examined their correlations with factors expected to constrain recruitment, namely seed release, seed arrival, moist germination beds, light levels, groundwater depth, groundwater recession rates, and shear stress. Germination/initial establishment rates were low due in part to low seed arrival rates. Only Salix gooddingii was abundant enough to model in detail, and while moist germination surfaces increased germination/initial establishment, rates were low overall. Survivorship rates for Salix gooddingii seedlings and for small individuals were not correlated with any examined covariates. Seedlings tolerated moderate competition, and the absence of major scouring, even during 6 year flows, enabled survival at sites with sufficiently shallow groundwater that seedlings were unaffected by groundwater recession rates

Data from: Conservation planning for offsetting the impacts of development: a case study of biodiversity and renewable energy in the Mojave Desert

Balancing society's competing needs of development and conservation requires careful consideration of tradeoffs. Renewable energy development and biodiversity conservation are often considered beneficial environmental goals. However, the direct footprint and disturbance of renewable energy can displace species' habitat and negatively impact populations and communities if sited without ecological consideration. To mitigate residual impacts, offsets have emerged as a potentially useful tool after trying to avoid, minimize, or restore affected sites. Yet where many species or many sites are involved, the problem of efficiently designing a set of offset sites becomes increasingly complex. Spatial conservation prioritization tools are designed to handle this problem, but have seen little application to offset siting and analysis. To address this need we designed an offset siting support tool for the Desert Renewable Energy Conservation Plan (DRECP) of California, and present a case study of hypothetical impacts from solar development in the Western Mojave subsection. We compare two offset scenarios designed to mitigate a hypothetical 15,331 ha derived from proposed utility-scale solar energy development (USSED) projects. The first prioritizes offsets based precisely on impacted features, while the second offsets impacts based on the potential to maximize biodiversity conservation gains in the region. The two methods only agree on 28% of their prioritized sites and differ in meeting species-specific offset goals. Differences between the two scenarios highlight the importance of clearly specifying choices and priorities for offset siting and mitigation in general. Similarly, the effects of background climate and land use change may lessen the durability or effectiveness of offsets if not considered. Our offset siting support tool was designed specifically for the DRECP area, but with minor code modification could work well in other offset analyses, and provide continuing support for a potentially innovative mitigation solution to environmental impacts