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Abstract Key message The non-linear seemingly unrelated regression mixed-effects model (NSURMEM) and generalized additive model (GAM) were applied for the first time in crown width (CW) additive models of larch (Larix gmelinii Rupr.), birch (Betula platyphylla Suk.), and poplar (Populus davidiana Dode). The crown radii in four directions (CR) exhibited different growth trends and responded differently to tree size and competition variables. In the absence of calibration, GAM was more accurate than NSURMEM for CR and CW predictions. Context Crown radii in four directions (CR) and crown width (CW) are fundamental indicators used to describe tree crowns. The complexity of the CR growth in four directions of different tree species in natural forests is often ignored. There is logical additivity among CR and CW that is also often overlooked. Furthermore, the existing methods applied to CW additive models have some drawbacks. Aims We aim to: (i) evaluate the utility of two new methods in developing CW additive models for larch (Larix gmelinii Rupr.), birch (Betula platyphylla Suk.), and poplar (Populus davidiana Dode) in natural secondary forests of Northeastern China; and (ii) explore the growth patterns of CR in four directions to gain important ecological insights. Methods The non-linear seemingly unrelated regression mixed-effects model (NSURMEM) and generalized additive model (GAM) were used to develop CW additive models and to explore crown growth patterns. The predictive ability of the additive models was evaluated using leave-one-plot-out cross-validation (LOOCV). Results At a fair level without calibration, GAM provided slightly better results than NSURMEM. The response of the four CR to tree size and competition variables is different and may be non-uniform due to complex stand conditions and tree growth strategies. Conclusion The newly provided methods applied to additive models are available for external datasets. GAM is recommended in the absence of calibration. This study has important implications for the understanding of natural forest dynamics and decision-making for critical stand management.

Abstract Background The high-altitude-adapted frog Rana kukunoris, occurring on the Tibetan plateau, is an excellent model to study life history evolution and adaptation to harsh high-altitude environments. However, genomic resources for this species are still underdeveloped constraining attempts to investigate the underpinnings of adaptation. Results The R. kukunoris genome was assembled to a size of 4.83 Gb and the contig N50 was 1.80 Mb. The 6555 contigs were clustered and ordered into 12 pseudo-chromosomes covering ~ 93.07% of the assembled genome. In total, 32,304 genes were functionally annotated. Synteny analysis between the genomes of R. kukunoris and a low latitude species Rana temporaria showed a high degree of chromosome level synteny with one fusion event between chr11 and chr13 forming pseudo-chromosome 11 in R. kukunoris. Characterization of features of the R. kukunoris genome identified that 61.5% consisted of transposable elements and expansions of gene families related to cell nucleus structure and taste sense were identified. Ninety-five single-copy orthologous genes were identified as being under positive selection and had functions associated with the positive regulation of proteins in the catabolic process and negative regulation of developmental growth. These gene family expansions and positively selected genes indicate regions for further interrogation to understand adaptation to high altitude. Conclusions Here, we reported a high-quality chromosome-level genome assembly of a high-altitude amphibian species using a combination of Illumina, PacBio and Hi-C sequencing technologies. This genome assembly provides a valuable resource for subsequent research on R. kukunoris genomics and amphibian genome evolution in general.

Abstract Classification of the genus Rhacophorus has been problematic. In particular there has been considerable controversy surrounding the phylogenetic relationships among Rhacophorus rhodopus, R. bipunctatus, and R. reinwardtii. To examine the relationship among these Rhacophorus species, we assembled the complete mitochondrial genome sequence of R. rhodopus. The R. rhodopus genome is 15,789 bp in length with 12 protein-coding genes (PCGs) (losing ND5), two ribosomal genes, 22 transfer RNA genes, and a control region (D-loop). Base composition of the overall sequence was 60.86% for A + T content and 39.14% for C + G content. Most of the PCGs used ATG as a start codon, except for the COX I gene, which used the ATA start codon. COX I and ND6 used AGG and ATP8 stop codons respectively, while ND3 and ND4L used the TAA stop codon. For the remaining seven genes, the stop codons was incomplete. In addition, both 5' and 3' of the control areas had distinct repeating regions. Based on three datasets and two methods (Bayesian inference (BI) and maximum likelihood (ML)), we reconstructed three phylogenetic trees to explore the taxonomic status of the species and the phylogenetic relationship among R. rhodopus, R. bipunctatus and R. reinwardtii. Our results indicated that these three species are non-monophyletic; thus, the phylogenetic relationship among them is complex and difficult to determine. Further, R. rhodopus is divided into three lineages from different parts of China. The two Rhacophorus samples showed very close phylogenetic relationship with R. rhodopus. Our results add to the mitochondrial genome database of amphibians and will help to disentangle the phylogenetic relationships within the Rhacophoridae.

In order to study shaft wall damage resulting from ore drawing in ore passes, a theoretical model for predicting the shaft wall damage to high-depth inclined ore passes is constructed based on field surveys of 25 ore passes in a deep mine in Yunnan, China. The mathematical expression of the total shaft wall damage volume is derived using the contact mechanics theory. Considering the structural characteristics of ore passes, and taking No. 1, 2, 3, and 9 ore passes as examples, combined with numerical simulation and an engineering case, the rationality of the proposed theoretical model is verified with respect to the initial collision position and the damage conditions of the shaft wall. The influence of, and sensitivity to, the ore block size P and the structural parameters of high-depth inclined ore passes on the total shaft wall damage volume Qtol are quantitatively analyzed. The results show that the calculation results of the theoretical model and numerical simulation are in good agreement with the actual engineering situations. Moreover, the ore-pass dip angle θ and the inclined angle of the chute α have a significant impact on the damage to the shaft wall, while the effects of the ore-pass depth H and the shaft diameter D are comparatively minor. With an increase in θ or α, Qtol generally first increases and then decreases. Qtol increases exponentially with P and increases steadily with D. H affects Qtol by influencing the collision frequency between the ore and the shaft wall. Therefore, in the mining design of deep mines, θ and α should be minimized as much as possible or adjusted to approach 90°, thereby reducing damage to the shaft wall. Secondly, ore block size should be strictly controlled to prevent collapses in the shaft wall caused by large ore blocks. This work provides technical support for the long-term safe operation of high-depth inclined ore passes.

The immediate roof of Shanxi sedimentary bauxite is hard clay rock, which maintain stable difficultly in goaf. It is necessary to ensure the stability of the goaf during the mine production period. The relevant research objects did not involve soft rock mass such as bauxite and hard clay and did not pay attention to the weakening characteristics of load-bearing structures under the action of weathering and rheology. This paper provides theoretical support for the safety production of bauxite and similar mines. In order to study the relationship between the stability of the protective roof-pillar bearing structure and time, this paper uses elastic thin plates and rheological theory to build the physical model of the bauxite protective roof-pillar bearing structure, and gives the calculation formula of the stand-up time of the bearing structure. The influence of factors such as the thickness of the protective roof, the uniform surface force coefficient of pillar, the span of the goaf and the thickness of the overlying rock layer on the stand-up time of the bearing structure is analyzed. The relationship between the ultimate bearing capacity and stand-up time of the bearing structure is quantified. The results show that the bearing capacity of the bearing structure is affected by the mechanical properties of the rock mass and the structural parameters of the goaf. Under the condition that the influencing factors of the mechanical parameters of the rock mass remain unchanged, the stand-up time T, which represents the bearing capacity of the bearing structure, is positively correlated with the thickness of the protective roof, positively correlated with the uniform surface force coefficient of the pillar, negatively correlated with the span of the goaf and negatively correlated with the thickness of the overlying rock layer. The engineering example verifies the rationality of theoretical calculation and provides a new idea for mining safety.

Crown width (CW) is an important indicator for assessing tree health, vitality, and stability, as well as being used to predict forestry models and evaluate forest dynamics. However, acquiring CW data is laborious and time-consuming, making it crucial to establish a convenient and accurate CW prediction model for forest management. In this study, we developed three models capable of conducting calibration: generalized models (GM), quantile regression models (QR), and mixed-effects models (MIXED). The aim was to effectively improve the prediction accuracy of CW using data from Dahurian larch (Larix gmelinii Rupr.) in Northeastern China. Different sampling designs were applied, including selecting the thickest, thinnest, intermediate, and random trees, with 1 to 10 sample trees for each design. The results showed that all models achieved accurate CW predictions. MIXED displayed the most superior fitting statistics than GM and QR. In model validation, with the increase in the number of sample trees, the model prediction accuracy gradually improved and the model differences gradually reduced. MIXED produced the smallest RMSE, MAE, and MAPE across all sampling designs. The intermediate tree sampling design with the best validation statistics for the given sample size was selected as the final sampling design. Under intermediate tree sampling design, MIXED required a minimum of five sample trees, while GM and QR required at least five and six sample trees for calibration, respectively. Generally, we suggested selecting MIXED as the final CW prediction model and using the intermediate tree sampling design of five trees per plot. This study could provide ideas and support for forest managers to accurately and efficiently predict CW.

CRISPR-based genome-editing tools have emerged as an efficient tool for functional genomics studies. Online tools and databases have been developed to facilitate the design and selection of CRISPR single guide RNA (sgRNA) for gene modifications. However, to the best of our knowledge, none of these tools or database are designated to cell surface proteins. In a previous study, we described the development and application of surfaceome CRISPR libraries targeting to cell surface proteins on human cells. Here, we present the design and construction of an online tool and database (https://crispr-surfaceome.siais.shanghaitech.edu.cn/home), named CRISPR-Surfaceome, for the design of highly efficient sgRNA targeting to the surface proteins on human cells. To show case and validate the efficiencies of sgRNAs designed by this online tool, we chose ICAM-1 gene for knockout studies and found that all the 10 designed ICAM-1 sgRNAs could efficiently generate knockout cells, with more than 80% gene disruption rates. These ICAM-1 knockout cells were found to be resistant to the infection of rhinovirus (RV), which utilizes ICAM-1 as the receptor. Therefore, CRISPR-Surfaceome can serve the research community for the functional genomics studies on cell surface proteins, such as identification of pathogen receptors and discovery of drug targets.

Abstract Background Previous studies have indicated that the programmed death molecule 1 (PD-1) signaling pathway may play a key role in rheumatoid arthritis (RA). However, the pathogenesis of rheumatoid arthritis-related interstitial lung disease (RA-ILD) is not clear. We examined the serum levels of soluble PD-1 in patients with RA and its relationship with RA-ILD. Methods Blood samples were obtained from 87 patients with RA (58 with ILD and 29 without ILD) and 45 healthy controls. Serum sPD-1 was measured by Enzyme-Linked Immunosorbent Assay. The pulmonary interstitial disease score was completed by a pulmonary physician and a radiologist through chest high-resolution computed tomography. Patients with RA-ILD were tested for lung function [e.g., forced vital capacity (FVC%), diffusing capacity of lungs for carbon monoxide (DLCO%)]. Associations between ILD and various markers, including sPD-1 and confounding factors, were investigated by logistic regression analysis. Diagnostic values of sPD-1 for the presence of ILD were investigated using receiver operating characteristic curve analysis. Results Serum sPD-1 levels were higher in RA patients with ILD than in RA patients without ILD and healthy controls (185.1 ± 109.0 pg/ml vs. 119.1 ± 77.5 pg/ml vs. 52.1 ± 21.7 pg/ml, P < 0.05). Serum sPD-1 levels were positively correlated with RF titer (P = 0.02, r = 0.249), anti-cyclic citrullinated peptide antibody status (P = 0.02, r = 0.243), and serum IgG levels (P < 0.001, r = 0.368), negatively associated with FVC% (P = 0.02, r = − 0.344), forced expiratory volume (FEV1%) (P = 0.01, r = − 0.354), total lung capacity (TLC%) (P = 0.046, r = − 0.302), and was independently associated with the presence of ILD in RA patients by multivariate logistic regression analysis. The sensitivity and specificity of sPD-1 levels for the detection of ILD in RA patients were 58.6% and 75.9%, respectively. The area under the curve was 0.689. Conclusion Serum sPD-1 levels were increased in RA patients with ILD. Increased sPD-1 may be a valuable biomarker to predict the presence of ILD in patients with RA.

Accurate large-scale biomass prediction is crucial for assessing forest carbon storage and dynamics. It can also inform sustainable forest management practices and climate change mitigation efforts. However, stand-level biomass models are still scarce worldwide. Our study aims to introduce the generalized additive model (GAM) as a convenient and efficient approach for forest biomass estimation. Data from 311 sample plots of three conifer species in northeastern China were used to evaluate the performance of the GAM model and compare it with traditional nonlinear seemingly unrelated regression (NSUR) models in predicting stand biomass, including total, aboveground, and component biomass. The results indicated that the goodness of fit of GAM was better than that of NSUR in two model systems. In the majority of cases, the scatter plots and prediction performance revealed that the stand total and component biomass models utilizing GAM outperformed those based on NSUR. Disregarding heteroscedasticity and requiring fewer statistical assumptions provide additional support for the replacement of NSUR-based models with GAM-based models. This study implies that the GAM approach has greater potential for developing a system of stand biomass models.

Climate change affects forest resource availability, growing season length, and thus forest biomass accumulation. However, only a limited number of studies have been conducted on forest biomass management based on climate effects, particularly at the stand-level. Thus, an allometric biomass equation based on conventional and climate-based stand biomass models, was developed and compared for larch trees (Larix spp.). A total of 160 experimental plots of larch plantations have been collected in Heilongjiang Province, Northeast China. In this study, we developed four types of additive model systems for stand-level biomass: two types of the stand-level biomass basic models (M-1 and M-2) with stand variables (stand basal area (BA) and stand mean height (Hm)) as the predictors, and two types of the proposed stand-level biomass climate-based models (M-3 and M-4) with stand variables (BA and Hm) and climatic variables (mean annual temperature (MAT) and annual precipitation (AP)) as the predictors. Accordingly, this study evaluated the effects of climatic variables (MAT and AP) and stand variables (BA and Hm) on the model’s performance. Model fitting and validation results revealed that the climatic variables significantly improved the model performance of the fitted equation by increasing the coefficient of determination (R2) values and reducing the root mean square error (RMSE) values. A higher R2 and a lower RMSE were consistently generated by M-2 and M-4, whereas M-1 and M-3 consistently generated a lower R2 and a higher RMSE. We found that the proposed stand-level biomass climate-based model type 4 (M-4) performed better than the other models and slightly better than in previous studies of climate-sensitive models. This study provided an additional and beneficial method of analyzing climate effects on stand-level biomass estimation.

Concrete mortar segregation during vertical pipeline gravity transportation will form a weak part in the shaft lining, which poses a challenge for deep mine shaft safety. The specific gravity difference between aggregate and slurry will cause relative motion; the relative velocity is detrimental to the mortar workability, which plays a significant role in mortar segregation. A prediction model of the relative velocity between slurry and aggregate was proposed and verified by numerical simulation results. This approach adopts the interference coefficient to revise the aggregate collision loss. The corresponding relationship among aggregate relative velocity, mortar rheological properties and particle shape was analysed to explain the mortar segregation mechanism. Segregation can be prevented by increasing the mortar viscosity and shape coefficient and decreasing the density difference and aggregate diameter to reduce the relative velocity. This work is favourable for concrete mortar quality control for gravity transportation and shaft lining construction safety.

The ultimately exposed roof area (UERA) of goaf is crucial to the safety and economics of underground mining. The prediction models do not consider the mechanical weakness of rock mass and ignore the influence of the joint damage factor, causing a large predicted exposure area with a high roof falling risk. This work adopted joint damage factor to derive a new UERA prediction model. The relationships between the UERA (S) and the span ratio (m), the density (λ) and the diameter of fracture (d) were analysed by the new prediction model. The results showed that the exposed area S and the span ratio m have a U-shaped curve relationship. The S decreases with the increase of m and then increases when m is beyond 2. The exposed roof area S is in an inversely proportional power-law relationship with the fracture surface density λ, and the curvature of the S-λ relationship curve decreases when d = 0.5 and λ > 7, and S is close to 0. There is a negative correlation between S and the fracture surface diameter d, the curvature of the S-d curve decreases with the increase of d and λ, and the variation rate increases first and then decreases with the increase of d; when λ = 0.5 and d > 9, S is close to 0. The predicted values of the UERA prediction model are 119.3, 112.8, and 114.6 m2 with different joint damage parameters, which are slightly smaller than the actual critical exposure area of a roof (S = 120 m2). The case study shows that the alternative prediction model is reasonable and acceptable and provides new theoretical support for the underground mining safety of sedimentary bauxite ore.

The accurate assessment of forest biomass is vital to climate change mitigation. Based on forest survey data, stand biomass models can effectively assess forest biomass carbon at large scales. However, traditional stand biomass models have ignored the potential effects of the climate on stand biomass estimation. There is still a lack of research on whether or not and in what ways the effects of the climate reduce uncertainty in biomass estimation and carbon accounting. Therefore, two types of stand biomass models, including basic stand biomass models (BBMs) and climate-sensitive stand biomass models (CBMs), were developed and tested using 311 plantation plots of Korean pine (Pinus koraiensis Siebold & Zucc.), Korean larch (Larix olgensisi A. Henry), and Mongolian pine (Pinus sylvestris var. mongolica Litv.) in Northeast China. The two types of models were developed by applying simultaneous equations based on nonlinear, seemingly unrelated, regression (NSUR) to ensure additivity of the stand total and components biomass (root, stem, branch, and needle). The results of fitting and leave-one-out cross-validation (LOOCV) indicated that the CBMs performed better than the corresponding BBMs. The RMSEs of the stand total biomass decreased by 3.5% to 10.6% for the three conifer species. The influence of temperature-related climate variables on the biomass of stand components was greater than that of precipitation-related climate variables. The sensitivity of the three conifer species to climate variables was ranked as Korean pine > Mongolian pine > Korean larch. This study emphasizes the importance of combining climate variables in stand biomass models to reduce the uncertainty and climate effects in forest biomass estimation, which will play a role in carbon accounting for forest ecosystems.

The Hongyuan breed Yak (Bos grunniens) belongs to a member of t the subfamily Bovinae. We provide a complete mitogenome of B. grunniens and analyze its phylogenetic relationship with other related species. Its mitogenome is a circular molecule with 16,322 bp in size, including 13 protein coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-loop, CR) that are conserved in most Bovidae mitogenomes. The total base composition of the B. grunniens mitogenome is 33.67% A, 27.29% T, 25.84% C, and 13.20% G. The gene composition, structure and the arrangement for B. grunniens are similar to those of most other Bovidae species. Phylogenetic analysis of mitochondrial genomes of 30 close species with Bayesian inference and maximum likelihood based on 13 protein-coding genes indicated that B. grunniens breed Hongyuan is more closely related to B. grunniens breed Qinghai Plateau than to B. grunniens breed Xuedong and B. grunniens breed Maiwa. The complete mitogenome of B. grunniens breed Hongyuan provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic relationships of Bovinae and related species.

The mitochondrial genome has proven to be a highly successful resource for the investigation of evolution and population genetics. Here, we present the complete mitochondrial genome of Fejervarya multistriata. The circle genome was found to be 17,759 bp in length, containing 13 protein-coding genes, 23 transfer RNA genes, 2 ribosomal RNA genes, and 1 noncoding control region that are conserved in most Dicroglossidae mitogenomes. The total base composition of the F. multistriata mitogenome is 28.04% A, 29.82% T, 26.99% C, and 15.15% G, which is typical for Amphibious animals’ mitochondrial genomes. Eight tRNAs are encoded on the light strand (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Glu and tRNA-Pro). Only one PCG is encoded on the light strand (ND6), whereas the other genes are located on the heavy strand. Phylogenetic analyses were performed on the concatenated dataset of 13 PCGs at nucleotide levels with maximum likelihood (ML) and Bayesian analysis (BI) methods. The results showed that F. multistriata and F. limnocharis integrated into a big branch and they have a close genetic relationship. This study could provide important molecular data for species identification and the phylogenetic relationship of Fejervarya and related species.

The Günther’s frog (Hylarana guentheri) belongs to a member of the family Ranidae. We provide a complete mitogenome of H. guentheri and examine its phylogenetic position with other related species. Its mitogenome is a closed circular molecule 18,698 bp in length including 13 protein coding genes, 22 tRNA coding genes, two rRNA-coding genes, and a control region (CR) that are conserved in most Ranidae mitogenomes. The overall base composition of the H. guentheri mitogenome is 29.27% A, 30.45% T, 26.14% C, and 14.15% G, which is typical for Amphibious animals’ mitochondrial genomes. The alignment of the Ranidae species control regions showed high levels of genetic variation and abundant AT content. Seven tandem repeats were found in the control region. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein-coding genes indicated that H. guentheri is more closely related to Nidirana okinavana than to Babina subaspera and B. holsti. The complete mitogenome of H. guentheri provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic relationships of Hylarana and related species.

Abstract This is the first study to describe the mitochondrial genome of the Himalayan Griffon, Gyps himalayensis, which is an Old World vulture belonging to the family Accipitridae and occurring along the Himalayas and the adjoining Tibetan Plateau. Its mitogenome is a closed circular molecule 17,381 bp in size containing 13 protein‐coding genes, 22 tRNA coding genes, two rRNA‐coding genes, a control region (CR), and an extra pseudo‐control region (CCR) that are conserved in most Accipitridae mitogenomes. The overall base composition of the G. himalayensis mitogenome is 24.55% A, 29.49% T, 31.59% C, and 14.37% G, which is typical for bird mitochondrial genomes. The alignment of the Accipitridae species control regions showed high levels of genetic variation and abundant AT content. At the 5′ end of the domain I region, a long continuous poly‐C sequence was found. Two tandem repeats were found in the pseudo‐control regions. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein‐coding genes indicated that the relationships at the family level were (Falconidae + (Cathartidae + (Sagittariidae + (Accipitridae + Pandionidae))). In the Accipitridae clade, G. himalayensis is more closely related to Aegypius monachus than to Spilornis cheela. The complete mitogenome of G. himalayensis provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic history of Gyps species.

Abstract Background Noninvasive biomarkers are urgently needed for patients with nonalcoholic steatohepatitis (NASH) to assist in diagnosis, monitoring disease progression and assessing treatment response. Recently several exploratory studies showed that circulating level of microRNA is associated with NASH and correlated with disease severity. Although these data were encouraging, the application of circulating microRNA as biomarkers for patient screening and stratification need to be further assessed under well-controlled conditions. Results The expression of circulating microRNAs were profiled in diet-induced NASH progression and regression models to assess the diagnostic and prognostic values and the translatability between preclinical mouse model and men. Since these mice had same genetic background and were housed in the same conditions, there were minimal confounding factors. Histopathological lesions were analyzed at distinct disease progression stages along with microRNA measurement which allows longitudinal assessment of microRNA as NASH biomarkers. Next, differentially expressed microRNAs were identified and validated in an independent cohorts of animals. Thirdly, these microRNAs were examined in a NASH regression model to assess whether they would respond to NASH treatment. MicroRNA profiling in two independent cohorts of animals validated the up-regulation of 6 microRNAs (miR-122, miR-192, miR-21, miR-29a, miR-34a and miR-505) in NASH mice, which was designated as the circulating microRNA signature for NASH. The microRNA signature could accurately distinguish NASH mice from lean mice, and it responded to chow diet treatment in a NASH regression model. To further improve the performance of microRNA-based biomarker, a new composite biomarker was proposed, which consists of miR-192, miR-21, miR-505 and ALT. The new composite biomarker outperformed the microRNA signature in predicting NASH mice which had NAS > 3, and deserves further validations in large scale studies. Conclusion The present study supported the translation of circulating microRNAs between preclinical models and humans in NASH pathogenesis and progression. The microRNA-based composite biomarker may be used for non-invasive diagnosis, clinical monitoring and assessing treatment response for NASH.

Stem taper function is an important concept in forest growth and yield modeling, and forest management. However, the additivity of the function and the inherent correlations between stem components (diameter outside bark—dob, diameter inside bark—dib, and double-bark thickness—dbt) are seldom considered. In this paper, a total disaggregation model (TDM) structure was developed based on the well-known Kozak (2004) model to ensure the additivity of the stem components. The reconstructed model was fitted with the data of 1281 felled Dahurian larch trees from three regions of Daxing’anling Mountains in Northeast China. The results from TDM were compared with other additive model structures including adjustment in proportion (AP), non-additive taper models (NAM), and three logical structures of NSUR (AMO, SMI, SMB). The results showed that the difference was significant among the three regions. The performance of TDM was slightly better than those of other model structures. Therefore, TDM was considered as another optimal additive system to estimate stem, bark thickness, and volume predicting for Dahurian larch in Northeast China besides NSUR, a method widely used in calculating additive volume or biomass throughout the world. We believe this work is cutting-edge, and that this methodology can be applied to other tree species.

In this study, the complete mitochondrial genome of big-eyed mountain keelback Pseudoxenodon macrops was sequenced adopting Illumina high-throughput sequencing technology. The complete mitogenome of the species was 19,444 bp in length, including 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and two non-coding control regions (CR). The overall base composition of mitogenome was 32.0% A, 25.5% T, 28.2% C, and 14.3% G. Most mitochondrial genes are encoded on the heavy strand, only ND6 and eight tRNA genes are on the light strand. We expect that the presented mitogenome can provide important data for future studies on phylogenetic relationship and population genetics of this species.

In this study, the complete mitochondrial genome of Duttaphrynus himalayanus was sequenced adopting Illumina high-throughput sequencing method. The complete mitogenome of the species was 17,172 bp in length, including 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and a non-coding control region (CR). The overall base composition of mitogenome was 29.7% A, 29.6% T, 26.0% C, and 14.7% G. Most mitochondrial genes are encoded on the heavy strand, only ND6 and eight tRNA genes on the light strand. The complete mitogenome of D. himalayanus can provide an important data for future studies on phylogenetic relationship and population genetics of this species.

In this study, we obtained the complete mitochondrial genome sequence of Nanorana chayuensis. The mitogenome length is 17,882 bp, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 1 non-coding control region (CR). Present data will contribute to further analysis of phylogenetic relationship and population genetics of this species.

The Asiatic toad Bufo gargarizans belongs to Bufonidae. This species is known from the Russian Far East, central, northern and north-eastern China, the Democratic People's Republic of Korea and Japan. In this study, the complete mitochondrial genome of B. gargarizans was sequenced. The mitogenome was 17,407 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the B. gargarizans is 28.9% A, 28.2% T, 27.5% C, and 15.3% G. Phylogenetic analysis showed B. gargarizans was closely related to B. bankorensis and B. tibetanus. The complete mitogenome of B. gargarizans can provide an important data for the studies on phylogenetic relationship and population genetics to further explore the taxonomic status of this species.

Crown architecture has long been evaluated for its impact on taper modeling. However, most of the research has focused on a limited number of crown dimensions. This study examined the effect of adding several crown dimensions in improving the diameter and volume estimates of Dahurian larch, Korean spruce, and Manchurian fir in northeast China. The crown dimensions included crown length, crown ratio, crown width, height to live crown base, diameter at the crown base, and crown shape. A well-known taper model of Clark et al. (1991) was fitted to the data of 276 trees from natural stands. To adjust the inherent autocorrelation in the data, we added a third-order continuous-time error structure in the model fit. Model fitting was carried out with the NLMIXED procedure (Non-linear Mixed Procedure), followed by the MODEL procedure of SAS using the generalized nonlinear least-squares method. Fit statistics and graphical assessments were used to evaluate the original and modified models. Above 98% of the total variance of d was explained by the models for all species. The addition of crown variables showed slight improvements for root mean square error (RMSE) values in the analyzed species. The RMSE plots indicated that the models with crown variables slightly improved the diameter and volume predictions for the species but only for the upper stem (>50%–90%). The study demonstrated that crown dimensions influence the stem taper, but the original model of Clark et al. (1991) reasonably realized that effect.

Mitochondrial genomes are important markers using to reconstruct phylogenetic status and reveal insect molecular evolution. In this study, the mitochondrial genome (mitogenome) of Anoplophora horsfieldi (Coleoptera: Chrysomelidae) was determined using high-throughput sequencing. The size of circular mitogenome is 15,796 bp and it includes a typical structure of 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs) and an adenine + thymine (A+T)-rich region. The base composition of the major strand is A: 39.74%, T: 39.57%, G: 8.22%, and C: 12.47%, with a A+T content of 79.31%. The genomic analyses indicated that its gene arrangement and content is similar to that of other Cucujiformia species. The Anoplophora species control region sequence with rich A+T content exhibited high genetic variability. All PCGs initiate with ATN and terminate with the TAA or TAG except for COXI-COXIII and ND3-ND5, where they end with an incomplete stop codon (T--). All tRNAs form clover-leaf structure only apart from trnS (AGN) which possess a reduced DHU arm. The motifs 'ATGATAA' between ND4L and ND4, was more conserved than that between trnS (UCN) and ND1 and between ATP8 and ATP6 in the mitogenomes of Cucujiformia. The 1,143 bp A+T-rich area includes a 16 bp poly-T stretch, 14 bp poly-A stretch region, three microsatellite-like repeats of (TA) n and three other random repetitive sequences. Based on 13 PCGs of 118 Cucujiformia mitogenomes, the phylogenetic analyses are reconstructed with both maximum likelihood and Bayesian analyses and a consistent topology is formed. The results show that A. horsfieldi grouped with A. glabripennis and A. chinensis with high nodal supports. It also supports such phylogenetic relationships of ((Lymexyloidea + Tenebrionoidea) + (Curculionoidea + (Chrysomeloidea + (Cucujoidea + (Cleroidea + Coccinelloidea))))) within Cucujiformia. Therefore, A. horsfieldi mitogenome enriches our understanding of the phylogenetic relationship of Chrysomelidae. In addition, it is used to establish phylogenetic trees and further study the phylogenetic relationship between Cucujiformia and Chrysomeloidea. [ABSTRACT FROM AUTHOR]

Mitochondrial genome is a very useful marker for determining the phylogenetic relationships. Hence in this study, the complete mitochondrial genome of Turdus merula was sequenced, described, and analyzed with Sanger sequencing technology. The complete mitochondrial genome of T. merula was 16,734 bp in length and encoded 37 genes, including 13 protein-coding genes, 22 tRNAs, 2 rRNA gene fragments, a control region (D-loop region) and gene arrangement was identical to that of other Passeriformes mitogenomes. The overall base composition included A, 29.34%; C, 32.50%; G, 14.82% and T, 23.34%. The motifs obtained by sequence comparison, "ATGAACCTAA" between ATP8 and ATP6, and "ATGCTAA" between ND4L and ND4, and "CAAGAAAGG" between COXI and tRNASer(UCN) were highly conservative in Passeriformes species. The monophyly of Passeriformes is divided into four major clades: Musicicapoidea, Sylvioidea, Passeroidea, and Corvoidea. The phylogeny analyses of Passerida was conducted with the clear support of dividing the group into three superfamilies: the Muscicapoidea, the Sylvioidea, and the Passeroidea, and Passeroidea is a sister taxon for Muscicapoidea and Sylvioidea, which are closely related to each other. We suggest that the genus Paradoxornis will be classified as family Sylviidae, while these two species (Luscinia cyanura and Monticola gularis) are placed in the family Muscicapidae. Moreover, Turdidae formed a sister group with Muscicapidae, which indicates that they are closely related and form the superfamily Muscicapoidea together with the Sturnidae families. The relationships between some species of the order Passeriformes may remain difficult to resolve despite an effort to collect additional characters for phylogenetic analysis. Current research of avian phylogeny should focus on adding molecular markers and taxa samples and use both effectively to reconstruct a better resolution for disputed species. [ABSTRACT FROM AUTHOR]

The tufted deer (Elaphodus cephalophus) is a unique species in the genus Elaphodus. Currently, very little is known about its nuclear and mitochondrial genomes and their phylogenetic position within the family Cervidae. In this study, we have determined the complete sequence of the mitochondrial genome of the tufted deer, by using a long polymerase chain reaction (PCR) technique. The entire mtDNA sequence is 16,196 bp in length, which compared with previous studies is the least, containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region (CR, D-loop). The overall base composition included 33.37 % A, 29.33 % T, 23.94 % C, and 13.36 % G. According to 13 protein-coding genes and phylogenetic analysis, Elaphodus may have a sister relationship with another deer group Muntiacus and they belong to the monophyletic genus. This study depicted mitochondrial genome characteristics for E. cephalophus and deepened the understanding of the phylogenetic relationship of Cervidae. [ABSTRACT FROM AUTHOR]