A prototype system for detecting the radio-frequency pulse associated with cosmic ray air showers

The development of a system to detect the radio-frequency (RF) pulse associated with extensive air showers of cosmic rays is described. This work was performed at the CASA/MIA array in Utah, with the intention of designing equipment that can be used in conjunction with the Auger Giant Array. A small subset of data (less than 40 out of a total of 600 hours of running time), taken under low-noise conditions, permitted upper limits to be placed on the rate for pulses accompanying showers of energies around $10^{17}$ eV.Comment: 53 pages, LaTeX, 19 figures, published in Nuclear Instruments and Methods. Revised version; some references update

Using social parasitism to test reproductive skew models in a primitively eusocial wasp

Remarkable variation exists in the distribution of reproduction (skew) among members of cooperatively breeding groups, both within and between species. Reproductive skew theory has provided an important framework for understanding this variation. In the primitively eusocial Hymenoptera, two models have been routinely tested: concessions models, which assume complete control of reproduction by a dominant individual, and tug-of-war models, which assume on-going competition among group members over reproduction. Current data provide little support for either model, but uncertainty about the ability of individuals to detect genetic relatedness and difficulties in identifying traits conferring competitive ability mean that the relative importance of concessions versus tug-of-war remains unresolved. Here, we suggest that the use of social parasitism to generate meaningful variation in key social variables represents a valuable opportunity to explore the mechanisms underpinning reproductive skew within the social Hymenoptera. We present a direct test of concessions and tug-of-war models in the paper wasp Polistes dominulus by exploiting pronounced changes in relatedness and power structures that occur following replacement of the dominant by a congeneric social parasite. Comparisons of skew in parasitized and unparasitized colonies are consistent with a tug-of-war over reproduction within P. dominulus groups, but provide no evidence for reproductive concessions

Effects of seasonal variation in prey abundance on field metabolism, water flux, and activity of a tropical ambush foraging snake

The responses of animals to seasonal food shortages can have important consequences for population dynamics and the structure and function of food webs. We investigated how an ambush foraging snake, the northern death adder Acanthophis praelongus, responds to seasonal fluctuations in prey availability in its tropical environment. In the dry season, field metabolic rates and water flux, as measured by doubly labeled water, were significantly lower than in the wet season. Unlike some other reptiles of the wet-dry tropics, death adders showed no seasonal difference in their resting metabolism. About 94% of the decrease in energy expended in the dry season was due to a decrease in activity and digestion, with lower body temperatures accounting for the remainder. In the dry season, death adders were less active and moved shorter distances between foraging sites than in the wet season. Analysis of energy expenditure suggested that adders fed no more than every 2-3 wk in the dry season but fed more frequently during the wet season. Unlike many lizards that cease feeding during the dry season, death adders remain active and attempt to maximize their energy intake year-round

Characterization of the bovine pregnancy-associated glycoprotein gene family – analysis of gene sequences, regulatory regions within the promoter and expression of selected genes

<p>Abstract</p> <p>Background</p> <p>The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the <it>Artiodactyla </it>order. In cattle, the <it>PAG </it>gene family is comprised of at least 22 transcribed genes, as well as some variants. Phylogenetic analyses have shown that the PAG family segregates into 'ancient' and 'modern' groupings. Along with sequence differences between family members, there are clear distinctions in their spatio-temporal distribution and in their relative level of expression. In this report, 1) we performed an <it>in silico </it>analysis of the bovine genome to further characterize the <it>PAG </it>gene family, 2) we scrutinized proximal promoter sequences of the <it>PAG </it>genes to evaluate the evolution pressures operating on them and to identify putative regulatory regions, 3) we determined relative transcript abundance of selected <it>PAGs </it>during pregnancy and, 4) we performed preliminary characterization of the putative regulatory elements for one of the candidate PAGs, <it>bovine </it>(<it>bo</it>) <it>PAG-2</it>.</p> <p>Results</p> <p>From our analysis of the bovine genome, we identified 18 distinct <it>PAG </it>genes and 14 pseudogenes. We observed that the first 500 base pairs upstream of the translational start site contained multiple regions that are conserved among all <it>boPAGs</it>. However, a preponderance of conserved regions, that harbor recognition sites for putative transcriptional factors (TFs), were found to be unique to the modern <it>boPAG </it>grouping, but not the ancient <it>boPAGs</it>. We gathered evidence by means of Q-PCR and screening of EST databases to show that <it>boPAG-2 </it>is the most abundant of all <it>boPAG </it>transcripts. Finally, we provided preliminary evidence for the role of ETS- and DDVL-related TFs in the regulation of the <it>boPAG-2 </it>gene.</p> <p>Conclusion</p> <p><it>PAGs </it>represent a relatively large gene family in the bovine genome. The proximal promoter regions of these genes display differences in putative TF binding sites, likely contributing to observed differences in spatial and temporal expression. We also discovered that <it>boPAG-2 </it>is the most abundant of all boPAG transcripts and provided evidence for the role of ETS and DDVL TFs in its regulation. These experiments mark the crucial first step in discerning the complex transcriptional regulation operating within the <it>boPAG </it>gene family.</p

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity

Assessing neural tuning for object perception in schizophrenia and bipolar disorder with multivariate pattern analysis of fMRI data.

IntroductionDeficits in visual perception are well-established in schizophrenia and are linked to abnormal activity in the lateral occipital complex (LOC). Related deficits may exist in bipolar disorder. LOC contains neurons tuned to object features. It is unknown whether neural tuning in LOC or other visual areas is abnormal in patients, contributing to abnormal perception during visual tasks. This study used multivariate pattern analysis (MVPA) to investigate perceptual tuning for objects in schizophrenia and bipolar disorder.MethodsFifty schizophrenia participants, 51 bipolar disorder participants, and 47 matched healthy controls completed five functional magnetic resonance imaging (fMRI) runs of a perceptual task in which they viewed pictures of four different objects and an outdoor scene. We performed classification analyses designed to assess the distinctiveness of activity corresponding to perception of each stimulus in LOC (a functionally localized region of interest). We also performed similar classification analyses throughout the brain using a searchlight technique. We compared classification accuracy and patterns of classification errors across groups.ResultsStimulus classification accuracy was significantly above chance in all groups in LOC and throughout visual cortex. Classification errors were mostly within-category confusions (e.g., misclassifying one chair as another chair). There were no group differences in classification accuracy or patterns of confusion.ConclusionsThe results show for the first time MVPA can be used successfully to classify individual perceptual stimuli in schizophrenia and bipolar disorder. However, the results do not provide evidence of abnormal neural tuning in schizophrenia and bipolar disorder

Relation of Patients Living Without a Partner or Spouse to Being Physically Active After Acute Coronary Syndromes (from the PULSE Accelerometry Substudy)

Living alone is associated with adverse outcomes after acute coronary syndromes (ACS). One potential mediator of the relation between partner status and outcomes after ACS is physical activity. To evaluate the association of partner status with physical activity after ACS, data from 107 participants enrolled in the Prescription Use, Lifestyle, and Stress Evaluation (PULSE) study, a prospective observational study of post-ACS patients, were analyzed. Accelerometers were used to measure physical activity after hospital discharge. The primary outcome measure was a maximum 10 hours of daytime activity 1 month after discharge. One month after discharge from ACS hospitalizations, participants without a partner or spouse exhibited 24.4% lower daytime activity than those with a partner or spouse (p = 0.003). After controlling for age, gender, body mass index, Charlson co-morbidity index, and traditional psychosocial and clinical cardiovascular correlates of post-ACS physical activity, partner status remained an independent predictor of post-ACS physical activity (20.5% lower daytime activity among those without a partner or spouse, p = 0.008). In conclusion, in this study of accelerometer-measured physical activity after an ACS hospitalization, those without a partner or spouse exhibit significantly less physical activity than those with a partner or spouse 1 month after discharge from the hospital. Low physical activity may be an important mediator of the prognosis associated with partner status after ACS