Inputs, outputs and living standards in rural China during the 1920s and 30s: a quantitative analysis

Since Kenneth Pomeranz’s Great Divergence that was published in 2000, the scholarly debate has been focused on when the divergence was likely to begin. But a lack of real data for the Pomeranz framework has been noticeable. For our purpose, real data are imperative. The primary-source data this study uses are from the first large-scale modern survey of the rural economy in China in the 1920s and 30s to establish correlations between inputs, outputs and living standards in China’s rural sector. This study views China’s traditional growth trajectory continuing from the Qing to troubled times of the 1920s and 1930s despite considerable negative externalities from a regime change. The present view is that given that the rural economy managed to hang on during the Republican Period despite many disadvantages Qing China would have performed at least at the 1920s-30s’ level. Our findings indicate that rural population did indeed eat quite well during the politically troubled time, supporting Pomeranz’s pathbreaking comparison of utility functions between China’s Yangzi Delta and Western Europe. Secondly, food consumption proved incentives for improvement in labour productivity. Thirdly, China’s peasants were rational operators to maximise their returns. Fourthly, China’s highyield farming depended on land and labour inputs along a production probability frontier, which explains the root cause of the Great Divergence. Finally, there was a ‘little divergence’ inside China which was dictated by rice production, which justifies the Yangzi Delta as the best scenario

Performance and mechanisms of the Maoist economy: a holistic approach, 1950-1980

This article probes performance and mechanisms of the Maoist economy from 1950 to 1980, a period commonly regarded as a turning point that ushered in a bumpy but new path for China’s new economic fortune, including industrialisation and modernisation. Mao and his government have often been regarded as a developer and moderniser for China. This study questions it. To that end, the Maoist economy is re-conceptualised, re-examined, and re-assessed with qualitative and quantitative evidence including empirical modelling. The key findings suggest that the Maoist economy was a closed one with industrial dependence on agriculture in an urbanrural zero-sum. In the end, despite the official propaganda agriculture declined, industrial workforce stagnated, and the population was poor. This gloomy performance justified the post-Mao reforms and opening up, a game changer that put China on a very different trajectory of growth and development

A Two-Dimensional Simulation Model of the Bicoid Gradient in Drosophila

BACKGROUND:Bicoid (Bcd) is a Drosophila morphogenetic protein responsible for patterning the anterior structures in embryos. Recent experimental studies have revealed important insights into the behavior of this morphogen gradient, making it necessary to develop a model that can recapitulate the biological features of the system, including its dynamic and scaling properties. METHODOLOGY/PRINCIPAL FINDINGS:We present a biologically realistic 2-D model of the dynamics of the Bcd gradient in Drosophila embryos. This model is based on equilibrium binding of Bcd molecules to non-specific, low affinity DNA sites throughout the Drosophila genome. It considers both the diffusion media within which the Bcd gradient is formed and the dynamic and other relevant properties of bcd mRNA from which Bcd protein is produced. Our model recapitulates key features of the Bcd protein gradient observed experimentally, including its scaling properties and the stability of its nuclear concentrations during development. Our simulation model also allows us to evaluate the effects of other biological activities on Bcd gradient formation, including the dynamic redistribution of bcd mRNA in early embryos. Our simulation results suggest that, in our model, Bcd protein diffusion is important for the formation of an exponential gradient in embryos. CONCLUSIONS/SIGNIFICANCE:The 2-D model described in this report is a simple and versatile simulation procedure, providing a quantitative evaluation of the Bcd gradient system. Our results suggest an important role of Bcd binding to non-specific, low-affinity DNA sites in proper formation of the Bcd gradient in our model. They demonstrate that highly complex biological systems can be effectively modeled with relatively few parameters

In utero gene expression in the Slc39a8(neo/neo) knockdown mouse

Slc39a8 encodes ZIP8, a divalent cation/bicarbonate symporter expressed in pluripotent mouse embryonic stem cells, and therefore ubiquitous in adult tissues; ZIP8 influxes Zn2+, Mn2+ and Fe2+. Slc39a8(neo/neo) knockdown mice exhibit 10–15% of wild-type ZIP8 mRNA and protein levels, and show pleiotropic phenotype of stunted growth, neonatal lethality, multi-organ dysmorphogenesis, and dysregulated hematopoiesis manifested as severe anemia. Herein we performed RNA-seq analysis of gestational day (GD)13.5 yolk sac and placenta, and GD16.5 liver, kidney, lung, heart and cerebellum,comparing Slc39a8(neo/neo) with Slc39a8(+/+) wild-type. Meta-data analysis of differentially- expressed genes revealed 29 unique genes from all tissues — having enriched GO categories associated with hematopoiesis and hypoxia and KEGG categories of complement, response to infection, and coagulation cascade — consistent with dysregulated hematopoietic stem cell fate. Based on transcription factor (TF) profiles in the JASPAR database, and searching for TF-binding sites enriched by Pscan, we identified numerous genes encoding zinc-finger and other TFs associated with hematopoietic stem cell functions. We conclude that, in this mouse model, deficient ZIP8-mediated divalent cation transport affects zinc-finger (e.g. GATA proteins) and other TFs interacting with GATA proteins (e.g. TAL1), predominantly in yolk sac. These data strongly support the phenotype of dysmorphogenesis and anemia seen in Slc39a8(neo/neo) mice in utero

Distance measurements via the morphogen gradient of Bicoid in Drosophila embryos

<p>Abstract</p> <p>Background</p> <p>Patterning along the anterior-posterior (A-P) axis in <it>Drosophila </it>embryos is instructed by the morphogen gradient of Bicoid (Bcd). Despite extensive studies of this morphogen, how embryo geometry may affect gradient formation and target responses has not been investigated experimentally.</p> <p>Results</p> <p>In this report, we systematically compare the Bcd gradient profiles and its target expression patterns on the dorsal and ventral sides of the embryo. Our results support a hypothesis that proper distance measurement and the encoded positional information of the Bcd gradient are along the perimeter of the embryo. Our results also reveal that the dorsal and ventral sides of the embryo have a fundamentally similar relationship between Bcd and its target Hunchback (Hb), suggesting that Hb expression properties on the two sides of the embryo can be directly traced to Bcd gradient properties. Our 3-D simulation studies show that a curvature difference between the two sides of an embryo is sufficient to generate Bcd gradient properties that are consistent with experimental observations.</p> <p>Conclusions</p> <p>The findings described in this report provide a first quantitative, experimental evaluation of embryo geometry on Bcd gradient formation and target responses. They demonstrate that the physical features of an embryo, such as its shape, are integral to how pattern is formed.</p

Aluminum porphyrins with quaternary ammonium halides as catalysts for copolymerization of cyclohexene oxide and CO2: metal–ligand cooperative catalysis

Bifunctional AlIII porphyrins with quaternary ammonium halides, 2-Cl and 2-Br, worked as excellent catalysts for the copolymerization of cyclohexene oxide (CHO) and CO2 at 120 °C. Turnover frequency (TOF) and turnover number (TON) reached 10 000 h−1 and 55 000, respectively, and poly(cyclohexene carbonate) (PCHC) with molecular weight of up to 281 000 was obtained with a catalyst loading of 0.001 mol%. In contrast, bifunctional MgII and ZnII counterparts, 3-Cl and 4-Cl, as well as a binary catalyst system, 1-Cl with bis(triphenylphosphine)iminium chloride (PPNCl), showed poor catalytic performances. Kinetic studies revealed that the reaction rate was first-order in [CHO] and [2-Br] and zero-order in [CO2], and the activation parameters were determined: ΔH‡ = 12.4 kcal mol−1, ΔS‡ = −26.1 cal mol−1 K−1, and ΔG‡ = 21.6 kcal mol−1 at 80 °C. Comparative DFT calculations on two model catalysts, AlIII complex 2′ and MgII complex 3′, allowed us to extract key factors in the catalytic behavior of the bifunctional AlIII catalyst. The high polymerization activity and carbonate-linkage selectivity originate from the cooperative actions of the metal center and the quaternary ammonium cation, both of which facilitate the epoxide-ring opening by the carbonate anion to form the carbonate linkage in the key transition state such as TS3b (ΔH‡ = 13.3 kcal mol−1, ΔS‡ = −3.1 cal mol−1 K−1, and ΔG‡ = 14.4 kcal mol−1 at 80 °C)

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

Single-cell transcriptomics reveals gene expression heterogeneity but suffers from stochastic dropout and characteristic bimodal expression distributions in which expression is either strongly non-zero or non-detectable. We propose a two-part, generalized linear model for such bimodal data that parameterizes both of these features. We argue that the cellular detection rate, the fraction of genes expressed in a cell, should be adjusted for as a source of nuisance variation. Our model provides gene set enrichment analysis tailored to single-cell data. It provides insights into how networks of co-expressed genes evolve across an experimental treatment. MAST is available at https://github.com/RGLab/MAST

Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA

BACKGROUND: Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2)regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level. CONCLUSIONS: Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.Jingyuan Song, Linchun Shi, Dezhu Li, Yongzhen Sun, Yunyun Niu, Zhiduan Chen, Hongmei Luo, Xiaohui Pang, Zhiying Sun, Chang Liu, Aiping Lv, Youping Deng, Zachary Larson-Rabin, Mike Wilkinson and Shilin Che

Investigating the predictability of essential genes across distantly related organisms using an integrative approach

Rapid and accurate identification of new essential genes in under-studied microorganisms will significantly improve our understanding of how a cell works and the ability to re-engineer microorganisms. However, predicting essential genes across distantly related organisms remains a challenge. Here, we present a machine learning-based integrative approach that reliably transfers essential gene annotations between distantly related bacteria. We focused on four bacterial species that have well-characterized essential genes, and tested the transferability between three pairs among them. For each pair, we trained our classifier to learn traits associated with essential genes in one organism, and applied it to make predictions in the other. The predictions were then evaluated by examining the agreements with the known essential genes in the target organism. Ten-fold cross-validation in the same organism yielded AUC scores between 0.86 and 0.93. Cross-organism predictions yielded AUC scores between 0.69 and 0.89. The transferability is likely affected by growth conditions, quality of the training data set and the evolutionary distance. We are thus the first to report that gene essentiality can be reliably predicted using features trained and tested in a distantly related organism. Our approach proves more robust and portable than existing approaches, significantly extending our ability to predict essential genes beyond orthologs

Potential of Core-Collapse Supernova Neutrino Detection at JUNO

JUNO is an underground neutrino observatory under construction in Jiangmen, China. It uses 20kton liquid scintillator as target, which enables it to detect supernova burst neutrinos of a large statistics for the next galactic core-collapse supernova (CCSN) and also pre-supernova neutrinos from the nearby CCSN progenitors. All flavors of supernova burst neutrinos can be detected by JUNO via several interaction channels, including inverse beta decay, elastic scattering on electron and proton, interactions on C12 nuclei, etc. This retains the possibility for JUNO to reconstruct the energy spectra of supernova burst neutrinos of all flavors. The real time monitoring systems based on FPGA and DAQ are under development in JUNO, which allow prompt alert and trigger-less data acquisition of CCSN events. The alert performances of both monitoring systems have been thoroughly studied using simulations. Moreover, once a CCSN is tagged, the system can give fast characterizations, such as directionality and light curve