Evolutionary algorithms for the selection of single nucleotide polymorphisms

BACKGROUND: Large databases of single nucleotide polymorphisms (SNPs) are available for use in genomics studies. Typically, investigators must choose a subset of SNPs from these databases to employ in their studies. The choice of subset is influenced by many factors, including estimated or known reliability of the SNP, biochemical factors, intellectual property, cost, and effectiveness of the subset for mapping genes or identifying disease loci. We present an evolutionary algorithm for multiobjective SNP selection. RESULTS: We implemented a modified version of the Strength-Pareto Evolutionary Algorithm (SPEA2) in Java. Our implementation, Multiobjective Analyzer for Genetic Marker Acquisition (MAGMA), approximates the set of optimal trade-off solutions for large problems in minutes. This set is very useful for the design of large studies, including those oriented towards disease identification, genetic mapping, population studies, and haplotype-block elucidation. CONCLUSION: Evolutionary algorithms are particularly suited for optimization problems that involve multiple objectives and a complex search space on which exact methods such as exhaustive enumeration cannot be applied. They provide flexibility with respect to the problem formulation if a problem description evolves or changes. Results are produced as a trade-off front, allowing the user to make informed decisions when prioritizing factors. MAGMA is open source and available at . Evolutionary algorithms are well suited for many other applications in genomics

AltitudeOmics: Baroreflex Sensitivity During Acclimatization to 5,260 m.

<b>Introduction:</b> Baroreflex sensitivity (BRS) is essential to ensure rapid adjustment to variations in blood pressure (BP). Little is known concerning the adaptive responses of BRS during acclimatization to high altitude at rest and during exercise. <b>Methods:</b> Twenty-one healthy sea-level residents were tested near sea level (SL, 130 m), the 1st (ALT1) and 16th day (ALT16) at 5,260 m using radial artery catheterization. BRS was calculated using the sequence method (direct interpretation of causal link between BP and heartrate). At rest, subjects breathed a hyperoxic mixture (250 mmHg O <sub>2</sub> , end tidal) to isolate the preponderance of CO <sub>2</sub> chemoreceptors. End-tidal CO <sub>2</sub> varied from 20 to 50 mmHg to assess peripheral chemoreflex. Rebreathing provoked incremental increase in CO <sub>2</sub> , increasing BP to assess baroreflex. During incremental cycling exercise to exhaustion, subjects breathed room air. <b>Results:</b> Resting BRS decreased in ALT1 which was exacerbated in ALT16. This decrease in ALT1 was reversible upon additional inspired CO <sub>2</sub> , but not in ALT16. BRS decrease during exercise was greater and occurred at lower workloads in ALT1 compared to SL. At ALT16, this decrease returned toward SL values. <b>Discussion/Conclusion:</b> This study is the first to report attenuated BRS in acute hypoxia, exacerbated in chronic hypoxia. In ALT1, hypocapnia triggered BRS reduction whilst in ALT16 resetting of chemoreceptor triggered BRS reduction. The exercise BRS resetting was impaired in ALT1 but normalized in ALT16. These BRS decreases indicate decreased control of BP and may explain deteriorations of cardiovascular status during exposure to high altitude

Mortality on Mount Everest, 1921-2006: descriptive study

Objective To examine patterns of mortality among climbers on Mount Everest over an 86 year period

The sleep of elite athletes at sea level and high altitude: A comparison of sea-level natives and high-altitude natives (ISA3600)

Background Altitude exposure causes acute sleep disruption in non-athletes, but little is known about its effects in elite athletes. The aim of this study was to examine the effects of altitude on two groups of elite athletes, that is, sea-level natives and high-altitude natives. Methods Sea-level natives were members of the Australian under-17 soccer team (n=14). High-altitude natives were members of a Bolivian under-20 club team (n=12). Teams participated in an 18-day (19 nights) training camp in Bolivia, with 6 nights at near sea level in Santa Cruz (430 m) and 13 nights at high altitude in La Paz (3600 m). Sleep was assessed on every day/night using activity monitors. Results The Australians’ sleep was shorter, and of poorer quality, on the first night at altitude compared with sea level. Sleep quality returned to normal by the end of the first week at altitude, but sleep quantity had still not stabilised at its normal level after 2 weeks. The quantity and quality of sleep obtained by the Bolivians was similar, or greater, on all nights at altitude compared with sea level. The Australians tended to obtain more sleep than the Bolivians at sea level and altitude, but the quality of the Bolivians’ sleep tended to be better than that of the Australians at altitude. Conclusions Exposure to high altitude causes acute and chronic disruption to the sleep of elite athletes who are sea-level natives, but it does not affect the sleep of elite athletes who are high-altitude natives

Wellness, fatigue and physical performance acclimatisation to a 2-week soccer camp at 3600 m (ISA3600)

Objectives To examine the time course of wellness, fatigue and performance during an altitude training camp (La Paz, 3600 m) in two groups of either sea-level (Australian) or altitude (Bolivian) native young soccer players. Methods Wellness and fatigue were assessed using questionnaires and resting heart rate (HR) and HR variability. Physical performance was assessed using HR responses to a submaximal run, a Yo-Yo Intermittent recovery test level 1 (Yo-YoIR1) and a 20 m sprint. Most measures were performed daily, with the exception of Yo-YoIR1 and 20 m sprints, which were performed near sea level and on days 3 and 10 at altitude. Results Compared with near sea level, Australians had moderate-to-large impairments in wellness and Yo-YoIR1 relative to the Bolivians on arrival at altitude. The acclimatisation of most measures to altitude was substantially slower in Australians than Bolivians, with only Bolivians reaching near sea-level baseline high-intensity running by the end of the camp. Both teams had moderately impaired 20 m sprinting at the end of the camp. Exercise HR had large associations (r>0.5–0.7) with changes in Yo-YoIR1 in both groups. Conclusions Despite partial physiological and perceptual acclimatisation, 2 weeks is insufficient for restoration of physical performance in young sea-level native soccer players. Because of the possible decrement in 20 m sprint time, a greater emphasis on speed training may be required during and after altitude training. The specific time course of restoration for each variable suggests that they measure different aspects of acclimatisation to 3600 m; they should therefore be used in combination to assess adaptation to altitude

The impact of altitude on the sleep of young elite soccer players (isa3600)

Background Altitude training is used by elite athletes to improve sports performance, but it may also disrupt sleep. The aim of this study was to examine the effects of two weeks at high altitude on the sleep of young elite athletes. Methods Participants (n=10) were members of the Australian under-17 soccer team on an 18-day (19-night) training camp in Bolivia, with 6 nights at near sea level in Santa Cruz (430 m) and 13 nights at high altitude in La Paz (3,600 m). Sleep was monitored using polysomnography during a baseline night at 430 m and three nights at 3,600 m (immediately after ascent, one week after ascent, two weeks after ascent). Data were analysed using effect size statistics. Results All results are reported as comparisons with baseline. Rapid eye movement (REM) sleep was likely lower immediately upon ascent to altitude, possibly lower after one week, and similar after two weeks. On all three nights at altitude, hypopneas and desaturations were almost certainly higher; oxygen saturation was almost certainly lower; and central apneas, respiratory arousals, and periodic breathing were very likely higher. The effects on REM sleep were common to all but one participant, but the effects on breathing were specific to only half the participants. Conclusions The immediate effects of terrestrial altitude of 3,600 m are to reduce the amount of REM sleep obtained by young elite athletes, and to cause 50% of them to have impaired breathing during sleep. REM sleep returns to normal after two weeks at altitude, but impaired breathing does not improve

Soccer activity profile of altitude versus sea-level natives during acclimatisation to 3600 m (ISA3600)

Objectives We investigated the effect of high altitude on the match activity profile of elite youth high altitude and sea level residents.Methods Twenty Sea Level (Australian) and 19 Altitude-resident (Bolivian) soccer players played five games, two near sea level (430 m) and three in La Paz (3600 m). Match activity profile was quantified via global positioning system with the peak 5 min period for distance ((D5peak)) and high velocity running (>4.17 m/s, HIVR5peak); as well as the 5 min period immediately subsequent to the peak for both distance (D5sub) and high-velocity running (HIVR5sub) identified using a rolling 5 min epoch. The games at 3600 m were compared with the average of the two near sea-level games.Results The total distance per minute was reduced by a small magnitude in the first match at altitude in both teams, without any change in low-velocity running. There were variable changes in HiVR, D5peak and HiVR5peak from match to match for each team. There were within-team reductions in D5peak in each game at altitude compared with those at near sea level, and this reduction was greater by a small magnitude in Australians than Bolivians in game 4. The effect of altitude on HiVR5peak was moderately lower in Australians compared with Bolivians in game 3. There was no clear difference in the effect of altitude on maximal accelerations between teams.Conclusions High altitude reduces the distance covered by elite youth soccer players during matches. Neither 13 days of acclimatisation nor lifelong residence at high altitude protects against detrimental effects of altitude on match activity profile

AltitudeOmics: Spontaneous Baroreflex Sensitivity During Acclimatization to 5,260 m: A Comparison of Methods

Baroreflex sensitivity (BRS) is essential to ensure rapid adjustment to variations in blood pressure (BP). Spontaneous baroreflex function can be assessed using continuous recordings of blood pressure. The goal of this study was to compare four methods for BRS quantification [the sequence, Bernardi's (BER), frequency and transfer function methods] to identify the most consistent method across an extreme range of conditions: rest and exercise, in normoxia, hypoxia, hypocapnia, and hypercapnia. Using intra-radial artery BP in young healthy participants, BRS was calculated and compared using the four methods in normoxia, acute and chronic hypoxia (terrestrial altitude of 5,260 m) in hypocapnia (hyperventilation), hypercapnia (rebreathing) and during ramp exercise to exhaustion. The sequence and BER methods for BRS estimation showed good agreement during the resting and exercise protocols, whilst the ultra- and very-low frequency bands of the frequency and transfer function methods were more discrepant. Removing respiratory frequency from the blood pressure traces affected primarily the sequence and BER methods and occasionally the frequency and transfer function methods. The sequence and BER methods contained more respiratory related information than the frequency and transfer function methods, indicating that the former two methods predominantly rely on respiratory effects of BRS. BER method is recommended because it is the easiest to compute and even though it tends to overestimate BRS compared to the sequence method, it is consistent with the other methods, whilst its interquartile range is the smallest