On Equivalence of Infinitary Formulas under the Stable Model Semantics

Propositional formulas that are equivalent in intuitionistic logic, or in its extension known as the logic of here-and-there, have the same stable models. We extend this theorem to propositional formulas with infinitely long conjunctions and disjunctions and show how to apply this generalization to proving properties of aggregates in answer set programming. To appear in Theory and Practice of Logic Programming (TPLP)

On the Semantics of Gringo

Input languages of answer set solvers are based on the mathematically simple concept of a stable model. But many useful constructs available in these languages, including local variables, conditional literals, and aggregates, cannot be easily explained in terms of stable models in the sense of the original definition of this concept and its straightforward generalizations. Manuals written by designers of answer set solvers usually explain such constructs using examples and informal comments that appeal to the user's intuition, without references to any precise semantics. We propose to approach the problem of defining the semantics of gringo programs by translating them into the language of infinitary propositional formulas. This semantics allows us to study equivalent transformations of gringo programs using natural deduction in infinitary propositional logic.Comment: Proceedings of Answer Set Programming and Other Computing Paradigms (ASPOCP 2013), 6th International Workshop, August 25, 2013, Istanbul, Turke

The Acute Physiological Responses of Eccentric Cycling During the Recovery Periods of a High Intensity Concentric Cycling Interval Session

Eccentric and concentric exercise is associated with disparate acute and chronic responses. We uniquely interspersed workload equivalent eccentric cycling during each recovery period of a high intensity interval training (HIIT) cycling trial to determine acute cardiopulmonary, thermal and psycho-physiological responses. Twelve males [age 28 years (SD 6), peak oxygen consumption 48 mL ⋅ kg-1 ⋅ min-1 (SD 6)] completed two high intensity interval cycling trials [4 x 5 min, 60% peak power output (PPO)] separated by 7-10 days. The CONR trial required participants to cycle concentrically during each recovery period (5 min, 30% PPO). The ECCR trial modified the recovery to be eccentric cycling (5 min, 60% PPO). High intensity workload (CONR: 187 ± 17; ECCR: 187 ± 21 W), oxygen consumption (CONR: 2.55 ± 0.17; ECCR: 2.68 ± 0.20 L ⋅ min-1), heart rate (CONR: 165 ± 7; ECCR: 171 ± 10 beats ⋅ min-1) and RPE legs (CONR: 15 ± 3; ECCR: 15 ± 3) were equivalent between trials. Eccentric cycling recovery significantly increased external workload (CONR: 93 ± 18; ECCR: 196 ± 24 W, P \u3c 0.01) yet lowered oxygen consumption (CONR: 1.51 ± 0.18; ECCR: 1.20 ± 0.20 L ⋅ min-1, P \u3c 0.05) while heart rate (CONR: 132 ± 13; ECCR: 137 ± 12 beats ⋅ min-1) and RPE of the legs (CONR: 11 ± 7; ECCR: 12 ± 7) remained equivalent. There was no significant difference in the aural temperature between the trials (ECCR: 37.3 ± 0.1°C; CONR: 37.4 ± 0.1°C, P \u3e 0.05), yet during recovery periods mean skin temperature was significantly elevated in the ECCR (ECCR: 33.9 ± 0.2°C; CONR: 33.3 ± 0.2°C, P \u3c 0.05). Participants preferred ECCR (10/12) and rated the ECCR as more achievable (82.8 ± 11.4 mm) than CONR (79.4 ± 15.9 mm, P \u3c 0.01). In conclusion, eccentric cycling during the recovery period of a HIIT training session, offers a novel approach to concurrent training methodology. The unique cardiopulmonary and skeletal muscle responses facilitate the achievement of both training stimuli within a single exercise bout

Motile cilia defects in diseases other than primary ciliary dyskinesia:The contemporary diagnostic and research role for transmission electron microscopy

Ultrastructural studies have underpinned the cell biological and clinical investigations of the varied roles of motile cilia in health and disease, with a long history since the 1950s. Recent developments from transmission electron microscopy (TEM; cryo-electron microscopy, electron tomography) have yielded higher resolution and fresh insights into the structure and function of these complex organelles. Microscopy in ciliated organisms, disease models, and in patients with ciliopathy diseases has dramatically expanded our understanding of the ubiquity, multisystem involvement, and importance of cilia in normal human development. Here, we review the importance of motile cilia ultrastructural studies in understanding the basis of diseases other than primary ciliary dyskinesia

The Winograd Schema Challenge and Reasoning about Correlation. In

Abstract The Winograd Schema Challenge is an alternative to the Turing Test that may provide a more meaningful measure of machine intelligence. It poses a set of coreference resolution problems that cannot be solved without human-like reasoning. In this paper, we take the view that the solution to such problems lies in establishing discourse coherence. Specifically, we examine two types of rhetorical relations that can be used to establish discourse coherence: positive and negative correlation. We introduce a framework for reasoning about correlation between sentences, and show how this framework can be used to justify solutions to some Winograd Schema problems

Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton

Ribonucleotide reductases (RNRs) are ancient enzymes that catalyze the reduction of ribonucleotides to deoxyribonucleotides. They are required for virtually all cellular life and are prominent within viral genomes. RNRs share a common ancestor and must generate a protein radical for direct ribonucleotide reduction. The mechanisms by which RNRs produce radicals are diverse and divide RNRs into three major classes and several subclasses. The diversity of radical generation methods means that cellular organisms and viruses typically contain the RNR best-suited to the environmental conditions surrounding DNA replication. However, such diversity has also fostered high rates of RNR misannotation within subject sequence databases. These misannotations have resulted in incorrect translative presumptions of RNR biochemistry and have diminished the utility of this marker gene for ecological studies of viruses. We discovered a misannotation of the RNR gene within the Prochlorococcus phage P-SSP7 genome, which caused a chain of misannotations within commonly observed RNR genes from marine virioplankton communities. These RNRs are found in marine cyanopodo- and cyanosiphoviruses and are currently misannotated as Class II RNRs, which are O2-independent and require cofactor B12. In fact, these cyanoviral RNRs are Class I enzymes that are O2-dependent and may require a di-metal cofactor made of Fe, Mn, or a combination of the two metals. The discovery of an overlooked Class I β subunit in the P-SSP7 genome, together with phylogenetic analysis of the α and β subunits confirms that the RNR from P-SSP7 is a Class I RNR. Phylogenetic and conserved residue analyses also suggest that the P-SSP7 RNR may constitute a novel Class I subclass. The reannotation of the RNR clade represented by P-SSP7 means that most lytic cyanophage contain Class I RNRs, while their hosts, B12-producing Synechococcus and Prochlorococcus, contain Class II RNRs. By using a Class I RNR, cyanophage avoid a dependence on host-produced B12, a more effective strategy for a lytic virus. The discovery of a novel RNR β subunit within cyanopodoviruses also implies that some unknown viral genes may be familiar cellular genes that are too divergent for homology-based annotation methods to identify

Fluorescent Detection of Bromoperoxidase Activity in Microalgae and Planktonic Microbial Communities Using Aminophenyl Fluorescein

Among planktonic communities haloperoxidase enzymes may play a role in the control of intracellular and extracellular reactive oxygen species, in the generation of halogenated organic compounds and in chemical interactions between microbes. We introduce a sensitive fluorometric assay with a large dynamic range that is based on the dearylation of aminophenyl fluorescein (APF) to fluorescein by highly reactive oxygen species. Bromoperoxidase and chloroperoxidase enzymes catalyze the reaction between hydrogen peroxide and halides to generate highly reactive hypohalite intermediates able to dearylate APF. The fundamentals and standardization of the approach are illustrated using a partially purified, vanadium-dependent bromoperoxidase from the red seaweed Corallina officinalis. Laboratory cultures of two polar diatoms, Porosira glacialis and Fragilariopsis cylindrus, are used to illustrate the sensitivity and potential applications of the approach for in vitro, in vivo and in situ measurements of bromoperoxidase activity. These two diatoms differ in biovolume-specific bromoperoxidase activity by 2-orders of magnitude, from 5.4 to 0.044 fmol fluorescein μm-3 h-1, respectively. The approach is also used to investigate the partition of haloperoxidase activity between different size fractions of summer coastal planktonic communities, illustrating that generally more than 50% of the haloperoxidase activity occurred in a >10 μm size fraction that was dominated by diatoms. The assay has the potential to be of value in many aspects of haloperoxidase research, including developing an improved understanding of the roles of haloperoxidase enzymes in microbial planktonic communities