Coping with Incomplete Data: Recent Advances

Handling incomplete data in a correct manner is a notoriously hard problem in databases. Theoretical approaches rely on the computationally hard notion of certain answers, while practical solutions rely on ad hoc query evaluation techniques based on three-valued logic. Can we find a middle ground, and produce correct answers efficiently? The paper surveys results of the last few years motivated by this question. We re-examine the notion of certainty itself, and show that it is much more varied than previously thought. We identify cases when certain answers can be computed efficiently and, short of that, provide deterministic and probabilistic approximation schemes for them. We look at the role of three-valued logic as used in SQL query evaluation, and discuss the correctness of the choice, as well as the necessity of such a logic for producing query answers

Designing an Equitable Strategy for Allocating Antiretroviral Treatments

A study by Wilson and Blower in the February issue of PLoS Medicine addressed the issue of ensuring equity in distributing AIDS medications. Reis and Capron discuss the study's implication

Volcanogenic Pseudo-Fossils From the ~3.48 Ga Dresser Formation, Pilbara, Western Australia

The ~ 3.48 billion-year-old Dresser Formation, Pilbara Craton, Western Australia, is a key geological unit for the study of Earth\u27s earliest life and the habitats it occupied. Here, we describe a new suite of spheroidal to lenticular microstructures that morphologically resemble some previously reported Archean microfossils. Correlative microscopy shows that these objects have a size distribution, wall ultrastructure, and chemistry that are incompatible with a microfossil origin and instead are interpreted as pyritized and silicified fragments of vesicular volcanic glass. Organic kerogenous material is associated with much of the altered volcanic glass; variable quantities of organic carbon line or fill the insides of some individual vesicles, while relatively large, tufted organic-rich laminae envelop multiple vesicles. The microstructures reported herein constitute a new type of abiogenic artifact (pseudo-fossil) that must be considered when evaluating potential signs of early life on Earth or elsewhere. In the sample studied here, where hundreds of these microstructures are present, the combined evidence permits a relatively straightforward interpretation as vesicular volcanic glass. However, reworked, isolated, and silicified microstructures of this type may prove particularly problematic in early or extraterrestrial life studies since they adsorb carbon onto their surfaces and are readily pyritized, mimicking a common preservation mechanism for bona fide microfossils. In those cases, nanoscale analysis of wall ultrastructure would be required to firmly exclude a biological origin

Dissecting the Re-Os molybdenite geochronometer

Rhenium and osmium isotopes have been used for decades to date the formation of molybdenite (MoS2), a common mineral in ore deposits and the world’s main source of molybdenum and rhenium. Understanding the distribution of parent 187Re and radiogenic daughter 187Os isotopes in molybdenite is critical in interpreting isotopic measurements because it can compromise the accurate determination and interpretation of mineralization ages. In order to resolve the controls on the distribution of these elements, chemical and isotope mapping of MoS2 grains from representative porphyry copper-molybdenum deposits were performed using electron microprobe and nano-scale secondary ion mass spectrometry. Our results show a heterogeneous distribution of 185,187Re and 192Os isotopes in MoS2, and that both 187Re and 187Os isotopes are not decoupled as previously thought. We conclude that Re and Os are structurally bound or present as nanoparticles in or next to molybdenite grains, recording a complex formation history and hindering the use of microbeam techniques for Re-Os molybdenite dating. Our study opens new avenues to explore the effects of isotope nuggeting in geochronometers

Oligodendroglia are particularly vulnerable to oxidative damage after neurotrauma in vivo

Loss of function following injury to the central nervous system is worsened by secondary degeneration of neurons and glia surrounding the injury and initiated by oxidative damage. However, it is not yet known which cellular populations and structures are most vulnerable to oxidative damage in vivo Using Nanoscale secondary ion mass spectrometry (NanoSIMS), oxidative damage was semi-quantified within cellular subpopulations and structures of optic nerve vulnerable to secondary degeneration, following a partial transection of the optic nerve in adult female PVG rats. Simultaneous assessment of cellular subpopulations and structures revealed oligodendroglia as the most vulnerable to DNA oxidation following injury. 5-ethynyl-2'-deoxyuridine (EdU) was used to label cells that proliferated in the first 3 days after injury. Injury led to increases in DNA, protein and lipid damage in OPCs and mature oligodendrocytes at 3 days, regardless of proliferative state, associated with a decline in the numbers of OPCs at 7 days. O4+ pre-oligodendrocytes also exhibited increased lipid peroxidation. Interestingly, EdU+ mature oligodendrocytes derived after injury demonstrated increased early susceptibility to DNA damage and lipid peroxidation. However, EdU- mature oligodendrocytes with high 8OHdG immunoreactivity were more likely to be caspase3+. By day 28, newly derived mature oligodendrocytes had significantly reduced MYRF mRNA indicating that the myelination potential of these cells may be reduced. The proportion of caspase3+ oligodendrocytes remained higher in EdU- cells. Innovative use of NanoSIMS together with traditional immunohistochemistry and in situ hybridisation have enabled the first demonstration of subpopulation specific oligodendroglial vulnerability to oxidative damage, due to secondary degeneration in vivo. SIGNIFICANCE STATEMENT. Injury to the central nervous system is characterised by oxidative damage in areas adjacent to the injury. However, the cellular subpopulations and structures most vulnerable to this damage remain to be elucidated. Here we use powerful NanoSIMS techniques to show increased oxidative damage in oligodendroglia and axons and to demonstrate that cells early in the oligodendroglial lineage are the most vulnerable to DNA oxidation. Further immunohistochemical and in situ hybridisation investigation reveals that mature oligodendrocytes derived after injury are more vulnerable to oxidative damage than their counterparts existing at the time of injury and have reduced MYRF mRNA, yet pre-existing oligodendrocytes are more likely to die

Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis.

BackgroundSponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea.ResultsThe two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome.ConclusionsHere, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutritional symbiotic interactions to holobiont function, and, via cascading effects, ecosystem functioning, in one of the earliest metazoan-microbe symbioses. Video abstract

Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility.

The skeleton of reef-building coral harbors diverse microbial communities that could compensate for metabolic deficiencies caused by the loss of algal endosymbionts, i.e., coral bleaching. However, it is unknown to what extent endolith taxonomic diversity and functional potential might contribute to thermal resilience. Here we exposed Goniastrea edwardsi and Porites lutea, two common reef-building corals from the central Red Sea to a 17-day long heat stress. Using hyperspectral imaging, marker gene/metagenomic sequencing, and NanoSIMS, we characterized their endolithic microbiomes together with 15N and 13C assimilation of two skeletal compartments: the endolithic band directly below the coral tissue and the deep skeleton. The bleaching-resistant G. edwardsi was associated with endolithic microbiomes of greater functional diversity and redundancy that exhibited lower N and C assimilation than endoliths in the bleaching-sensitive P. lutea. We propose that the lower endolithic primary productivity in G. edwardsi can be attributed to the dominance of chemolithotrophs. Lower primary production within the skeleton may prevent unbalanced nutrient fluxes to coral tissues under heat stress, thereby preserving nutrient-limiting conditions characteristic of a stable coral-algal symbiosis. Our findings link coral endolithic microbiome structure and function to bleaching susceptibility, providing new avenues for understanding and eventually mitigating reef loss

Intermobility of barium, strontium, and lead in chloride and sulfate leach solutions

Production of radionuclide-free copper concentrates is dependent on understanding and controlling the deportment of daughter radionuclides (RNs) produced from 238U decay, specifically 226Ra, 210Pb, and 210Po. Sulfuric acid leaching is currently employed in the Olympic Dam processing plant (South Australia) to remove U and fluorine from copper concentrates prior to smelting but does not adequately remove the aforementioned RN. Due to chemical similarities between lead and alkaline earth metals (including Ra), two sets of experiments were designed to understand solution interactions between Sr, Ba, and Pb at various conditions. Nanoscale secondary ion mass spectrometry (NanoSIMS) isotopic spatial distribution maps and laser ablation inductively coupled-plasma mass spectrometry transects were performed on laboratory-grown crystals of baryte, celestite, and anglesite which had been exposed to different solutions under different pH and reaction time conditions. Analysis of experimental products reveals three uptake mechanisms: overgrowth of nearly pure SrSO4 and PbSO4 on baryte; incorporation of minor of Pb and Ba into celestite due to diffusion; and extensive replacement of Pb by Sr (and less extensive replacement of Pb by Ba) in anglesite via coupled dissolution-reprecipitation reactions. The presence of H2SO4 either enhanced or inhibited these reactions. Kinetic modelling supports the experimental results, showing potential for extrapolating the (Sr, Ba, Pb)SO4 system to encompass RaSO4. Direct observation of grain-scale element distributions by nanoSIMS aids understanding of the controlling conditions and mechanisms of replacement that may be critical steps for Pb and Ra removal from concentrates by allowing construction of a cationic replacement scenario targeting Pb or Ra, or ideally all insoluble sulfates. Experimental results provide a foundation for further investigation of RN uptake during minerals processing, especially during acid leaching. The new evidence enhances understanding of micro- to nanoscale chemical interactions and not only aids determination of where radionuclides reside during each processing stage but also guides development of flowsheets targeting their removal.Mark Rollog, Nigel J. Cook, Paul Guagliardo, Kathy Ehrig, Sarah E. Gilbert and Matt Kilbur