Alternative Awaiting and Broadcast for Two-Way Relay Fading Channels

We investigate a two-way relay (TWR) fading channel where two source nodes wish to exchange information with the help of a relay node. Given traditional TWR protocols, transmission rates in both directions are known to be limited by the hop with lower capacity, i.e., the min operations between uplink and downlink. In this paper, we propose a new transmission protocol, named as alternative awaiting and broadcast (AAB), to cancel the min operations in the TWR fading channels. The operational principles, new upper bound on ergodic sum-capacity (ESC) and convergence behavior of average delay of signal transmission (ST) (in relay buffer) for the proposed AAB protocol are analyzed. Moreover, we propose a suboptimal encoding/decoding solution for the AAB protocol and derive an achievable ergodic sum-rate (ESR) with corresponding average delay of ST. Numerical results show that 1) the proposed AAB protocol significantly improves the achievable ESR compared to the traditional TWR protocols, 2) considering the average delay of system service (SS) (in source buffer), the average delay of ST induced by the proposed AAB protocol is very small and negligible.Comment: to appear in IEEE Transactions on Vehicular Technology, 201

Pairwise Check Decoding for LDPC Coded Two-Way Relay Block Fading Channels

Partial decoding has the potential to achieve a larger capacity region than full decoding in two-way relay (TWR) channels. Existing partial decoding realizations are however designed for Gaussian channels and with a static physical layer network coding (PLNC). In this paper, we propose a new solution for joint network coding and channel decoding at the relay, called pairwise check decoding (PCD), for low-density parity-check (LDPC) coded TWR system over block fading channels. The main idea is to form a check relationship table (check-relation-tab) for the superimposed LDPC coded packet pair in the multiple access (MA) phase in conjunction with an adaptive PLNC mapping in the broadcast (BC) phase. Using PCD, we then present a partial decoding method, two-stage closest-neighbor clustering with PCD (TS-CNC-PCD), with the aim of minimizing the worst pairwise error probability. Moreover, we propose the minimum correlation optimization (MCO) for selecting the better check-relation-tabs. Simulation results confirm that the proposed TS-CNC-PCD offers a sizable gain over the conventional XOR with belief propagation (BP) in fading channels.Comment: to appear in IEEE Trans. on Communications, 201

Probing Chromatin Compaction and Its Epigenetic States in situ With Single-Molecule Localization-Based Super-Resolution Microscopy

Chromatin organization play a vital role in gene regulation and genome maintenance in normal biological processes and in response to environmental insults. Disruption of chromatin organization imposes a significant effect on many cellular processes and is often associated with a range of pathological processes such as aging and cancer. Extensive attention has been attracted to understand the structural and functional studies of chromatin architecture. Biochemical assays coupled with the state-of-the-art genomic technologies have been traditionally used to probe chromatin architecture. Recent advances in single molecule localization microscopy (SMLM) open up new opportunities to directly visualize higher-order chromatin architecture, its compaction status and its functional states at nanometer resolution in the intact cells or tissue. In this review, we will first discuss the recent technical advantages and challenges of using SMLM to image chromatin architecture. Next, we will focus on the recent applications of SMLM for structural and functional studies to probe chromatin architecture in key cellular processes. Finally, we will provide our perspectives on the recent development and potential applications of super-resolution imaging of chromatin architecture in improving our understanding in diseases

Ionic Liquids as Bifunctional Cosolvents Enhanced CO₂ Conversion Catalysed by NADH-Dependent Formate Dehydrogenase

Efficient CO2 conversion by formate dehydrogenase is limited by the low CO2 concentrations that can be reached in traditional buffers. The use of ionic liquids was proposed as a manner to increase CO2 concentration in the reaction system. It has been found, however, that the required cofactor (NADH) heavily degraded during the enzymatic reaction and that acidity was the main reason. Acidity, indeed, resulted in reduction of the conversion of CO2 into formic acid and contributed to overestimate the amount of formic acid produced when the progression of the reaction was followed by a decrease in NADH absorbance (method N). Stability of NADH and the mechanism of NADH degradation was investigated by UV, NMR and by DFT calculations. It was found that by selecting neutral-basic ionic liquids and by adjusting the concentration of the ionic liquid in the buffer, the concentration of NADH can be maintained in the reaction system with little loss. Conversion of CO2 to methanol in BmimBF(4) (67.1%) was more than twice as compared with the conversion attained by the enzymatic reaction in phosphate buffer (24.3%)

Huatuo-26M, a Large-scale Chinese Medical QA Dataset

In this paper, we release a largest ever medical Question Answering (QA) dataset with 26 million QA pairs. We benchmark many existing approaches in our dataset in terms of both retrieval and generation. Experimental results show that the existing models perform far lower than expected and the released dataset is still challenging in the pre-trained language model era. Moreover, we also experimentally show the benefit of the proposed dataset in many aspects: (i) trained models for other QA datasets in a zero-shot fashion; and (ii) as external knowledge for retrieval-augmented generation (RAG); and (iii) improving existing pre-trained language models by using the QA pairs as a pre-training corpus in continued training manner. We believe that this dataset will not only contribute to medical research but also facilitate both the patients and clinical doctors. See \url{https://github.com/FreedomIntelligence/Huatuo-26M}

Allopatric divergence and hybridization within Cupressus chengiana (Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China

Having a comprehensive understanding of population structure, genetic differentiation and demographic history is important for the conservation and management of threatened species. High‐throughput sequencing (HTS) provides exciting opportunities to address a wide range of factors for conservation genetics. Here, we generated HTS data and identified 266,884 high‐quality single nucleotide polymorphisms from 82 individuals of Cupressus chengiana , to assess population genomics across the species' full range, comprising the Daduhe River (DDH), Minjiang River (MJR) and Bailongjiang River (BLJ) catchments in western China. admixture , principal components analysis and phylogenetic analyses indicated that each region contains a distinct lineage, with high levels of differentiation between them (DDH, MJR and BLJ lineages). MJR was newly distinguished compared to previous surveys, and evidence including coalescent simulations supported a hybrid origin of MJR during the Quaternary. Each of these three lineages should be recognized as an evolutionarily significant unit (ESU), due to isolation, differing genetic adaptations and different demographic history. Currently, each ESU faces distinct threats, and will require different conservation strategies. Our work shows that population genomic approaches using HTS can reconstruct the complex evolutionary history of threatened species in mountainous regions, and hence inform conservation efforts, and contribute to the understanding of high biodiversity in mountains.Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809Award Number: 31622015Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809Award Number: 31590821Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809Award Number: 31370261Funding provided by: National Basic Research Program of China*Crossref Funder Registry ID: Award Number: 2014CB954100Funding provided by: Sichuan University Fundamental Research Funds for the Central Universities*Crossref Funder Registry ID: Award Number: SCU2019D013Funding provided by: Sichuan University Fundamental Research Funds for the Central Universities*Crossref Funder Registry ID: Award Number: SCU2018D006Funding provided by: National Basic Research Program of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100012166Award Number: 2014CB954100Funding provided by: Sichuan University Fundamental Research Funds for the Central UniversitiesCrossref Funder Registry ID: Award Number: SCU2019D013We identified 266,884 high-quality SNPs from 82 individuals to assess population genomics of Cupressus chengiana across its full range. To get a high-quality reference, single-molecule real-time (SMRT) sequencing was used to obtain the full-length transcriptome of C. chengiana. A total of 82 samples were collected for RNA-seq. We used bwa-mem to align the quality-filtered reads of each individual to the refences sequences. We used the "mpileup" command in SAMTOOLS to identify SNPs. Data were filtered with the following processes: SNPs with a mapping quality <30, a mapping depth <10, genotyping rate <50% per group, minor allele frequency (MAF) <5%, or in 5bps windows around any indel

Phylogeography and allopatric divergence of cypress species (Cupressus L.) in the Qinghai-Tibetan Plateau and adjacent regions

Additional files can be found at http://www.biomedcentral.com/1471-2148/10/194Background Although allopatric speciation is viewed as the most common way in which species originate, allopatric divergence among a group of closely related species has rarely been examined at the population level through phylogeographic analysis. Here we report such a case study on eight putative cypress (Cupressus) species, which each have a mainly allopatric distribution in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. The analysis involved sequencing three plastid DNA fragments (trnD-trnT, trnS-trnG and trnL-trnF) in 371 individuals sampled from populations at 66 localities. Results Both phylogenetic and network analyses showed that most DNA haplotypes recovered or haplotype-clustered lineages resolved were largely species-specific. Across all species, significant phylogeographic structure (NST > GST, P < 0.05) implied a high correlation between haplotypes/lineages and geographic distribution. Two species, C. duclouxiana and C. chengiana, which are distributed in the eastern QTP region, contained more haplotypes and higher diversity than five species with restricted distributions in the western highlands of the QTP. The remaining species, C. funebris, is widely cultivated and contained very little cpDNA diversity. Conclusions It is concluded that the formation of high mountain barriers separating deep valleys in the QTP and adjacent regions caused by various uplifts of the plateau since the early Miocene most likely promoted allopatric divergence in Cupressus by restricting gene flow and fixing local, species-specific haplotypes in geographically isolated populations. The low levels of intraspecific diversity present in most species might stem from population bottlenecks brought about by recurrent periods of unfavorable climate and more recently by the negative impacts of human activities on species' distributions. Our findings shed new light on the importance of geographical isolation caused by the uplift of the QTP on the development of high plant species diversity in the QTP biodiversity hotspot.Publisher PDFPeer reviewe

Diversity patterns and conservation gaps of Magnoliaceae species in China

Postponed access: the file will be available after 2023-12-27Magnoliaceae, a primitive group of angiosperms and distinguished ornamental plants with more than 100 species in China, is one of the most threatened plant family in the wild due to logging, habitat loss, over-collection and climate change. To provide a scientific guide of its conservation for policymakers, we explore the diversity patterns of 114 Magnoliaceae species in China using three diversity indices (species richness, weighted endemism, β-diversity) with a spatial resolution of 10 km by 10 km. Two methods, the top 5% richness algorithm and complementary algorithm, are used to identify diversity hotspots. Conservation gaps are recognized by overlapping the diversity hotspots with Chinese nature reserves. Our results indicate that Magnoliaceae species richness and weighted endemism are high in tropical to subtropical low montane forests in southern China, exceptionally high in southernmost Yunnan and boundary of Guizhou, Guangxi and Hunan. The β-diversity are scattered in southern China, suggesting a different species composition among grid cells. We identify 2524 grids as diversity hotspots for Magnoliaceae species in China, with 24 grids covered by three diversity indices (first-level diversity hotspots), 561 grids covered by two indices (second-level diversity hotspots) simultaneously and 1939 grids (76.8%) covered by only one index (third-level diversity hotspots). The first-level diversity hotspots include over 70% of the critically endangered Magnoliaceae species and are the priority areas for Magnoliaceae conservation. However, only 24% of the diversity hotspots fall in nature reserves and only ten grids are from the first-level diversity hotspots. Zhejiang, Guizhou and Fujian have less than 20% of diversity hotspots covered by nature reserves and need attention in future Magnoliaceae conservation. Using multiple diversity indices and algorithms, our study identifies diversity hotspots and conservation gaps and provides scientific basis for Magnoliaceae conservation in future.acceptedVersio

Variational formulas of higher order mean curvatures

In this paper, we establish the first variational formula and its Euler-Lagrange equation for the total $2p$-th mean curvature functional $\mathcal {M}_{2p}$ of a submanifold $M^n$ in a general Riemannian manifold $N^{n+m}$ for $p=0,1,...,[\frac{n}{2}]$. As an example, we prove that closed complex submanifolds in complex projective spaces are critical points of the functional $\mathcal {M}_{2p}$, called relatively $2p$-minimal submanifolds, for all $p$. At last, we discuss the relations between relatively $2p$-minimal submanifolds and austere submanifolds in real space forms, as well as a special variational problem.Comment: 13 pages, to appear in SCIENCE CHINA Mathematics 201

Global patterns of species richness of the holarctic alpine herb Saxifraga: The role of temperature and habitat heterogeneity

Postponed access: the file will be available after 2022-08-03The effects of contemporary climate, habitat heterogeneity and long-term climate change on species richness are well studied for woody plants in forest ecosystems, but poorly understood for herbaceous plants, especially in alpine–arctic ecosystems. Here, we aim to test if the previously proposed hypothesis based on the richness–environment relationship could explain the variation in richness patterns of the typical alpine–arctic herbaceous genus Saxifraga. Using a newly compiled distribution database of 437 Saxifraga species, we estimated the species richness patterns for all species, narrow- and wide-ranged species. We used generalized linear models and simultaneous autoregressive models to evaluate the effects of contemporary climate, habitat heterogeneity and historical climate on species richness patterns. Partial regressions were used to determine the independent and shared effects of different variables. Four widely used models were tested to identify their predictive power in explaining patterns of species richness. We found that temperature was negatively correlated with the richness patterns of all and wide-ranged species, and that was the most important environmental factor, indicating a strong conservatism of its ancestral temperate niche. Habitat heterogeneity and long-term climate change were the best predictors of the spatial variation of narrow-ranged species richness. Overall, the combined model containing five predictors can explain ca. 40%–50% of the variation in species richness. We further argued that additional evolutionary and biogeographical processes might have also played an essential role in shaping the Saxifraga diversity patterns and should be considered in future studies.acceptedVersio