The ISCIP Analyst, Volume XV, Issue 12

This repository item contains a single issue of The ISCIP Analyst, an analytical review journal published from 1996 to 2010 by the Boston University Institute for the Study of Conflict, Ideology, and Policy

Instruments and Methods: Direct measurement of sliding at the glacier bed

Sliding at the base of Trapridge Glacier, Yukon Territory, Canada, was measured using a “drag spool”. We describe this simple and inexpensive instrument as well as its installation and operation. From 1990 to 1992 seven sites were instrumented with drag spools. At six of the sites basal sliding, during the period of observation, accounted for 50-70% of the total flow observed at the glacier surface. The contribution from ice creep is known to be small, so most of the remaining surface motion must be attributed to subglacial sediment deformation. For the seventh site the observed sliding rate was ~ 90% of the total flow, an indication that the sliding contribution varies spatially across the bed. Diurnal variations in the response of one of our instruments appear to be correlated to subglacial water-pressure fluctuations and are interpreted in terms of changes in sliding velocity rather than the opening and closing of basal cavities

Construction of self-dual normal bases and their complexity

Recent work of Pickett has given a construction of self-dual normal bases for extensions of finite fields, whenever they exist. In this article we present these results in an explicit and constructive manner and apply them, through computer search, to identify the lowest complexity of self-dual normal bases for extensions of low degree. Comparisons to similar searches amongst normal bases show that the lowest complexity is often achieved from a self-dual normal basis

Multidisciplinary Investigations of Alpine Ice Patches in Southwest Yukon, Canada: Paleoenvironmental and Paleobiological Investigations

Since the discovery of dung-rich alpine ice patches in southwest Yukon in 1997, continuing multidisciplinary studies have provided a unique window on the biology, climate, and hunting activity in this region over much of the Holocene. Aerial surveys have identified 72 ice patches of variable size, and 65 patches have been ground-surveyed for organic remains. Of these, 35 yielded an abundance of biological specimens, including caribou and other rare large mammal remains, mummified small mammals and birds, and artifacts spanning 8000 years. The dung provides pollen and plant macrofossils for analysis and paleoenvironmental reconstruction, as well as dietary, genetic, and parasitic information. Stratigraphically controlled sampling of dung within ice layers has yielded a geochronology placing their formation as early as 8300 to 8000 years BP. Ice patch formation was nearly continuous except for an interval between 6700 and 4700 years BP and another between 1440 and 1030, when warm or dry conditions (or both) resulted in no net ice accumulation. Resumption of ice accumulation over the following 500 years likely culminated in the Little Ice Age. The size of the ice patches during this period is made evident by a lichen-free zone that haloes each patch. More recently, interpretation of air photos from 1946 to 2001 has found a significant reduction in ice patch dimensions. Daily temperature records for Whitehorse (1942-2001) were used to calculate melting degree-day values that account for a large part of the variation in ice patch size, indicating that while considerable melting has likely occurred since the end of the Little Ice Age, the ice patches are highly sensitive to decadal changes in temperature.Depuis la découverte de plaques de glace alpines riches en excréments d'animaux dans le sud-ouest du Yukon en 1997, des études multidisciplinaires continues offrent une fenêtre unique sur la biologie, le climat et les activités de chasse de la région pendant presque toute la période de l'Holocène. À l'aide de relevés aériens, il a été possible d'identifier 72 plaques de glace de tailles différentes. Des relevés sur le terrain ont été effectués sur 65 de ces plaques pour récupérer des restes organiques, et 18 d'entre-elles ont révélé une abondance d'espèces biologiques et des restes de grands mammifères rares (y compris le caribou), des petits mammifères et des oiseaux momifiés, et des artéfacts datant jusqu'à 8000 ans. Les excréments d'animaux permettent d'analyser des macrofossiles de pollen et de plantes afin de faire une reconstruction paléoécologique, ainsi que d'obtenir des renseignements sur le régime alimentaire, la génétique et les parasites. À l'aide de la géochronologie, l'échantillonnage des excréments d'animaux contrôlé par stratigraphie a permis de dater la formation des excréments à aussi loin que 8300 à 8000 ans B.P. La formation des plaques de glace a été presque continue, à l'exception d'une période entre 6700 et 4700 ans B.P. et d'une autre entre 1440 et 1030, lorsque des conditions chaudes ou sèches ou les deux n'ont pas permis à la glace de s'accumuler. La reprise de l'accumulation de glace au cours des 500 dernières années a vraisemblablement provoqué le petit âge glaciaire. La taille des plaques de glace au cours de cette période est facilement calculable grâce aux zones sans lichen qui encerclent chaque plaque. Des études plus récentes de photos aériennes prises entre 1946 et 2001 ont permis de constater une réduction marquée de la taille des plaques de glace. Les données des températures quotidiennes de Whitehorse (de 1942 à 2001) ont été utilisées pour calculer la valeur du degré-jour de fonte qui est en grande partie responsable de la variation de la taille des plaques de glace. Ces données indiquent que même si le plus gros de la fonte s'est produit depuis la fin du petit âge glaciaire, les plaques de glace réagissent beaucoup aux changements de température décennaux

In Pursuit of Prehistoric Caribou on Thandlät, Southern Yukon

In 1997, the first author noted a large concentration of caribou (Rangifer sp.) fecal pellets and a caribou antler on a permanent snow patch in the Kusawa Lake area of southern Yukon. Caribou are completely absent from this area today. Coring of the snow patch revealed continuous deposits of fecal pellets to depths of at least 160 cm. The proximal portion of a wooden dart or arrow shaft fragment recovered on the edge of the snow patch represents one of the few organic examples of mid-Holocene hunting technology ever found in Canada. An age of 2450 BP ± 50 years was obtained for the fecal material from approximately 1.6 m below the surface of the snow patch, and the dart was dated at 4360 BP ± 50 years. These dates indicate that aboriginal Yukon hunters have been harvesting caribou at this location for at least 4000 years. The Thandlät site offers a rare opportunity to explore a number of questions regarding the prehistoric ecology of large caribou populations, the implications of climate change for caribou populations, and human use of high-elevation hunting sites.En 1997, le premier auteur a découvert une concentration élevée de boulettes fécales (Rangifer sp.) et des bois de caribou sur une congère dans la région du lac Kusawa, dans le sud du Yukon. Il n'y a plus de caribous dans cette région. Le carottage de la congère a révélé des dépôts de boulettes jusqu'à une profondeur de 160 cm. Un fragment de dard ou de la flèche en bois trouvé sur le bord de la congère représente une des rares découvertes au Canada relatives à ce type d'arme. Il a été déterminé que les matières fécales prélevées dans la congère, à environ 1,6 m de profondeur, sont âgées de 2450 BP ± 50 ans, et que le dard aurait 4360 BP ± 50 ans. Ces dates montrent que les Autochtones du Yukon chassaient déjà le caribou à cet endroit il y a 4000 ans. Le site Thandlät est un des rares endroits où l'on peut observer divers aspects préhistoriques des grandes populations de caribou, des effets des changements climatiques sur les populations de caribous et des activités de chasse à grande altitude

SPA: A Probabilistic Algorithm for Spliced Alignment

Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of the repertoire of splice variants, and to gain insight into the mechanisms of alternative splicing, it is essential that cDNAs are very accurately mapped to their respective genomes. Currently available algorithms for cDNA-to-genome alignment do not reach the necessary level of accuracy because they use ad hoc scoring models that cannot correctly trade off the likelihoods of various sequencing errors against the probabilities of different gene structures. Here we develop a Bayesian probabilistic approach to cDNA-to-genome alignment. Gene structures are assigned prior probabilities based on the lengths of their introns and exons, and based on the sequences at their splice boundaries. A likelihood model for sequencing errors takes into account the rates at which misincorporation, as well as insertions and deletions of different lengths, occurs during sequencing. The parameters of both the prior and likelihood model can be automatically estimated from a set of cDNAs, thus enabling our method to adapt itself to different organisms and experimental procedures. We implemented our method in a fast cDNA-to-genome alignment program, SPA, and applied it to the FANTOM3 dataset of over 100,000 full-length mouse cDNAs and a dataset of over 20,000 full-length human cDNAs. Comparison with the results of four other mapping programs shows that SPA produces alignments of significantly higher quality. In particular, the quality of the SPA alignments near splice boundaries and SPA's mapping of the 5′ and 3′ ends of the cDNAs are highly improved, allowing for more accurate identification of transcript starts and ends, and accurate identification of subtle splice variations. Finally, our splice boundary analysis on the human dataset suggests the existence of a novel non-canonical splice site that we also find in the mouse dataset. The SPA software package is available at http://www.biozentrum.unibas.ch/personal/nimwegen/cgi-bin/spa.cgi

The Atacama Cosmology Telescope: Cross-Correlation of Cosmic Microwave Background Lensing and Quasars

We measure the cross-correlation of Atacama cosmology telescope cosmic microwave background (CMB) lensing convergence maps with quasar maps made from the Sloan Digital Sky Survey DR8 SDSS-XDQSO photometric catalog. The CMB lensing quasar cross-power spectrum is detected for the first time at a significance of 3.8σ, which directly confirms that the quasar distribution traces the mass distribution at high redshifts z\u3e1. Our detection passes a number of null tests and systematic checks. Using this cross-power spectrum, we measure the amplitude of the linear quasar bias assuming a template for its redshift dependence, and find the amplitude to be consistent with an earlier measurement from clustering; at redshift z≈1.4, the peak of the distribution of quasars in our maps, our measurement corresponds to a bias of b=2.5±0.6. With the signal-to-noise ratio on CMB lensing measurements likely to improve by an order of magnitude over the next few years, our results demonstrate the potential of CMB lensing cross-correlations to probe astrophysics at high redshifts

Expanding the Direct HetR Regulon in Anabaena sp. Strain PCC 7120

In response to a lack of environmental combined nitrogen, the filamentous cyanobacterium Anabaena sp. strain PCC 7120 differentiates nitrogen-fixing heterocyst cells in a periodic pattern. HetR is a transcription factor that coordinates the regulation of this developmental program. An inverted repeat-containing sequence in the hepA promoter required for proheterocyst-specific transcription was identified based on sequence similarity to a previously characterized binding site for HetR in the promoter of hetP. The binding affinity of HetR for the hepA site is roughly an order of magnitude lower than that for the hetP binding site. A BLAST search of the Anabaena genome identified 166 hepA-like sites that occur as single or tandem sites (two binding sites separated by 13 bp). The vast majority of these sites are present in predicted intergenic regions. HetR bound five representative single binding sites in vitro, and binding was abrogated by transversions in the binding sites that conserved the inverted repeat nature of the sites. Binding to four representative tandem sites was not observed. Transcriptional fusions of the green fluorescent protein gene gfp with putative promoter regions associated with the representative binding sites indicated that HetR could function as either an activator or repressor and that activation was cell-type specific. Taken together, we have expanded the direct HetR regulon and propose a model in which three categories of HetR binding sites, based on binding affinity and nucleotide sequence, contribute to three of the four phases of differentiation