In-Flight Fatigue Crack Monitoring of an Aircraft Engine Cowling

This research investigates the feasibility of implementing an in-flight fatigue crack monitoring system in an airplane to identify fatigue crack growth. An acoustic emission data acquisition system coupled with a Kohonen self organizing map neural network were used to perform the analysis. Fatigue cracking was responsible for ripping the top of a fuselage off an Aloha Airline’s Boeing 737-200 as it carried passengers over the Pacific Ocean, killing some aboard. This tragedy is perhaps a precursor of problems to come, as our nation’s aircraft age. These planes experience fatigue as they perform their daily routine of ferrying passengers from location to location. Fatigue can initiate cracking within the aircraft’s structure and at least damage a small expendable part of the plane, or at most damage a vital part of the airplane leading to disaster as happened to the Aloha Airline’s flight. In an attempt to curb this sort of devastation, this research involves the development of an in-flight fatigue crack monitoring system. Such a system would have the ability to identify possible crack sources before the crack would have the chance to cause significant damage. Advantages of this type of system would be first, an obvious safety cushion, and second, lower maintenance costs because routine parts replacement and inspection could be minimized

Evolutionary rates and gene dispensability associate with replication timing in the Archaeon Sulfolobus islandicus

In bacterial chromosomes, the position of a gene relative to the single origin of replication generally reflects its replication timing, how often it is expressed, and consequently, its rate of evolution. However, because some archaeal genomes contain multiple origins of replication, bias in gene dosage caused by delayed replication should be minimized and hence the substitution rate of genes should associate less with chromosome position. To test this hypothesis, six archaeal genomes from the genus Sulfolobus containing three origins of replication were selected, conserved orthologs were identified, and the evolutionary rates (dN and dS) of these orthologs were quantified. Ortholog families were grouped by their consensus position and designated by their proximity to one of the three origins (O1, O2, O3). Conserved orthologs were concentrated near the origins and most variation in genome content occurred distant from the origins. Linear regressions of both synonymous and nonsynonymous substitution rates on distance from replication origins were significantly positive, the rates being greatest in the region furthest from any of the origins and slowest among genes near the origins. Genes near O1 also evolved faster than those near O2 and O3, which suggest that this origin may fire later in the cell cycle. Increased evolutionary rates and gene dispensability are strongly associated with reduced gene expression caused in part by reduced gene dosage during the cell cycle. Therefore, in this genus of Archaea as well as in many Bacteria, evolutionary rates and variation in genome content associate with replication timing

Why genes evolve faster on secondary chromosomes in bacteria

In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs within each genus. Both evolutionary rate parameters were faster among orthologs found on secondary chromosomes than those on the primary chromosome. Further, in every bacterial genome with multiple chromosomes that we studied, genes on secondary chromosomes exhibited significantly weaker codon usage bias than those on primary chromosomes. Faster evolution and reduced codon bias could in turn result from global effects of chromosome position, as genes on secondary chromosomes experience reduced dosage and expression due to their delayed replication, or selection on specific gene attributes. These alternatives were evaluated using orthologs common to genomes with multiple chromosomes and genomes with single chromosomes. Analysis of these ortholog sets suggested that inherently fast-evolving genes tend to be sorted to secondary chromosomes when they arise; however, prolonged evolution on a secondary chromosome further accelerated substitution rates. In summary, secondary chromosomes in bacteria are evolutionary test beds where genes are weakly preserved and evolve more rapidly, likely because they are used less frequently

Why Genes Evolve Faster on Secondary Chromosomes in Bacteria

In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs within each genus. Both evolutionary rate parameters were faster among orthologs found on secondary chromosomes than those on the primary chromosome. Further, in every bacterial genome with multiple chromosomes that we studied, genes on secondary chromosomes exhibited significantly weaker codon usage bias than those on primary chromosomes. Faster evolution and reduced codon bias could in turn result from global effects of chromosome position, as genes on secondary chromosomes experience reduced dosage and expression due to their delayed replication, or selection on specific gene attributes. These alternatives were evaluated using orthologs common to genomes with multiple chromosomes and genomes with single chromosomes. Analysis of these ortholog sets suggested that inherently fast-evolving genes tend to be sorted to secondary chromosomes when they arise; however, prolonged evolution on a secondary chromosome further accelerated substitution rates. In summary, secondary chromosomes in bacteria are evolutionary test beds where genes are weakly preserved and evolve more rapidly, likely because they are used less frequently

Evolutionary Rates and Gene Dispensability Associate with Replication Timing in the Archaeon Sulfolobus islandicus

In bacterial chromosomes, the position of a gene relative to the single origin of replication generally reflects its replication timing, how often it is expressed, and consequently, its rate of evolution. However, because some archaeal genomes contain multiple origins of replication, bias in gene dosage caused by delayed replication should be minimized and hence the substitution rate of genes should associate less with chromosome position. To test this hypothesis, six archaeal genomes from the genus Sulfolobus containing three origins of replication were selected, conserved orthologs were identified, and the evolutionary rates (dN and dS) of these orthologs were quantified. Ortholog families were grouped by their consensus position and designated by their proximity to one of the three origins (O1, O2, O3). Conserved orthologs were concentrated near the origins and most variation in genome content occurred distant from the origins. Linear regressions of both synonymous and nonsynonymous substitution rates on distance from replication origins were significantly positive, the rates being greatest in the region furthest from any of the origins and slowest among genes near the origins. Genes near O1 also evolved faster than those near O2 and O3, which suggest that this origin may fire later in the cell cycle. Increased evolutionary rates and gene dispensability are strongly associated with reduced gene expression caused in part by reduced gene dosage during the cell cycle. Therefore, in this genus of Archaea as well as in many Bacteria, evolutionary rates and variation in genome content associate with replication timing

On the human appropriation of wetland primary production

Humans are changing the Earth\u27s surface at an accelerating pace, with significant consequences for ecosystems and their biodiversity. Landscape transformation has far-reaching implications including reduced net primary production (NPP) available to support ecosystems, reduced energy supplies to consumers, and disruption of ecosystem services such as carbon storage. Anthropogenic activities have reduced global NPP available to terrestrial ecosystems by nearly 25%, but the loss of NPP from wetland ecosystems is unknown. We used a simple approach to estimate aquatic NPP from measured habitat areas and habitat-specific areal productivity in the largest wetland complex on the USA west coast, comparing historical and modern landscapes and a scenario of wetland restoration. Results show that a 77% loss of wetland habitats (primarily marshes) has reduced ecosystem NPP by 94%, C (energy) flow to herbivores by 89%, and detritus production by 94%. Our results also show that attainment of habitat restoration goals could recover 12% of lost NPP and measurably increase carbon flow to consumers, including at-risk species and their food resources. This case study illustrates how a simple approach for quantifying the loss of NPP from measured habitat losses can guide wetland conservation plans by establishing historical baselines, projecting functional outcomes of different restoration scenarios, and establishing performance metrics to gauge success

Sounds of Indo-Pacific humpback dolphins (Sousa chinensis) in West Hong Kong: A preliminary description

Vocalizations of Indo-Pacific humpback dolphins (Sousa chinensis) in west Hong Kong waters were described from 12 recordings in 2010. A broadband hydrophone system recorded sounds. Vocalizations were characterized as broadband click trains, burst pulses, and narrowband frequency modulated sounds, including whistles generally similar to those of some other delphinid cetaceans. A comparison of results to previous humpback dolphin sound descriptions for Moreton Bay, Australia found broad similarities except for the apparent absence of “quacks” and “grunts” in the present study, which are of low frequency and thus were possibly masked by anthropogenic and other low frequency noise in the Hong Kong habitat.This is the publisher’s final pdf. The published article is copyrighted by Acoustical Society of America and can be found at: http://asadl.org/jasa/resource/1/jasman

Faculty Roundtable Discussion

SELECTING INITIAL REGIMENS MR. FROST (MODERATOR): I want to ask Dr. Saag, the question that I think is probably one of the most frequently asked. What do you start treatment with? Suppose a new patient, with no retroviral history, comes to you with a CD4 count between 400 and 500 and a viral load of 10,000 to 15,000 copies. DR. SAAG: There is more to consider in initial therapies than just retroviral load and CD4 count. It is also about who are they as a person, how motivated are they, and are they ready to start therapy? DR. SAAG: Alright. Then in talking to you, I would find out whether you want to be hyperaggressive or whether you want to be more conservative in treatment approach

Question and Answer Session

PROPHYLAXIS OF OPPORTUNISTIC INFECTIONS QUESTION: In your clinic do you stop prophylaxis for PCP when patients go up above a CD4 count of 200? DR. CURRIER: Not routinely. I enroll the patients in the ongoing study, if they are interested. Sometimes patients stop prophylaxis on their own and do not tell me that they have decided to discontinue it. But I have not been routinely recommending discontinuation without more data. MR. FROST (MODERATOR): What about mycobacterium avium complex (MAC)? DR. CURRIER: It is [stopped]. But I do not go around discontinuing it as a matter of routine