Sum rules for an atomic hyperfine structure in a magnetic field

Sum rules for the energy levels of a hyperfine multiplet in a constant uniform magnetic field is presented. It is found that for any values of the electron angular moment and the nuclear spin there are certain linear combinations of energy levels which do not depend on the magnetic field and can be used to determine the unperturbated hfs separation in the presence of perturbing magnetic field. It is also demonstrated that there are other linear combinations which are linear with the external magnetic field and hence can be used to determine bound values of the electron and nuclear magnetic moments. The accuracy of the approximation within which the result is valid is also discussed

Comparative Energetics of Mammalian Thermoregulatory Physiology

Endothermy allows species to decouple body temperature from environmental temperatures but does not equate to endothermic species maintaining those constant temperatures. Instead, heterothermy fluctuating body temperatures, both in and outside of torpor is common and allows endotherms to expand the limits of thermoneutrality. Thermolability is likely to be more common in the tropics and subtropics, where species live within or above their thermoneutral zone. My dissertation research focused on the heterothermic-homeothermic continuum, specifically quantifying where on the continuum different species fall at certain times and why those species have evolved to be at those points. I quantified the thermal profile of Sundamys muelleri, a tropical, nocturnal rodent. S. muelleri increased evaporative water loss and subcutaneous body temperature at ambient temperatures of 33°C, indicating an upper thermal limit, although metabolic rate showed no increase up to the highest ambient temperature (38.2°C), suggesting this species will tolerate future climatic changes. I then studied the extremely thermally-labile Tenrec ecaudatus. Although there was a wide range of intraindividual variability in metabolic rate and body temperature at both the higher and lower ambient temperatures, I identified a lower thermal limit thermoneutrality of 19.1°C. I then investigated how detailed climate variables may affect thermolability in Chiropteran species across biogeographical zones. I quantified how thermolability phenotypes in bats are globally distributed but found no relationship between thermoregulatory variables of body temperature and lower thermal limits and climatic variables. The unique thermoregulatory adaptations in Chiroptera gives us insights into the physiology and evolution of thermolability in endotherms. Finally, I focused on thermolability at the limits of thermoneutrality in Rodentia, the most diverse and specious clade of Mammalia. Body temperatures at the upper limits of thermoneutrality and the differential between the upper limit and the body temperature at that limit increase with latitude. However, the thermoneutral zone was wider for species with ranges at latitudes closer to the equator than the poles. Lower latitude species have lower temperatures at upper thermal limits and maintain their body temperatures closer to those limits. Through my research we can see how thermolability is shaped by evolutionary history, phylogeny, biogeographical patterns, and climate

Ultrafast dynamics of coherences in the quantum Hall system

Using three-pulse four-wave-mixing optical spectroscopy, we study the ultrafast dynamics of the quantum Hall system. We observe striking differences as compared to an undoped system, where the 2D electron gas is absent. In particular, we observe a large off-resonant signal with strong oscillations. Using a microscopic theory, we show that these are due to many-particle coherences created by interactions between photoexcited carriers and collective excitations of the 2D electron gas. We extract quantitative information about the dephasing and interference of these coherences.Comment: 4 pages, 4 figures, to be published in Phys. Rev. Let

Habitat quality, torpor expression and pathogen transmission in little brown bats (Myotis lucifugus)

Protection of habitat can improve survival and reproductive fitness of threatened and endangered wildlife, particularly if that habitat helps individuals maintain energy balance. Temperate bats are heterothermic and rely on torpor to save energy during winter hibernation and, to a lesser extent, during summer. However, torpor delays parturition and slows lactation for females, and inhibits sperm production for males, so reproductive bats should select warm roosts to help them avoid torpor. Torpor may also slow healing rates, which could have implications for bats that survive the winter with white-nose syndrome (WNS), a devastating fungal skin disease impacting hibernating North American bats. WNS survivors must emerge from hibernation and initiate reproduction while also healing from extensive wing damage caused by the disease. Warm roosting habitat could help WNS survivors avoid torpor to heal and reproduce more quickly, enhancing population recoveries. However, reduced torpor expression and increased activity and exploration could increase the chance of bats acquiring pathogens and parasites from substrates in their environment. I tested the hypotheses that warm roosting habitat: 1) reduces use of torpor by endangered little brown bats (Myotis lucifugus); but 2) increases the risk of pathogen acquisition from substrates in the environment. I captured bats from a fall swarm and housed individuals in outdoor flight enclosures equipped with either four heated or four unheated roost boxes. I quantified torpor expression using skin temperature dataloggers and used ultraviolet (UV) fluorescent powder as a proxy pathogen which I applied to one of the four roost boxes in each tent. Bats provided with warm roosts used less torpor (p<0.0001), but the amount of time a bat spent in torpor (p=0.26), had no effect on intensity of infection with the proxy pathogen. My data highlight roost temperature as a driver of torpor expression in little brown bats but suggest that heated roosts will not speed rates of pathogen or parasite acquisition from the environment. This result supports the potential of enhancement of summer roosting habitat as a management strategy for WNS.Master of Science in Bioscience, Technology, and Public Polic

Salvaging Affymetrix probes after probe-level re-annotation

Background: Affymetrix GeneChips can be re-annotated at the probe-level by breaking up the original probe-sets and recomposing new probe-sets based on up-to-date genomic knowledge, such as available in Entrez Gene. This results in custom Chip Description Files (CDF). Using these custom CDFs improves the quality of the data and thus the results of related gene expression studies. However, 44-71% of the probes on a GeneChip are lost in this re-annotation process. Although generally aimed at less known genes, losing these probes obviously means a substantial loss of expensive experiment data. Biologists are therefore very reluctant to adopt this approach. Findings: We aimed to re-introduce the non-affected Affymetrix probe-sets after these re-annotation procedures. For this, we developed an algorithm (CDF-Merger) and applied it to standard Affymetrix CDFs and custom Brainarray CDFs to obtain Hybrid CDFs. Thus, salvaging lost Affymetrix probes with our CDF-Merger restored probe content up to 94%. Because the salvaged probes (up to 54% of the probe content on the arrays) represent less-reliable probe-sets, we made the origin of all probe-set definitions traceable, so biologists can choose at any time in their analyses, which subset of probe-sets they want to use. Conclusion: The availability of up-to-date Hybrid CDFs plus R environment allows for easy implementation of our approach

Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example

BACKGROUND: A complete gene-expression microarray should preferably detect all genomic sequences that can be expressed as RNA in an organism, i.e. the transcriptome. However, our knowledge of a transcriptome of any organism still is incomplete and transcriptome information is continuously being updated. Here, we present a strategy to integrate heterogeneous sequence information that can be used as input for an up-to-date microarray design. FINDINGS: Our algorithm consists of four steps. In the first step transcripts from different resources are grouped into Transcription Clusters (TCs) by looking at the similarity of all transcripts. TCs are groups of transcripts with a similar length. If a transcript is much smaller than a TC to which it is highly similar, it will be annotated as a subsequence of that TC and is used for probe design only if the probe designed for the TC does not query the subsequence. Secondly, all TCs are mapped to a genome assembly and gene information is added to the design. Thirdly TC members are ranked according to their trustworthiness and the most reliable sequence is used for the probe design. The last step is the actual array design. We have used this strategy to build an up-to-date zebrafish microarray. CONCLUSIONS: With our strategy and the software developed, it is possible to use a set of heterogeneous transcript resources for microarray design, reduce the number of candidate target sequences on which the design is based and reduce redundancy. By changing the parameters in the procedure it is possible to control the similarity within the TCs and thus the amount of candidate sequences for the design. The annotation of the microarray is carried out simultaneously with the design

The Effect of Time Variation in the Higgs Vacuum Expectation Value on the Cosmic Microwave Background

A time variation in the Higgs vacuum expectation value alters the electron mass and thereby changes the ionization history of the universe. This change produces a measurable imprint on the pattern of cosmic microwave background (CMB) fluctuations. The nuclear masses and nuclear binding energies, as well as the Fermi coupling constant, are also altered, with negligible impact on the CMB. We calculate the changes in the spectrum of the CMB fluctuations as a function of the change in the electron mass. We find that future CMB experiments could be sensitive to |\Delta m_e/m_e| \sim |\Delta G_F/G_F| \sim 10^{-2} - 10^{-3}. However, we also show that a change in the electron mass is nearly, but not exactly, degenerate with a change in the fine-structure constant. If both the electron mass and the fine-structure constant are time-varying, the corresponding CMB limits are much weaker, particularly for l < 1000.Comment: 6 pages, 3 figures, Fig. 3 modified, other minor correction