Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains

Background The HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation, among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method [1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal sequence data. We present serial evolutionary networks as a longitudinal representation of the mutational pathways of a viral population in a within-host environment. The longitudinal representation of the evolutionary networks was complemented with charts of clinical markers to facilitate correlation analysis between pertinent clinical information and the evolutionary relationships. Results Analysis based on the predicted networks suggests the following:: significantly stronger recombination signals (p = 0.003) for the inferred ancestors of the X4 strains, recombination events between different lineages and recombination events between putative reservoir virus and those from a later population, an early star-like topology observed for four of the patients who died of AIDS. A significantly higher number of recombinants were predicted at sampling points that corresponded to peaks in the viral load levels (p = 0.0042). Conclusion Our results indicate that serial evolutionary networks of HIV sequences enable systematic statistical analysis of the implicit relations embedded in the topology of the structure and can greatly facilitate identification of patterns of evolution that can lead to specific hypotheses and new insights. The conclusions of applying our method to empirical HIV data support the conventional wisdom of the new generation HIV treatments, that in order to keep the virus in check, viral loads need to be suppressed to almost undetectable levels.

Logical simulation of communication subsystem for Universal Serial Bus (USB)

The primary purpose of this thesis was to design a logical simulation of a communication sub block to be used in the effective communication of digital data between the host and the peripheral devices. The module designed is a Serial interface engine in the Universal Serial Bus that effectively controls the flow of data for communication between the host and the peripheral devices with the emphasis on the study of timing and control signals, considering the practical aspects of them. In this study an attempt was made to realize data communication in the hardware using the Verilog Hardware Description language, which is supported by most popular logic synthesis tools. Various techniques like Cyclic Redundancy Checks, bit-stuffing and Non Return to Zero are implemented in the design to provide enhanced performance of the module.

Vibrations of 1D non-conservative elastic continuum due to passage of a MDOF damped oscillator

Peer reviewed

Bella Abzug votes for passage of ERA in NY with husband Martin Abzug to her right

General note: Title and date provided by Bettye Lane.

NY Mayor Ed Koch speaks at gay civil rights demonstration in support of Intro 2 passage

General note: Title and date provided by Bettye Lane.

GAA protesting at City Hall for passage of Intro 475 gay civil rights bill

General note: Title and date provided by Bettye Lane.

Gays demonstrate outside City Hall for passage of Intro 475

General note: Title and date provided by Bettye Lane.

Dr. Bruce Voeller with partner at protest for passage of civil rights bill Intro 475

General note: Title and date provided by Bettye Lane. Digital reproduction

Gays protest outside of NY City Hall for passage of civil rights bill Intro 475

General note: Title and date provided by Bettye Lane.

La relation entre les positions du tronc et les stratégies motrices utilisées par les personnes hémiparétiques lors du passage de la position assise à debout

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

La relation entre les positions du tronc et les stratégies motrices utilisées par les personnes hémiparétiques lors du passage de la position assise à debout

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Abundance of tintinnids in waters of the Argentine Shelf and the Drake Passage 2002-2003

The relationship between the abundance and diversity of tintinnids and the concentration of chlorophyll a (Chl a) was contrasted between neritic and oceanic waters of the SW Atlantic during autumn and summer. Chl a and tintinnid abundance and biomass reached maximum values (17.53 µg/L, 2.76 x 10**3 ind./L and 6.29 µg C/L, respectively) in shelf waters during summer, and their mean values generally differed by one order of magnitude between environments. Peaks in species richness (13) and Shannon diversity index (2.12) were found in the shelf-ocean boundary, but both variables showed nonsignificant differences between areas. Species richness correlated significantly with both Chl a and abundance. Such relationships, which followed a negative linear or quadratic function in the shelf and a positive linear function in oceanic waters, are thought to reflect either the competitive dominance of one species or a relatively wide spectrum of tintinnid size-classes, respectively.

Ciliate abundance in waters of the Argentine shelf and the Drake Passage, the south-western Atlantic

Ciliates from sub-surface waters of the Argentine shelf and the Drake Passage under austral summer and autumn conditions were examined and compared for the first time. In both environments, the taxonomic structure of ciliates was related to temperature and salinity, and aloricate oligotrichs dominated in density (80%) over loricate oligotrichs, litostomatids and prostomatids, while the microplanktonic fraction prevailed in terms of biomass (90%) over the nanociliates. Myrionecta rubra was found all along the Argentine shelf only in autumn, but showed isolated peaks of abundance (10**3 ind./L) during summer. Mean values of density and biomass of total ciliates decreased ca. 2-fold from the shelf-slope to oceanic waters, while potential maximum production of aloricate oligotrichs decreased 9-fold, in relation with the drop in chlorophyll a concentration and the latitudinal decline of temperature, also reflected in maximum growth rates. Fifty percent of total ciliate abundance was represented by local increases (maximum: 20 000 ind./L and 25 µg C/L), which were spatially superimposed with ranges of seawater temperature and chlorophyll a concentrations of 10-15°C and 0.6-6 µg/L, respectively and were found in the nearby of fronts located on the shelf and the slope.