The role of climate in human mitochondrial DNA evolution: A reappraisal

AbstractPrevious studies have proposed that selection has been involved in the differentiation of human mitochondrial DNA (mtDNA) and climate was the main driving force. This viewpoint, however, gets no support from the subsequent studies and remains controversial thus far. To clarify this issue, a total of 237 complete mtDNA sequences belonging to autochthonous lineages from South Asia, Oceania, and East Asia were collected to seek for the imprint of selection. Based on nonsynonymous (N) and synonymous (S) substitutions analysis, our results confirmed that purifying selection was the predominant force during the evolution of human mtDNA. However, no significant and extensive difference was detected among these three regions, which did not support the climate adaptation hypothesis but preferred random genetic drift to be the main factor in shaping the current landscape of human mtDNA, at least those from Asian and Oceanian regions

PosterLayout: A New Benchmark and Approach for Content-aware Visual-Textual Presentation Layout

Content-aware visual-textual presentation layout aims at arranging spatial space on the given canvas for pre-defined elements, including text, logo, and underlay, which is a key to automatic template-free creative graphic design. In practical applications, e.g., poster designs, the canvas is originally non-empty, and both inter-element relationships as well as inter-layer relationships should be concerned when generating a proper layout. A few recent works deal with them simultaneously, but they still suffer from poor graphic performance, such as a lack of layout variety or spatial non-alignment. Since content-aware visual-textual presentation layout is a novel task, we first construct a new dataset named PosterLayout, which consists of 9,974 poster-layout pairs and 905 images, i.e., non-empty canvases. It is more challenging and useful for greater layout variety, domain diversity, and content diversity. Then, we propose design sequence formation (DSF) that reorganizes elements in layouts to imitate the design processes of human designers, and a novel CNN-LSTM-based conditional generative adversarial network (GAN) is presented to generate proper layouts. Specifically, the discriminator is design-sequence-aware and will supervise the "design" process of the generator. Experimental results verify the usefulness of the new benchmark and the effectiveness of the proposed approach, which achieves the best performance by generating suitable layouts for diverse canvases.Comment: Accepted to CVPR 2023. Dataset and code are available at https://github.com/PKU-ICST-MIPL/PosterLayout-CVPR202

Dynamic DNA Methylation During Aging: A “Prophet” of Age-Related Outcomes

The biological markers of aging used to predict physical health status in older people are of great interest. Telomere shortening, which occurs during the process of cell replication, was initially considered a promising biomarker for the prediction of age and age-related outcomes (e.g., diseases, longevity). However, the high instability in detection and low correlation with age-related outcomes limit the extension of telomere length to the field of prediction. Currently, a growing number of studies have shown that dynamic DNA methylation throughout human lifetime exhibits strong correlation with age and age-related outcomes. Indeed, many researchers have built age prediction models with high accuracy based on age-dependent methylation changes in certain CpG loci. For now, DNA methylation based on epigenetic clocks, namely epigenetic or DNA methylation age, serves as a new standard to track chronological age and predict biological age. Measures of age acceleration (Δage, DNA methylation age – chronological age) have been developed to assess the health status of a person. In addition, there is evidence that an accelerated epigenetic age exists in patients with certain age-related diseases (e.g., Alzheimer’s disease, cardiovascular disease). In this review, we provide an overview of the dynamic signatures of DNA methylation during aging and emphasize its practical utility in the prediction of various age-related outcomes

Insights into long noncoding RNAs of naked mole rat (Heterocephalus glaber) and their potential association with cancer resistance

Additional file 4: Table S3. Differential expressed lncRNAs identified in naked mole rat (Heterocephalus glaber) genome

IPS Observation System for Miyun 50m Radio Telescope and Its Acceptance Observation

Ground-based observation of Interplanetary Scintillation(IPS) is an important approach of monitoring solar wind. A ground-based IPS observation system is newly implemented on 50m radio telescope, Miyun station, National Astronomical Observatories, Chinese Academy of Sciences(NAOC). This observation system is constructed for purpose of observing the solar wind speed and scintillation index by using the normalized cross-spectrum of simultaneous dual-frequency IPS measurement. The system consists of a universal dual-frequency front-end and a dual-channel multi-function back-end specially designed for IPS. After careful calibration and testing, IPS observations on source 3C273B and 3C279 are successfully carried out. The preliminary observation results show that this newly developed observation system is capable of doing IPS observation.The system sensitivity for IPS observation can reach over 0.3Jy in terms of IPS polarization correlator with 4MHz bandwidth and 2s integration time.Comment: 8 pages, 7 figure

Distilling Artificial Recombinants from Large Sets of Complete mtDNA Genomes

BACKGROUND: Large-scale genome sequencing poses enormous problems to the logistics of laboratory work and data handling. When numerous fragments of different genomes are PCR amplified and sequenced in a laboratory, there is a high imminent risk of sample confusion. For genetic markers, such as mitochondrial DNA (mtDNA), which are free of natural recombination, single instances of sample mix-up involving different branches of the mtDNA phylogeny would give rise to reticulate patterns and should therefore be detectable. METHODOLOGY/PRINCIPAL FINDINGS: We have developed a strategy for comparing new complete mtDNA genomes, one by one, to a current skeleton of the worldwide mtDNA phylogeny. The mutations distinguishing the reference sequence from a putative recombinant sequence can then be allocated to two or more different branches of this phylogenetic skeleton. Thus, one would search for two (or three) near-matches in the total mtDNA database that together best explain the variation seen in the recombinants. The evolutionary pathway from the mtDNA tree connecting this pair together with the recombinant then generate a grid-like median network, from which one can read off the exchanged segments. CONCLUSIONS: We have applied this procedure to a large collection of complete human mtDNA sequences, where several recombinants could be distilled by our method. All these recombinant sequences were subsequently corrected by de novo experiments--fully concordant with the predictions from our data-analytical approach

Trace the Accretion Geometry of H 1743--322 with Type C Quasi-periodic Oscillations in Multiple Outbursts

We present a systematic analysis of type C quasi-periodic oscillation (QPO) observations of H 1743--322 throughout the Rossi X-ray Timing Explorer (RXTE) era. We find that, while different outbursts have significant flux differences, they show consistent positive correlations between the QPO fractional root-mean-square (rms) amplitude and non-thermal fraction of the emission, which indicate an independence of the intrinsic QPO rms on individual outburst brightness in H 1743--322. However, the dependence of the QPO rms on frequency is different between the outburst rise and decay phases, where QPO fractional rms of the decay phase is significantly lower than that of the rise phase at low frequencies. The spectral analysis also reveals different ranges of coronal temperature between the two outburst stages. A semi-quantitative analysis shows that the Lense-Thirring precession model could be responsible for the QPO rms differences, requiring a variable coronal geometric shape. However, the variable-Comptonization model could also account for the findings. The fact that the rms differences and the hysteresis traces in the hardness-intensity diagram (HID) accompany each other indicates a connection between the two phenomena. By correlating the findings with QPO phase lags and the quasi-simultaneous radio flux previously published, we propose there could be corona-jet transitions in H 1743--322 similar to those that have been recently reported in GRS 1915+105.Comment: 21 pages, 12 figure