174,168 research outputs found
Natural variation in Drosophila melanogaster
No full textThis work is dedicated to studying natural variation in D. melanogaster at the DNA sequence and gene expression level. In addition I present a new version of the DNA polymorphism analysis program VariScan, which includes significant improvements.
In CHAPTER 1 I describe a genome scan of single nucleotide polymorphism in two natural D. melanogaster populations (from Africa and Europe) on the third chromosome. Together with polymorphism data previously published for the X chromosome of the same populations, this allows a comparative study of the polymorphism patterns of the X chromosome and an autosome. The frequency spectrum of mutations and the patterns of linkage disequilibrium are investigated. The observed patterns indicate that there is a significant difference in the behavior of the two chromosomes, as has already been suggested by previous studies. To uncover the reasons for this a coalescent based maximum likelihood method is applied that incorporates the effects of demographic history and unequal sex ratios. For the African population the differential behavior of the chromosomes can be explained by its demographic history and an excess of females. In Europe, a population bottleneck and an excess of males alone cannot explain the patterns we observe. The additional action of positive selection in this population is proposed as a possible explanation.
In CHAPTER 2 I investigate the variation in gene expression of the two aforementioned populations. Whole-genome microarrays are used to study levels of expression for 88% of all known genes in eight adult males from both populations. The observed levels of expression variation are equal in Africa and Europe, despite the fact that DNA sequence variation is much higher in Africa. This is evidence for the action of stabilizing selection governing levels of expression polymorphism. Supporting this view, genes involved in many different functions, and are therefore on strong selective constraint, show less variation than do genes with only few functions. The experimental design allows the search for genes which differ in their expression patterns between Europe and Africa and might therefore have undergone adaptive evolution. Detected candidates include genes putatively involved in insecticide resistance and food choice. Surprisingly, many genes over-expressed in Africa are involved in the formation and function of the flying apparatus.
In CHAPTER 3 I present version 2 of the program VariScan. This program was designed to analyse patterns of DNA sequence polymorphism on a chromosomal scale. The functionality of the core analysis tool, the wavelet decomposition, is described. In addition, multiple improvements to the previous version are presented. The program now supports the “pairwise deletion” option. This is essential for analysing data at the chromosome scale, since such data often contains incomplete information. It is now possible to add outgroup information, which allows the calculation of additional statistics. Furthermore, the separate analysis of different predefined chromosomal regions is added as an option. To increase the user friendliness, a graphical user interface is now included as part of the software package. Finally, VariScan is applied to published and computer-generated data and the ability of the wavelet-based analysis to uncover chromosomal regions with interesting DNA polymorphism patterns is demonstrated
An accurate shock-capturing finite-difference method to solve the Savage-Hutter equations in avalanche dynamics
No full textThe Savage-Hutter equations of granular avalanche flows are a hyperbolic system of equations for the distribution of depth and depth-averaged velocity components tangential to the sliding bed. They involve two phenomenological parameters, the internal and the bed friction angles, which together define the earth pressure coefficient which assumes different values depending upon whether the flow is either diverging or contracting. Because of the hyperbolicity of the equations, since velocities may be supercritical, shock waves are often formed in avalanche flows. Numerical schemes solving these free surface flows must cope with smooth as well as non-smooth solutions. In this paper the Savage-Hutter equations in conservative form are solved with a shock-capturing technique, including a front-tracking method. This method can perform for parabolic similarity solutions for which the Lagrangian scheme is excellent, and it is even better in other situations when the latter fails
QR factorization over tunable processor grids
No full textThe increasing complexity of modern computer architectures has greatly influenced algorithm design. Algorithm performance on these architectures is now determined by the movement of data. Therefore,
modern algorithms should prioritize minimizing communication.
In this work, we present a new parallel QR factorization algorithm solved over a
tunable processor grid in a distributed memory environment. The processor grid can be
tuned between one and three dimensions, resulting in tradeoffs in the asymptotic costs of
synchronization, horizontal bandwidth,
flop count, and memory footprint. This parallel algorithm is
the first to efficiently extend the Cholesky-QR2 algorithm to matrices with an
arbitrary number of rows and columns. Along its critical path of execution on P processors, our tunable algorithm improves upon the horizontal bandwidth cost of the existing
Cholesky-QR2 algorithm by up to a factor of c^2 when solved over a c x d x c processor grid
subject to P = c^2 d and E[1,P^1/3].
The costs attained by our algorithm are asymptotically
equivalent to state-of-the-art QR factorization algorithms that have yet to
be implemented.
We argue that ours achieves better practicality and
flexibility while still attaining minimal communication.Open Restriction set for Item 102919 on 2017-08-21T15:06:31Z with date null by [email protected] by Janice Progen ([email protected]) on 2017-08-21T15:47:32Z
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Previous issue date: 2017-05Ope
Correction: "Density Functional Theory and Experimental Determination of Band Gaps and Lattice Parameters in Kesterite Cu2ZnSn(SxSe1-x)(4)" (vol 11, pg 10463, 2020)
No full textThe authors regret that one of their coauthors, Oliver S. Hutter, was omitted from the original publication due to an oversight. Dr. Hutter was responsible for performing a large part of the experiments on bulk crystalline materials. The authors therefore take this opportunity to include Dr. Hutter on the author list and extend their apologies to him for the earlier oversight
A Structural Model of the Complex Formed by Phospholamban and the Calcium Pump of Sarcoplasmic Reticulum Obtained by Molecular Mechanics
No full textPhospholamban (PLN) is an intrinsic membrane protein of 52 amino acids that modulates the activity of the reticular Ca2+ ion pump. We recently,solved the three-dimensional structure of chemically synthesized, unphosphoryloted, monomeric PLN (C41F) by high-resolution nuclear magnetic resonance spectroscopy in chloroform/methanol. The structure is composed of two alpha-helical regions connected by a beta urn- (Type III). We used this structure and the crystallographic structure of the sarcoplasmic reticulum calcium pump (SERCA) co-workers and modeled into, its E-2 form by Stokes (1KJU) or by Toyoshima (1FQU). We applied restrained and unrestrained energy optimizations and used the AMBER molecular mechanics force field to model the complex formed between PLN and the pump. The results indicate that transmembrane helix 6 (M6) of the SERCA pump is energetically favored, with respect to the other trans membrane helices, as the PLN, binding partner within the membrane and is the only, one of these helices that also permits contact between the N-terminal residues of PLN and the critical cytosolic binding loop region of the pump. This result is in agreement with published biochemical data and with the predictions of previous mutagenesis work on the membrane sector of the pump. The model reveals that PLN does not span the entire width of the membrane, that is, its hydrophobic C-terminal end is located near the center of the transmembrane region of the SERCA pump. The model also shows that interaction with M6 is stabilized by additional contacts made by PLN to M4. The contact between the N-terminal portion of PLN and the pump is stabilized by a number of salt and hydrogen-bond bridges, which may be abolished by phosphorylation of PLN. The contacts between the cytosolic portions of PLN and the pump are only observed in the E-2-conformation of the pump. Our model of the complex also offers a plausible structural explanation for the preference of protein kinase A for phosphorylation of Ser16 of PLN
Following up the Kepler field: Masses of Targets for transit timing and atmospheric characterization
No full textThese are posterior samples from TTV models presented in "Following up the Kepler field: Masses of Targets for transit timing and atmospheric characterization" by D. Jontof-Hutter, D., A. Wolfgang A., E. B. Ford, J. J. Liassauer, D. C. Fabrycky and J. F. Rowe
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Application-independent protocol for predicting the efficiency of lithium-ion battery cells in operations
No full textDespite a continuous reduction in battery prices, investment in storage systems carries a high risk. Indeed, many applications lack an adequate test protocol and method to predict the performance of batteries in operations. In this paper, we focus on lithium-ion battery energy storage systems (BESS), for which we introduce a novel method. With this method, predicting the efficiency of lithium-ion BESS becomes possible for any application from a single set of measurements. We show that evaluating the battery resistance as a function of the C-rate provides general âcapability chartsâ based on which the efficiency can be evaluated under arbitrary operation profiles. Application-specific test procedures therefore become unnecessary. We have applied the novel procedure on three different lithium-ion cell technologies and illustrate its accuracy in the example of grid-connected BESS used for primary control reserve
Boophis boppa Hutter, Lambert, Cobb, Andriampenomanana & Vences, 2015, sp. nov.
No full textBoophis boppa sp. nov. Suggested common English name. Boppa’s Bright-eyed treefrog Suggested common Malagasy name. Fity maso hazo Sahona ny Boppa Remarks. Previously referred to as Boophis sp. 1 (aff. ankaratra) (Andreone et al. 2007), Boophis aff. ankaratra ‘Antoetra slow’ (Glaw & Vences 2007), and Boophis sp. 18 (Vieites et al. 2009). Holotype (Figs. 2–3 A). KU 336824, an adult male collected by Carl R. Hutter and Zo F. Andriampenomanana on 18 January 2014, at Maharira within Ranomafana National Park (21 ° 20 '06.3"S, 47 ° 24 ' 28.31 "E; 1233 m, above sea level [a.s.l.]), Fianarantsoa province, Madagascar. Paratypes. Adult female KU 336829 and adult male KU 336826 collected on 21 January 2013 by Carl R. Hutter and Shea M. Lambert with same locality data as holotype. Adult males KU 336828, KU 336825, KU 336827, with same collection data as holotype. Referred specimens. UADBA-Uncatalogued (CRH 080), UADBA-Uncatalogued (CRH 168), UADBA- Uncatalogued (CRH 178) with same collection data as holotype. Etymology. This species in named in honor of Nicholas Jay Pritzker, devoted grandfather, father and husband, brilliant businessman, philanthropist, amateur scientist, committed conservationist; and board member, supporter and long-time friend of Conservation International. The name ‘Boppa’ is an affectionate nickname used by his children and grandchildren. This dedication is courtesy of his youngest son Isaac, who has generously supported amphibian research in Madagascar, including this study and future taxonomic research as well. The species name is used as an invariable noun in apposition to the genus name. Diagnosis. Boophis boppa (Figs. 2–4) is placed in the family Mantellidae, subfamily Boophinae, and genus Boophis, as diagnosed by Glaw & Vences (2006). The new species shares the following combination of morphological traits with all other Boophis: presence of intercalary element between ultimate and penultimate phalanges of fingers and toes; presence of nuptial pads and absence of femoral glands in males; absence of gular glands in males; terminal discs of fingers and toes enlarged; lateral metatarsalia separated by webbing; and absence of outer metatarsal tubercle. Furthermore, phylogenetic analyses support the placement of the new species in the genus Boophis. Boophis boppa is placed in the Boophis albipunctatus group as supported by the phylogenetic analyses. Additionally, the following combination of characters provide additional evidence for the inferred phylogenetic relationships: small body size (male SVL 90 %; PP> 0.95; Fig. 8). Uncorrected p-distances using the 16 S fragment indicate that B. ankaratra has the lowest distance to the new species, at 1.9–3.7 %. Additionally, we find that variation in genetic distance among B. boppa and B. ankaratra is not related to geographic proximity. The lowest distance of 1.9 % (Imaitso Forest; FMGV 1697) does not correspond to proximate localities and the highest distance of 3.7 % is from Ranomafana National Park (Ranomena; ZCMV 5989). This variability in distances is likely a result of varying amounts of sequence overlap being compared. Overall, these results provide strong evidence that the species is a separately evolving lineage and does not reproduce with other species in the complex. Distribution (Fig. 1). Boophis boppa is known from Ranomafana National Park (RNP), but has only been found at high elevation sites (~ 1046–1312 m, a.s.l.). In addition to the type locality of Maharira, DNA sequences also confirm that specimens FAZC 11454, 11462, and 11480 collected from Farihimazava forest near Antoetra (20 ° 50 '06"S, 47 ° 19 ' 57 "E, 1380–1420 m, a.s.l.; ca. 55 km north west of the type locality; see Andreone et al. 2007) are conspecific. Additionally, tadpoles ZCMV 9739 collected at Imaloka (RNP: 21 ° 14 ' 32 "S, 47 ° 27 ' 55 "E, 1020 m, a.s.l.) and ZSM 1164 / 2007 from Sakaroa (RNP: 21 ° 15 '00.1"S, 47 ° 24 ' 53.6 "E) belong to Boophis boppa. The species has a known elevational distribution of ca. 1020–1400 m, a.s.l. Natural history (Fig. 12). Boophis boppa was locally abundant but thus far only found in undisturbed, primary forests along fast moving streams and was occasionally found along slow flowing tributaries adjacent to fast streams. Males of the species typically were calling at night from the surfaces of vegetation less than three meters in height (Fig. 12 A–B). Females of B. boppa were rarely encountered and were only observed while in amplexus (Fig. 12 C). We also confirm that Boophis boppa is syntopic with Boophis ankaratra at Maharira and that the two species can be found calling less than a meter apart. This is also consistent with Andreone et al. (2007), which found B. boppa (i.e. Boophis aff. ankaratra) and B. ankaratra to occur sympatrically. Other syntopic species of Boophis at Maharira include: B. madagascariensis, B. majori, B. aff. marojezensis, B. aff. picturatus, B. popi, and B. reticulatus. Conservation status. The new species is known from Ranomafana National Park and its vicinity, extending into the Antoetra area. While it is known from a geographic area less than ~ 5,000 km 2, there are no known immediate threats, reductions in quality or extent of habitat, or observed declines as the species is well protected within Ranomafana National Park. Therefore, the new species meets only criterion (B 1), and could become endangered in the future if the situation changes at Ranomafana, for instance through population declines from chytridiomycosis, which has been detected in the park (Bletz et al. 2015). We recommend a conservation status of Near Threatened, following IUCN (2001) criteria.Published as part of Hutter, Carl R., Lambert, Shea M., Cobb, Kerry A., Andriampenomanana, Zo Faniry & Vences, Miguel, 2015, A new species of bright-eyed treefrog (Mantellidae) from Madagascar, with comments on call evolution and patterns of syntopy in the Boophis ankaratra complex, pp. 531-555 in Zootaxa 4034 (3) on pages 537-546, DOI: 10.11646/zootaxa.4034.3.6, http://zenodo.org/record/23809
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