Allocation in Practice

How do we allocate scarcere sources? How do we fairly allocate costs? These are two pressing challenges facing society today. I discuss two recent projects at NICTA concerning resource and cost allocation. In the first, we have been working with FoodBank Local, a social startup working in collaboration with food bank charities around the world to optimise the logistics of collecting and distributing donated food. Before we can distribute this food, we must decide how to allocate it to different charities and food kitchens. This gives rise to a fair division problem with several new dimensions, rarely considered in the literature. In the second, we have been looking at cost allocation within the distribution network of a large multinational company. This also has several new dimensions rarely considered in the literature.Comment: To appear in Proc. of 37th edition of the German Conference on Artificial Intelligence (KI 2014), Springer LNC

The Complexity of Computing Minimal Unidirectional Covering Sets

Given a binary dominance relation on a set of alternatives, a common thread in the social sciences is to identify subsets of alternatives that satisfy certain notions of stability. Examples can be found in areas as diverse as voting theory, game theory, and argumentation theory. Brandt and Fischer [BF08] proved that it is NP-hard to decide whether an alternative is contained in some inclusion-minimal upward or downward covering set. For both problems, we raise this lower bound to the Theta_{2}^{p} level of the polynomial hierarchy and provide a Sigma_{2}^{p} upper bound. Relatedly, we show that a variety of other natural problems regarding minimal or minimum-size covering sets are hard or complete for either of NP, coNP, and Theta_{2}^{p}. An important consequence of our results is that neither minimal upward nor minimal downward covering sets (even when guaranteed to exist) can be computed in polynomial time unless P=NP. This sharply contrasts with Brandt and Fischer's result that minimal bidirectional covering sets (i.e., sets that are both minimal upward and minimal downward covering sets) are polynomial-time computable.Comment: 27 pages, 7 figure

Caribbean Sea Soundscapes: Monitoring Humpback Whales, Biological Sounds, Geological Events, and Anthropogenic Impacts of Vessel Noise

Assessing marine soundscapes provides an understanding of the biological, geological and anthropogenic composition of a habitat, including species diversity, community composition, and human impacts. For this study, nine acoustic recorders were deployed between December 2016 and June 2017 off six Caribbean islands in several Marine Parks: the Dominican Republic (DR), St. Martin (SM), Guadeloupe east and west (GE, GW), Martinique (MA), Aruba (AR), and Bonaire (BO). Humpback whale song was recorded at five sites on four islands (DR, SM, GE, GW, and MA) and occurred on 49–93% of recording days. Song appeared first at the DR site and began 4–6 weeks later at GE, GW, and MA. No song was heard in AR and BO, the southernmost islands. A 2-week period was examined for the hourly presence of vessel noise and the number and duration of ship passages. Hourly vessel presence ranged from low (20% – DR, 30% – SM), medium (52% – MA, 54% – BO, 77% – GE) to near continuous (99% – GW; 100% – AR). Diurnal patterns were observed at BO, GE, and MA with few to no vessels present during night time hours, possibly reflecting the activity of recreational craft and fishing vessels. At the DR and GW sites, vessel traffic was ubiquitous for most of the day, likely reflecting heavy cruise ship and container ship presence. Soundscapes were diverse across islands with persistent fish choruses, sporadic sperm whale (Physeter macrocephalus) and dolphin (Delphinidae) presence at BO, minke whales (Balaenoptera acutorostrata) from late December to late February at MA and an earthquake recorded across all sites. These analyses provide an important first step in characterizing the health and species richness in Caribbean marine parks and demonstrate a surprising high anthropogenic foot print. Vessel traffic in particular contributes adversely to marine soundscapes, masking marine mammal sounds, potentially changing typical animal behavior and raising the risk of ship strike

Référentiel de connaissances pour un numérique éco-responsable

L’objectif de ce document est de définir un référentiel/socle de connaissances commun pour les enseignements sur le numérique responsable (impacts du numérique et comment les limiter1), à destination de formations en informatique ou d’autres filières incluant des cours d’informatique.Nous cherchons à répondre à la question suivante :Quelles connaissances devrait apporter une formation en informatique à des étudiantes et étudiants pour leur permettre d’apporter des réponses aux enjeux environnementaux et sociétaux dans leur vie professionnelle et citoyenne ?Ce document est donc focalisé sur les impacts du numérique, mais certains aspects plus généraux(enjeux environnementaux, contexte économique...) sont néanmoins abordés car nécessaires à la compréhension des aspects informatiques.Ce référentiel vise à fournir des notions et références utiles, mais n’a pas vocation à remplacer un cours

HPat provides a link between deadenylation and decapping in metazoa

A proline-rich region in the Drosophila Pat1 homologue works with the protein's C-terminal domain to recruit decapping and deadenylase complexes to target mRNAs

Scanning Tunneling Microscopy in TTF-TCNQ :direct proof of phase and amplitude modulated charge density waves

Charge density waves (CDW) have been studied at the surface of a cleaved TTF-TCNQ single crystal using a low temperature scanning tunneling microscope (STM) under ultra high vacuum (UHV) conditions. All CDW phase transitions of TTF-TCNQ have been identified. The measurement of the modulation wave vector along the a direction provides the first evidence for the existence of domains comprising single plane wave modulated structures in the temperature regime where the transverse wave vector of the CDW is temperature dependent, as hinted by the theory more than 20 years ago.Comment: To appear in Phys.Rev.Rapid. Com

Characterization of an OmpA-like outer membrane protein of the acidophilic iron-oxidizing bacterium, Acidithiobacillus ferrooxidans

An OmpA family protein (FopA) previously reported as one of the major outer membrane proteins of an acidophilic iron-oxidizing bacterium Acidithiobacillus ferrooxidans was characterized with emphasis on the modification by heat and the interaction with peptidoglycan. A 30-kDa band corresponding to the FopA protein was detected in outer membrane proteins extracted at 75°C or heated to 100°C for 10 min prior to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). However, the band was not detected in outer membrane proteins extracted at ≤40°C and without boiling prior to electrophoresis. By Western blot analysis using the polyclonal antibody against the recombinant FopA, FopA was detected as bands with apparent molecular masses of 30 and 90 kDa, suggesting that FopA existed as an oligomeric form in the outer membrane of A. ferrooxidans. Although the fopA gene with a sequence encoding the signal peptide was successfully expressed in the outer membrane of Escherichia coli, the recombinant FopA existed as a monomer in the outer membrane of E. coli. FopA was detected in peptidoglycan-associated proteins from A. ferrooxidans. The recombinant FopA also showed the peptidoglycan-binding activity

Disrupting the Acyl Carrier Protein/SpoT Interaction In Vivo: Identification of ACP Residues Involved in the Interaction and Consequence on Growth

In bacteria, Acyl Carrier Protein (ACP) is the central cofactor for fatty acid biosynthesis. It carries the acyl chain in elongation and must therefore interact successively with all the enzymes of this pathway. Yet, ACP also interacts with proteins of diverse unrelated function. Among them, the interaction with SpoT has been proposed to be involved in regulating ppGpp levels in the cell in response to fatty acid synthesis inhibition. In order to better understand this mechanism, we screened for ACP mutants unable to interact with SpoT in vivo by bacterial two-hybrid, but still functional for fatty acid synthesis. The position of the selected mutations indicated that the helix II of ACP is responsible for the interaction with SpoT. This suggested a mechanism of recognition similar to one used for the enzymes of fatty acid synthesis. Consistently, the interactions tested by bacterial two-hybrid of ACP with fatty acid synthesis enzymes were also affected by the mutations that prevented the interaction with SpoT. Yet, interestingly, the corresponding mutant strains were viable, and the phenotypes of one mutant suggested a defect in growth regulation

Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability

BACKGROUND: The emergence of eukaryotes was characterized by the expansion and diversification of several ancient RNA-binding domains and the apparent de novo innovation of new RNA-binding domains. The identification of these RNA-binding domains may throw light on the emergence of eukaryote-specific systems of RNA metabolism. RESULTS: Using sensitive sequence profile searches, homology-based fold recognition and sequence-structure superpositions, we identified novel, divergent versions of the Sm domain in the Scd6p family of proteins. This family of Sm-related domains shares certain features of conventional Sm domains, which are required for binding RNA, in addition to possessing some unique conserved features. We also show that these proteins contain a second previously uncharacterized C-terminal domain, termed the FDF domain (after a conserved sequence motif in this domain). The FDF domain is also found in the fungal Dcp3p-like and the animal FLJ22128-like proteins, where it fused to a C-terminal domain of the YjeF-N domain family. In addition to the FDF domains, the FLJ22128-like proteins contain yet another divergent version of the Sm domain at their extreme N-terminus. We show that the YjeF-N domains represent a novel version of the Rossmann fold that has acquired a set of catalytic residues and structural features that distinguish them from the conventional dehydrogenases. CONCLUSIONS: Several lines of contextual information suggest that the Scd6p family and the Dcp3p-like proteins are conserved components of the eukaryotic RNA metabolism system. We propose that the novel domains reported here, namely the divergent versions of the Sm domain and the FDF domain may mediate specific RNA-protein and protein-protein interactions in cytoplasmic ribonucleoprotein complexes. More specifically, the protein complexes containing Sm-like domains of the Scd6p family are predicted to regulate the stability of mRNA encoding proteins involved in cell cycle progression and vesicular assembly. The Dcp3p and FLJ22128 proteins may localize to the cytoplasmic processing bodies and possibly catalyze a specific processing step in the decapping pathway. The explosive diversification of Sm domains appears to have played a role in the emergence of several uniquely eukaryotic ribonucleoprotein complexes, including those involved in decapping and mRNA stability

The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock

RNA-binding proteins (RBPs) establish the cellular fate of a transcript, but an understanding of these processes has been limited by a lack of identified specific interactions between RNA and protein molecules. Using MS2 RNA tagging, we have purified proteins associated with individual mRNA species induced by osmotic stress, STL1 and GPD1. We found members of the Lsm1-7/Pat1 RBP complex to preferentially bind these mRNAs, relative to the non-stress induced mRNAs, HYP2 and ASH1. To assess the functional importance, we mutated components of the Lsm1-7/Pat1 RBP complex and analyzed the impact on expression of osmostress gene products. We observed a defect in global translation inhibition under osmotic stress in pat1 and lsm1 mutants, which correlated with an abnormally high association of both non-stress and stress-induced mRNAs to translationally active polysomes. Additionally, for stress-induced proteins normally triggered only by moderate or high osmostress, in the mutants the protein levels rose high already at weak hyperosmosis. Analysis of ribosome passage on mRNAs through co-translational decay from the 5' end (5P-Seq) showed increased ribosome accumulation in lsm1 and pat1 mutants upstream of the start codon. This effect was particularly strong for mRNAs induced under osmostress. Thus, our results indicate that, in addition to its role in degradation, the Lsm1-7/Pat1 complex acts as a selective translational repressor, having stronger effect over the translation initiation of heavily expressed mRNAs. Binding of the Lsm1-7/Pat1p complex to osmostress-induced mRNAs mitigates their translation, suppressing it in conditions of weak or no stress, and avoiding a hyperresponse when triggered