Predicting species abundance distributions by simultaneously using number and biomass as units of measurement

The universal observation that some species in an ecological community are common, but many more are rare, is neatly encapsulated in a species abundance distribution (SAD)1. However, the shape of the distribution can depend on the currency used to measure abundance 2. Here we show how the SADs for numerical abundance and biomass are related and how this relationship can be used to predict the form of the SAD. When plotted in log numerical abundance, log biomass space, species points lie within an approximately triangular area the limits of which are set by body size range, and the upper limit of abundance in both metrics. Under the simplifying, but reasonable, assumption that the observed scatter of species within this region is random, the shape of the SAD is immediately derived from simple geometrical considerations. For the SAD of numerical abundance this is a power curve. The biomass SAD can be either a power curve or, more frequently, a unimodal curve, which can approximate a log normal. This log triangular random placement model serves as a null hypothesis against which actual communities can be compared. Data from two intensively surveyed local communities indicate that it can give a good approximation, with species scattered within a triangle. Further, we can predict the consequences, for the SAD, of size-selective sampling protocols. We argue that mechanistic models of SADs must be able to account for the relative abundance of species in alternative currencies. Moreover, this approach will shed light on niche packing and may have application in environmental monitoring

Hfq binding changes the structure of Escherichia coli small noncoding RNAs OxyS and RprA, which are involved in the riboregulation of rpoS

OxyS and RprA are two small noncoding RNAs (sRNAs) that modulate the expression of rpoS, encoding an alternative sigma factor that activates transcription of multiple Escherichia coli stress-response genes. While RprA activates rpoS for translation, OxyS down-regulates the transcript. Crucially, the RNA binding protein Hfq is required for both sRNAs to function, although the specific role played by Hfq remains unclear. We have investigated RprA and OxyS interactions with Hfq using biochemical and biophysical approaches. In particular, we have obtained the molecular envelopes of the Hfq–sRNA complexes using small-angle scattering methods, which reveal key molecular details. These data indicate that Hfq does not substantially change shape upon complex formation, whereas the sRNAs do. We link the impact of Hfq binding, and the sRNA structural changes induced, to transcript stability with respect to RNase E degradation. In light of these findings, we discuss the role of Hfq in the opposing regulatory functions played by RprA and OxyS in rpoS regulation

Editorial: From Pedagogic Research to Embedded E-Learning

This Special Issue of Reflecting Education arises from the work of the PREEL project (From Pedagogic Research to Embedded e-Learning) at the Institute of Education from 2006-2008. This project was one of nine HEA/JISC (Higher Education Academy and Joint Information Systems Committee) Pilot Pathfinder Projects and followed on from our involvement in the Pilot Benchmarking of e-Learning Programme. In the benchmarking exercise we identified a lack of coordination between research and practice in e-learning at the IoE as one of our crucial weaknesses, and so our Pilot Pathfinder project concentrated on this theme of building links between e-learning research and practice

Metacognitive Awareness of Facial Affect in Higher-Functioning Children and Adolescents with Autism Spectrum Disorder

Higher-functioning participants with and without autism spectrum disorder (ASD) viewed a series of face stimuli, made decisions regarding the affect of each face, and indicated their confidence in each decision. Confidence significantly predicted accuracy across all participants, but this relation was stronger for participants with typical development than participants with ASD. In the hierarchical linear modeling analysis, there were no differences in face processing accuracy between participants with and without ASD, but participants with ASD were more confident in their decisions. These results suggest that individuals with ASD have metacognitive impairments and are overconfident in face processing. Additionally, greater metacognitive awareness was predictive of better face processing accuracy, suggesting that metacognition may be a pivotal skill to teach in interventions

Foundation Models and Fair Use

Existing foundation models are trained on copyrighted material. Deploying these models can pose both legal and ethical risks when data creators fail to receive appropriate attribution or compensation. In the United States and several other countries, copyrighted content may be used to build foundation models without incurring liability due to the fair use doctrine. However, there is a caveat: If the model produces output that is similar to copyrighted data, particularly in scenarios that affect the market of that data, fair use may no longer apply to the output of the model. In this work, we emphasize that fair use is not guaranteed, and additional work may be necessary to keep model development and deployment squarely in the realm of fair use. First, we survey the potential risks of developing and deploying foundation models based on copyrighted content. We review relevant U.S. case law, drawing parallels to existing and potential applications for generating text, source code, and visual art. Experiments confirm that popular foundation models can generate content considerably similar to copyrighted material. Second, we discuss technical mitigations that can help foundation models stay in line with fair use. We argue that more research is needed to align mitigation strategies with the current state of the law. Lastly, we suggest that the law and technical mitigations should co-evolve. For example, coupled with other policy mechanisms, the law could more explicitly consider safe harbors when strong technical tools are used to mitigate infringement harms. This co-evolution may help strike a balance between intellectual property and innovation, which speaks to the original goal of fair use. But we emphasize that the strategies we describe here are not a panacea and more work is needed to develop policies that address the potential harms of foundation models

Methylxanthine treatment for apnea in preterm infants [Intervention Review]

Background: Recurrent apnea is common in preterm infants, particularly at very early gestational ages. These episodes of loss of effective breathing can lead to hypoxemia and bradycardia that may be severe enough to require resuscitation including use of positive pressure ventilation. Methylxanthines (such as caffeine or theophylline) have been used to stimulate breathing and prevent apnea and its consequences. Objectives: To determine the effects of methylxanthine treatment on the incidence of apnea and the use of intermittent positive pressure ventilation (IPPV), and other clinically important effects in preterm infants with recurrent apnea. Search strategy: Searches were made of the Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library, Issue 4, 2007), the Oxford Database of Perinatal Trials, MEDLINE (1966 to January 2008), EMBASE (1982 - January 2008), previous reviews including cross references, abstracts, conferences and symposia proceedings, expert informants, journal hand searching mainly in the English language. Selection criteria: All trials utilizing random or quasi-random patient allocation in which methylxanthine (theophylline or caffeine) was compared with placebo or no treatment for apnea in preterm infants were included. Data collection and analysis: Methodological quality was assessed independently by the two review authors. Data were extracted independently by the two review authors. Treatment effects were expressed as relative risk (RR) and risk difference (RD) and their 95% confidence intervals, using a fixed effect model. For significant results, the inverse of the risk difference (1/RD) was used to calculate the number needed to treat (NNT). Main results: The results of five trials that enrolled a total of 192 preterm infants with apnea indicate that methylxanthine therapy leads to a reduction in apnea and use of IPPV in the first two to seven days. There are insufficient data to adequately evaluate side effects and no data to examine effects within different gestational age groups. There are no data in the included studies that examine long-term effects. Authors' conclusions: Methylxanthines are effective in reducing the number of apneic attacks and the use of mechanical ventilation in the two to seven days after starting treatment. In view of its lower toxicity, caffeine would be the preferred drug. The effects of methylxanthines on long-term outcomes will be addressed in data from the trial awaiting assessment (CAP Trial 2006). Copyrigh

Rare earth elements (REEs) in the tropical South Atlantic and quantitative deconvolution of their non-conservative behavior

This study presents new concentration measurements of dissolved rare earth elements (dREEs) along a full-depth east–west section across the tropical South Atlantic (∼12°S), and uses these data to investigate the oceanic cycling of the REEs. Enrichment of dREEs, associated with the redox cycling of Fe–Mn oxides, is observed in the oxygen minimum zone (OMZ) off the African shelf. For deeper-waters, a multi-parameter mixing model was developed to deconvolve the relative importance of physical transport (i.e., water mass mixing) from biogeochemical controls on the dREE distribution in the deep Atlantic. This approach enables chemical processes involved in REE cycling, not apparent from the measurements alone, to be distinguished and quantified. Results show that the measured dREE concentrations below ∼1000 m are dominantly controlled (>75%) by preformed REE concentrations resulting from water mass mixing. This result indicates that the linear correlation between dREEs and dissolved Si observed in Atlantic deep waters results from the dominantly conservative behavior of these tracers, rather than from similar chemical processes influencing both dREEs and Si. Minor addition of dREEs (∼10% of dNd and ∼5% of dYb) is observed in the deep (>∼4000 m) Brazil Basin, resulting from either remineralization of particles in-situ or along the flow path. Greater addition of dREEs (up to 25% for dNd and 20% for dYb) is found at ∼1500 m and below ∼4000 m in the Angola Basin near the African continental margin. Cerium anomalies suggest that different sources are responsible for these dREE addition plumes. The 1500 m excess is most likely attributed to dREE release from Fe oxides, whereas the 4000 m excess may be due to remineralization of calcite. Higher particulate fluxes and a more sluggish ocean circulation in the Angola Basin may explain why the dREE excesses in this basin are significantly higher than that observed in the Brazil Basin. Hydrothermal venting over the mid-Atlantic ridge acts as a regional net sink for light REEs, but has little influence on the net budget of heavy REEs. The combination of dense REE measurements with water mass deconvolution is shown to provide quantitative assessment of the relative roles of physical and biogeochemical processes in the oceanic cycling of REEs