Likelihood-Based Estimation of a Proportional-Hazard, Competing- Risk Model with Grouped Duration Data

This short paper demonstrates two important results related to the estimation of competing-risk models under the proportional-hazards assumption with grouped duration data. First I show that the model with non-parametric baseline hazards is unidentifiable with only grouped duration data. Therefore one has to make functional form assumption for any meaningful inference. Secondly I demonstrate that under some parametric assumption such as piecewise constant baseline hazards, the sample likelihood function has explicit analytical form. Therefore there is no need for approximation. The approximation formula adopted by Deng et al (2000) and religiously followed by others is only a quasi likelihood function.competing risk models, duration models, default risk

Productivity, water and nitrogen utilization of intensified dryland farming with annual forages on the Chinese Loess plateau

Understanding the relationships of productivity performance and water utilization and soil nitrogen dynamics after annual forage planting during the fallow period (F) in winter wheat (Triticum aestivum L.; W) mono-cropping is critically important for maintaining sustainable livestock and grain production in semiarid regions. We used 2 years (2017–2019) of data to investigate soil nitrogen dynamics, production, water utilization, and fallow efficiency when forage rape (Brassica campestris L.; R) and common vetch (Vicia sativa L.; V) were planted in a 3-month summer fallow of the W-F-W-F cropping system. Three cropping systems were comprised of winter wheat-summer fallow-winter wheat-summer fallow (W-F-W-F), winter wheat-forage rape-winter wheat-forage rape (W-R-W-R), and winter wheat-forage rape-winter wheat-common vetch (W-R-W-V). The results showed that the annual forage planting decreased the average NO3−-N content by 54.8% compared with the W-F-W-F cropping system. Compared with the W-F-W-F cropping system, planting annual forage in summer fallow increased the average system forage production by 4.93 t ha−1. Local total annual precipitation can meet crop-water requirements, and the limiting factor for agricultural production was the drought due to the uneven seasonal distribution of precipitation. In comparison to the W-F-W-F cropping system, annual forage planting decreased the average available soil moisture storage by 50.3 mm above the 80 cm soil layer. Compared with that in the W-R-W-R (23.21 t ha−1) and W-F-W-F (30.25 t ha−1) cropping systems, the crop productivity in the W-R-W-V cropping system (33.23 t ha−1) was relatively stable and high because the reduction in subsequent winter wheat yield (2.96 t ha−1) was adequately offset by the forage yield (5.15 t ha−1). Adding forage rape to the W-F-W-F cropping system decreased system crop-water productivity (CWP) by 40.9%. However, the CWP, precipitation use efficiency (PUE), and soil nitrate in the W-R-W-V cropping system increased by 30.4, 30.1, 110.9, and 82.0%, respectively, compared with those in the W-R-W-R cropping system. Therefore, the W-R-W-V cropping system is recommended for better water and fertility management as well as grain and forage production in semiarid regions. However, further study is required to involve drought years for better evaluation of the effect of long-term precipitation variability on the crop productivity

Metabolism and transcriptome profiling provides insight into the genes and transcription factors involved in monoterpene biosynthesis of borneol chemotype of Cinnamomum camphora induced by mechanical damage

Background The borneol chemotype of Cinnamomum camphora (BCC), a monoterpene-rich woody plant species, is the sole source prescribed by the Chinese Pharmacopoeia for the production of natural D-borneol, a major monoterpene in BCC used for millennia as a topical analgesic in China. Nevertheless, the possible gene-regulatory roles of transcription factors (TFs) in BCC’s monoterpenoid biosynthesis remained unknown. Here, a joint analysis of the transcriptome and terpenoid metabolome of BCC induced by mechanical damage (MD) was used to comprehensively explore the interaction between TFs and terpene synthase (TPS) unigenes that might participate in monoterpene biosynthesis in BCC. Results Gas chromatography–mass spectrometry analysis detected 14 monoterpenes and seven sesquiterpenes. All but two monoterpenes underwent a significantly increased accumulation after the MD treatment. RNA sequencing data revealed that 10 TPS, 82 MYB, 70 AP2/ERF, 38 BHLH, 31 WRKY, and 29 bZIP unigenes responded to the MD treatment. A correlation analysis revealed that three monoterpene synthase genes (CcTPS1, CcTPS3, CcTPS4) highly correlated with multiple monoterpenes, namely D-borneol, camphor, and bornyl acetate, which could be responsible for monoterpenoid biosynthesis in BCC. Furthermore, five WRKY, 15 MYB, 10 ERF/AP2, five bZIP, and two BHLH genes had strong, positive correlations with CcTPS1 or CcTPS4, judging by their high coefficient values (R2 > 0.8). The bioinformatics results were verified by quantitative real-time PCR. Conclusion This study provides insight into the genes involved in the biosynthesis and regulation of monoterpene in BCC and thus provides a pool of candidate genes for future mechanistic analyses of how monoterpenes accumulate in BCC

Comparative Analysis of the Complete Mitochondrial Genomes for Development Application

This present research work reports the comparative analysis of the entire nucleotide sequence of mitochondrial genomes of Serranochromis robustus and Buccochromis nototaenia and phylogenetic analyses of their protein-coding genes in order to establish their phylogenetic relationship within Cichlids. The mitochondrial genomes of S. robustus and B. nototaenia are 16,583 and 16,580 base pairs long, respectively, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and one control region (D-loop) which is 888 and 887 base pairs long, respectively, showing the same gene order and identical number of gene or regions with other well-elucidated mitogenomes of Cichlids. However, with exception of cytochrome-c oxidase subunit-1 (COX-1) gene, all the identified PCGs were initiated by ATG-codons. Structurally, 11 tRNA genes in B. nototaenia species and 9 tRNA genes in S. robustus species, folded into typical clover-leaf secondary structure created by the regions of self-complementarity within tRNA. All the 22 tRNA genes in both species lack variable loop. Moreover, 28 genes which include 12-protein-coding genes are encoded on the H-strand and the remaining 9 genes including one protein-coding gene are encoded on the L-strand. Thirteen sequences of concatenated mitochondrial protein-coding genes were aligned using MUSCLE, and the phylogenetic analyses performed using maximum likelihood and Bayesian inference showed that S. robustus and B. nototaenia had a broad phylogenetic relationship. These results may be a useful tool in resolving higher-level relationships in organisms and a useful dataset for studying the evolution of the Cichlidae mitochondrial genome, since Cichlids are well-known model species in the study of evolutionary biology, because of their extreme morphological, biogeographical, parental care behavior for eggs and larvae and phylogenetic diversities

Single cell atlas for 11 non-model mammals, reptiles and birds.

The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening of animal cells could reveal the expression patterns of viral entry genes in different hosts. However, such exploration for SARS-CoV-2 remains limited. Here, we perform single-nucleus RNA sequencing for 11 non-model species, including pets (cat, dog, hamster, and lizard), livestock (goat and rabbit), poultry (duck and pigeon), and wildlife (pangolin, tiger, and deer), and investigated the co-expression of ACE2 and TMPRSS2. Furthermore, cross-species analysis of the lung cell atlas of the studied mammals, reptiles, and birds reveals core developmental programs, critical connectomes, and conserved regulatory circuits among these evolutionarily distant species. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and putative zoonotic reservoirs

Log-concave Probability Distributions: Theory and Statistical Testing

Log-concavity, Increasing Hazard Rate, Non-parametric Testing

Statistical Inference of a Bivariate Proportional Hazard Model with Grouped Data

Proportional Hazard, Bivariate Durations, Grouped Data