Improving alignment accuracy on homopolymer regions for semiconductor-based sequencing technologies

BACKGROUND: Ion Torrent and Ion Proton are semiconductor-based sequencing technologies that feature rapid sequencing speed and low upfront and operating costs, thanks to the avoidance of modified nucleotides and optical measurements. Despite of these advantages, however, Ion semiconductor sequencing technologies suffer much reduced sequencing accuracy at the genomic loci with homopolymer repeats of the same nucleotide. Such limitation significantly reduces its efficiency for the biological applications aiming at accurately identifying various genetic variants. RESULTS: In this study, we propose a Bayesian inference-based method that takes the advantage of the signal distributions of the electrical voltages that are measured for all the homopolymers of a fixed length. By cross-referencing the length of homopolymers in the reference genome and the voltage signal distribution derived from the experiment, the proposed integrated model significantly improves the alignment accuracy around the homopolymer regions. CONCLUSIONS: Besides improving alignment accuracy on homopolymer regions for semiconductor-based sequencing technologies with the proposed model, similar strategies can also be used on other high-throughput sequencing technologies that share similar limitations

Intensification of mesoscale convective systems in the East Asian rainband over the past two decades

As one of the major producers of extreme precipitation, mesoscale convective systems (MCSs) have received much attention. Recently, MCSs over several hotpots, including the Sahel and US Great Plains, have been found to intensify under global warming. However, relevant studies on the East Asian rainband, another MCS hotpot, are scarce. Here, by using a novel rain-cell tracking algorithm on a high spatiotemporal resolution satellite precipitation product, we show that both the frequency and intensity of MCSs over the East Asian rainband have increased by 21.8% and 9.8% respectively over the past two decades (2000–2021). The more frequent and intense MCSs contribute nearly three quarters to the total precipitation increase. The changes in MCSs are caused by more frequent favorable large-scale water vapor-rich environments that are likely to increase under global warming. The increased frequency and intensity of MCSs have profound impacts on the hydroclimate of East Asia, including producing extreme events such as severe flooding

Human-induced intensified seasonal cycle of sea surface temperature

Abstract Changes in the seasonal cycle of sea surface temperature (SST) have far-reaching ecological and societal implications. Previous studies have found an intensified SST seasonal cycle under global warming, but whether such changes have emerged in historical records remains largely unknown. Here, we reveal that the SST seasonal cycle globally has intensified by 3.9 ± 1.6% in recent four decades (1983–2022), with hotspot regions such as the northern subpolar gyres experiencing an intensification of up to 10%. Increased greenhouse gases are the primary driver of this intensification, and decreased anthropogenic aerosols also contribute. These changes in anthropogenic emissions lead to shallower mixed layer depths, reducing the thermal inertia of upper ocean and enhancing the seasonality of SST. In addition, the direct impacts of increased ocean heat uptake and suppressed seasonal amplitude of surface heat flux also contribute in the North Pacific and North Atlantic. The temperature seasonal cycle is intensified not only at the ocean surface, but throughout the mixed layer. The ramifications of this intensified SST seasonal cycle extend to the seasonal variation in upper-ocean oxygenation, a critical factor for most ocean ecosystems

Phase and Amplitude Changes in Rainfall Annual Cycle Over Global Land Monsoon Regions Under Global Warming

Abstract Land monsoon rainfall has a distinct annual cycle. Under global warming, whether the phase and amplitude of this annual cycle would be changed is still unclear. Here, a global investigation is conducted using 34 CMIP6 and 34 CMIP5 models under a high emission scenario. Seasonal delays would occur in the Southern Hemisphere (SH) American (3.43 days), Northern Hemisphere (NH) African (5.98 days) and SH African (3.76 days) monsoon regions, while no robust signal is found in other monsoon regions. Except NH American monsoon, amplitude is enhanced in all the monsoon regions. Compared to amplitude, the phase changes dominate the future changes of precipitation in the SH American, NH African and SH African monsoon regions. In these phase‐dominated regions, atmospheric energetic framework is proved to be reliable at regional scale and the enhanced effective atmospheric heat capacity is found to be the dominant factor

Initialized Decadal Predictions by LASG/IAP Climate System Model FGOALS-s2: Evaluations of Strengths and Weaknesses

Decadal prediction experiments are conducted by using the coupled global climate model FGOALS-s2, following the CMIP 5 protocol. The paper documents the initialization procedures for the decadal prediction experiments and summarizes the predictive skills of the experiments, which are assessed through indicators adopted by the IPCC AR5. The observational anomalies of surface and subsurface ocean temperature and salinity are assimilated through a modified incremental analysis update (IAU) scheme. Three sets of 10-year-long hindcast and forecast runs were started every five years in the period of 1960–2005, with the initial conditions taken from the assimilation runs. The decadal prediction experiment by FGOALS-s2 shows significant high predictive skills in the Indian Ocean, tropical western Pacific, and Atlantic, similar to the results of the CMIP5 multimodel ensemble. The predictive skills in the Indian Ocean and tropical western Pacific are primarily attributed to the model response to the external radiative forcing associated with the change of atmospheric compositions. In contrast, the high skills in the Atlantic are attributed, at least partly, to the improvements in the prediction of the Atlantic multidecadal variability coming from the initialization

Location and Intensity Changes of the North Equatorial Countercurrent Tied to ITCZ Under Global Warming

Abstract Previous studies have suggested that global ocean circulation would be significantly changed under global warming, while the change of North Equatorial Countercurrent (NECC) and its mechanisms are still unclear. Here, we investigate the location and intensity changes of NECC under global warming based on CESM1 high‐resolution long‐term simulations from the perspective of the Inter‐Tropical Convergence Zone (ITCZ), considering the close connection between NECC and ITCZ and well‐established changes of ITCZ. It is found that the annual‐mean NECC shifts equatorward of 0.39° and weakens by 21.71% in the RCP8.5 scenario at the end of 21st century. The NECC change is seasonally dependent, with maximum shift and weakening during spring, consistent with the changes of ITCZ. Both the location and intensity changes of ITCZ are important in the NECC changes, especially for spring. The weakening and equatorward shift of ITCZ contributes almost equally to the strongest decrease of spring NECC (47.63%)

Trends in surface equivalent potential temperature: A more comprehensive metric for global warming and weather extremes.

Trends in surface air temperature (SAT) are a common metric for global warming. Using observations and observationally driven models, we show that a more comprehensive metric for global warming and weather extremes is the trend in surface equivalent potential temperature (Thetae_sfc) since it also accounts for the increase in atmospheric humidity and latent energy. From 1980 to 2019, while SAT increased by 0.79[Formula: see text], Thetae_sfc increased by 1.48[Formula: see text] globally and as much as 4[Formula: see text] in the tropics. The increase in water vapor is responsible for the factor of 2 difference between SAT and Thetae_sfc trends. Thetae_sfc increased more uniformly (than SAT) between the midlatitudes of the southern hemisphere and the northern hemisphere, revealing the global nature of the heating added by greenhouse gases (GHGs). Trends in heat extremes and extreme precipitation are correlated strongly with the global/tropical trends in Thetae_sfc. The tropical amplification of Thetae_sfc is as large as the arctic amplification of SAT, accounting for the observed global positive trends in deep convection and a 20% increase in heat extremes. With unchecked GHG emissions, while SAT warming can reach 4.8[Formula: see text] by 2100, the global mean Thetae_sfc can increase by as much as 12[Formula: see text], with corresponding increases of 12[Formula: see text] (median) to 24[Formula: see text] (5% of grid points) in land surface temperature extremes, a 14- to 30-fold increase in frequency of heat extremes, a 40% increase in the energy available for tropical deep convection, and an up to 60% increase in extreme precipitation

Advances in understanding the changes of tropical rainfall annual cycle: a review

Aided by progress in the theoretical understanding, new knowledge on tropical rainfall annual cycle changes under global warming background has been advanced in the past decade. In this review, we focus on recent advances in understanding the changes of tropical rainfall annual cycle, including its four distinct features: amplitude, pattern shift, phase and wet/dry season length changes. In a warming climate, the amplitude of tropical rainfall annual cycle is enhanced, more evidently over ocean, while the phase of tropical rainfall annual cycle is delayed, mainly over land. The former is explained by the wet-get-wetter mechanism and the latter is explained by the enhanced effective atmospheric heat capacity and increased convective barrier. The phase delay over land has already emerged in the past four decades. The pattern shift under warming is marked by two features: equatorward shift of the inter-tropical convergence zone throughout the year and the land-to-ocean precipitation shift in the rainy season. The former is explained by the upped-ante mechanism and/or related to the enhanced equatorial warming in a warmer world. The latter is suggested to be caused by the opposite land and ocean surface temperature annual cycle changes in the tropics. Over tropical rainforest regions such as Amazon and Congo Basin, the dry season has lengthened in the recent decades, but the fundamental reason is still unclear. Despite the notable progress of the last decade, many gaps remain in understanding the mechanism, quantifying and attributing the emergence, narrowing the inter-model uncertainty, and evaluating the impact of tropical rainfall annual cycle changes, motivating future work guided by some directions proposed in this review