Effects of passage history and sampling bias on phylogenetic reconstruction of human influenza A evolution

In this paper we determine the extent to which host-mediated mutations and a known sampling bias affect evolutionary studies of human influenza A. Previous phylogenetic reconstruction of influenza A (H3N2) evolution using the hemagglutinin gene revealed an excess of nonsilent substitutions assigned to the terminal branches of the tree. We investigate two hypotheses to explain this observation. The first hypothesis is that the excess reflects mutations that were either not present or were at low frequency in the viral sample isolated from its human host, and that these mutations increased in frequency during passage of the virus in embryonated eggs. A set of 22 codons known to undergo such “host-mediated” mutations showed a significant excess of mutations assigned to branches attaching sequences from egg-cultured (as opposed to cell-cultured) isolates to the tree. Our second hypothesis is that the remaining excess results from sampling bias. Influenza surveillance is purposefully biased toward sequencing antigenically dissimilar strains in an effort to identify new variants that may signal the need to update the vaccine. This bias produces an excess of mutations assigned to terminal branches simply because an isolate with no close relatives is by definition attached to the tree by a relatively long branch. Simulations show that the magnitude of excess mutations we observed in the hemagglutinin tree is consistent with expectations based on our sampling protocol. Sampling bias does not affect inferences about evolution drawn from phylogenetic analyses. However, if possible, the excess caused by host-mediated mutations should be removed from studies of the evolution of influenza viruses as they replicate in their human hosts.

The Mice at play in the CALIFA survey. A case study of a gas-rich major merger between first passage and coalescence

We present optical integral field spectroscopy (IFS) observations of the Mice, a major merger between two massive (≳10^11 M_⊙) gas-rich spirals NGC 4676A and B, observed between first passage and final coalescence. The spectra provide stellar and gas kinematics, ionised gas properties, and stellar population diagnostics, over the full optical extent of both galaxies with ~1.6 kpc spatial resolution. The Mice galaxies provide a perfect case study that highlights the importance of IFS data for improving our understanding of local galaxies. The impact of first passage on the kinematics of the stars and gas has been significant, with strong bars most likely induced in both galaxies. The barred spiral NGC 4676B exhibits a strong twist in both its stellar and ionised gas disk. The edge-on disk galaxy NGC 4676A appears to be bulge free, with a strong bar causing its “boxy” light profile. On the other hand, the impact of the merger on the stellar populations has been minimal thus far. By combining the IFS data with archival multiwavelength observations we show that star formation induced by the recent close passage has not contributed significantly to the total star formation rate or stellar mass of the galaxies. Both galaxies show bicones of high ionisation gas extending along their minor axes. In NGC 4676A the high gas velocity dispersion and Seyfert-like line ratios at large scaleheight indicate a powerful outflow. Fast shocks (vs ~ 350 km s^-1) extend to ~6.6 kpc above the disk plane. The measured ram pressure (P/k = 4.8 × 10^6 K cm^-3) and mass outflow rate (~8−20 M_⊙ yr^-1) are similar to superwinds from local ultra-luminous infrared galaxies, although NGC 4676A only has a moderate infrared luminosity of 3 × 10^10 L_⊙. Energy beyond what is provided by the mechanical energy of the starburst appears to be required to drive the outflow. Finally, we compare the observations to mock kinematic and stellar population maps extracted from a hydrodynamical merger simulation. The models show little enhancement in star formation during and following first passage, in agreement with the observations. We highlight areas where IFS data could help further constrain the models.

The Role of Passage Topic Knowledge in Typical and Poor Comprehenders' Recall

This dissertation examines the role of topic knowledge (TK) in comprehension among typical readers and those with Specifically Poor Comprehension (SPC), i.e., those who demonstrate deficits in understanding what they read despite adequate decoding. Previous studies of poor comprehension have focused on weaknesses in specific skills, such as word decoding and inferencing ability, but this dissertation examined a different factor: whether deficits in availability and use of TK underlie poor comprehension. It is well known that TK tends to facilitate comprehension among typical readers, but its interaction with working memory and word decoding is unclear, particularly among participants with deficits in these skills. Across several passages, we found that SPCs do in fact have less TK to assist their interpretation of a text. However, we found no evidence that deficits in working memory or word decoding ability make it difficult for children to benefit from their TK when they have it. Instead, children across the skill spectrum are able to draw upon TK to assist their interpretation of a passage. Because TK is difficult to assess and studies vary in methodology, another goal of this dissertation was to compare two methods for measuring it. Both approaches score responses to a concept question to assess TK, but in the first, a human rater assigns a score whereas in the second, a computer algorithm, Latent Semantic Analysis (LSA; Landauer & Dumais, 1997) assigns a score. We found similar results across both methods of assessing TK, suggesting that a continuous measure is not appreciably more sensitive to variations in knowledge than discrete human ratings. This study contributes to our understanding of how best to measure TK, the factors that moderate its relationship with recall, and its role in poor comprehension. The findings suggest that teaching practices that focus on expanding TK are likely to improve comprehension across readers with a variety of abilities.

Improving Colorado Mountain Highway Culvert Stream Crossings for Trout Passage

Highways can be effective barriers to animal migration. Where highways cross over streams, a passageway, typically a culvert, not designed for fish access can cut off an organism from miles of habitat. Traditional methods of culvert design, to convey floodwaters, reduced access to aquatic and riparian range. The Colorado Department of Transportation likely has numerous culverts that restrict aquatic passage. This paper provides guidance to CDOT for assessment of stream geomorphic conditions affecting culvert performance for fish passage, understanding aquatic organism habitat requirements, and incorporating ecological parameters into culvert designs that benefit fish and other organisms. A case study illustrates culvert problems in a difficult geomorphic setting including a fish passage assessment to evaluate stream stability for long-term culvert reliability.