NONAME system description, volume 1

Description of NONAME program and system for determining and analyzing satellite orbits and estimating geodetic parameter

Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2

<p>Abstract</p> <p>Background</p> <p>The availability of whole-genome sequences allows for the identification of the entire set of protein coding genes as well as their regulatory regions. This can be accomplished using multiple complementary methods that include ESTs, homology searches and <it>ab initio </it>gene predictions. Previously, the Genie gene-finding algorithm was trained on a small set of <it>Chlamydomonas </it>genes and shown to improve the accuracy of gene prediction in this species compared to other available programs. To improve <it>ab initio </it>gene finding in <it>Chlamydomonas</it>, we assemble a new training set consisting of over 2,300 cDNAs by assembling over 167,000 <it>Chlamydomonas </it>EST entries in GenBank using the EST assembly tool PASA.</p> <p>Results</p> <p>The prediction accuracy of our cDNA-trained gene-finder, GreenGenie2, attains 83% sensitivity and 83% specificity for exons on short-sequence predictions. We predict about 12,000 genes in the version <it>v3 Chlamydomonas </it>genome assembly, most of which (78%) are either identical to or significantly overlap the published catalog of <it>Chlamydomonas </it>genes <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. 22% of the published catalog is absent from the GreenGenie2 predictions; there is also a fraction (23%) of GreenGenie2 predictions that are absent from the published gene catalog. Randomly chosen gene models were tested by RT-PCR and most support the GreenGenie2 predictions.</p> <p>Conclusion</p> <p>These data suggest that training with EST assemblies is highly effective and that GreenGenie2 is a valuable, complementary tool for predicting genes in <it>Chlamydomonas reinhardtii</it>.</p

Simultaneous existence of two spin-wave modes in ultrathin Fe/GaAs(001) films studied by Brillouin Light Scattering: experiment and theory

A double-peaked structure was observed in the {\it in-situ} Brillouin Light Scattering (BLS) spectra of a 6 \AA$$ thick epitaxial Fe/GaAs(001) film for values of an external magnetic field $H$, applied along the hard in plane direction, lower than a critical value $H_c\simeq 0.9$ kOe. This experimental finding is theoretically interpreted in terms of a model which assumes a non-homogeneous magnetic ground state characterized by the presence of perperpendicular up/down stripe domains. For such a ground state, two spin-wave modes, namely an acoustic and an optic mode, can exist. Upon increasing the field the magnetization tilts in the film plane, and for $H \ge H_{c}$ the ground state is homogeneous, thus allowing the existence of just a single spin-wave mode. The frequencies of the two spin-wave modes were calculated and successfully compared with the experimental data. The field dependence of the intensities of the corresponding two peaks that are present in the BLS spectra was also estimated, providing further support to the above-mentioned interpretation.Comment: Shortened version (7 pages). Accepted for publication in Physical Review

Is "Real" Effort More Real?

In recent years, a growing number of studies have researchers opting to use "real" effort designs for laboratory experiments where subjects complete an actual task to exert effort rather than using what is perhaps a more traditional design of stylized effort where subjects simply choose an effort level from a pre-defined set. The commonly argued reason for real effort is that it makes the results more generalizable and field relevant. Some researchers go further and make a distinction between trivial and useful real effort, i.e. whether the task is only relevant for the experiment or if it leads to tangible production for some purpose outside of the experiment, and claim that the useful effort model is even more likely to be generalizable. We present an experiment designed to test whether these three modes of effort, stylized, trivial, and useful, have any impact on behavior in a public goods setting. We find that all three forms of effort lead to identical decision making and then discuss how these results help to inform us about the use of real effort in laboratory experiments

Is "Real" Effort More Real?

In recent years, a growing number of studies have researchers opting to use "real" effort designs for laboratory experiments where subjects complete an actual task to exert effort rather than using what is perhaps a more traditional design of stylized effort where subjects simply choose an effort level from a pre-defined set. The commonly argued reason for real effort is that it makes the results more generalizable and field relevant. Some researchers go further and make a distinction between trivial and useful real effort, i.e. whether the task is only relevant for the experiment or if it leads to tangible production for some purpose outside of the experiment, and claim that the useful effort model is even more likely to be generalizable. We present an experiment designed to test whether these three modes of effort, stylized, trivial, and useful, have any impact on behavior in a public goods setting. We find that all three forms of effort lead to identical decision making and then discuss how these results help to inform us about the use of real effort in laboratory experiments

Comparison of Outcomes Following a Switch from a Brand to an Authorized vs. Independent Generic Drug

Authorized generics are identical in formulation to brand drugs, manufactured by the brand company but marketed as a generic. Generics, marketed by generic manufacturers, are required to demonstrate pharmaceutical and bioequivalence to the brand drug, but repetition of clinical trials is not required. This retrospective cohort study compared outcomes for generics and authorized generics, which serves as a generic vs. brand proxy that minimizes bias against generics. For the seven drugs studied between 1999-2014, 5,234 unique patients were on brand drug prior to generic entry and 4,900 (93.6%) switched to a generic. During the 12-months following the brand-to-generic switch, patients using generics vs. authorized generics were similar in terms of outpatient visits, urgent care visits, hospitalizations, and medication discontinuation. The likelihood of emergency department visits was slightly higher for authorized generics compared with generics. These data suggest that generics were clinically no worse than their proxy brand comparator

In-beam internal conversion electron spectroscopy with the SPICE detector

The SPectrometer for Internal Conversion Electrons (SPICE) has been commissioned for use in conjunction with the TIGRESS $\gamma$-ray spectrometer at TRIUMF's ISAC-II facility. SPICE features a permanent rare-earth magnetic lens to collect and direct internal conversion electrons emitted from nuclear reactions to a thick, highly segmented, lithium-drifted silicon detector. This arrangement, combined with TIGRESS, enables in-beam $\gamma$-ray and internal conversion electron spectroscopy to be performed with stable and radioactive ion beams. Technical aspects of the device, capabilities, and initial performance are presented

Self-Affirmation Improves Problem-Solving under Stress

High levels of acute and chronic stress are known to impair problem-solving and creativity on a broad range of tasks. Despite this evidence, we know little about protective factors for mitigating the deleterious effects of stress on problem-solving. Building on previous research showing that self-affirmation can buffer stress, we tested whether an experimental manipulation of self-affirmation improves problem-solving performance in chronically stressed participants. Eighty undergraduates indicated their perceived chronic stress over the previous month and were randomly assigned to either a self-affirmation or control condition. They then completed 30 difficult remote associate problem-solving items under time pressure in front of an evaluator. Results showed that self-affirmation improved problem-solving performance in underperforming chronically stressed individuals. This research suggests a novel means for boosting problem-solving under stress and may have important implications for understanding how self-affirmation boosts academic achievement in school settings. © 2013 Creswell et al