Search Results (20)

As software systems continue to increase in complexity and scale, the number of reported bugs also grows. Bug reports are essential artifacts in software maintenance, supporting critical tasks such as detecting duplicate reports, predicting bug severity, and assigning priority levels. Although stop word removal is a common text preprocessing step in natural language processing, its effectiveness in deep learning-based bug report analysis has not been thoroughly evaluated. This study investigates the impact of stop word removal on three core bug report classification tasks. The analysis uses a dataset containing over 1.9 million bug reports from eight large-scale open-source projects, including Eclipse, FreeBSD, GCC, Gentoo, Kernel, RedHat, Sourceware, and WebKit. Five deep learning models are applied: convolutional neural networks, long short-term memory networks, gated recurrent units, Transformers, and BERT. Each model is evaluated on its performance with and without stop word removal during preprocessing. The results show that the F1 score difference was less than 0.01 in over 85% of comparisons, so stop word removal has little to no effect on predictive performance in eight open-source projects. Average F1-scores remain consistent across all tasks and models, with 0.36 for duplicate detection, 0.33 for severity prediction, and 0.33 for priority prediction. Statistical significance tests confirm that the observed differences are not meaningful across datasets or model types. The findings suggest that stop word removal is not necessary in deep learning-based bug report analysis. Removing this step may simplify preprocessing pipelines without reducing accuracy, particularly in large-scale and real-world software engineering applications. Full article

This paper revisits the effects of financial market openness and stock market returns on economic development in the Gulf Cooperation Council countries over the period 1993–2022. We performed the panel stationarity test advanced that accommodates the presence of multiple structural breaks and exploits the cross-section variations. Empirical results from several panel tests provide strong support for the long-run positive effect of financial market openness on economic growth and a long-run negative association between stock market returns and growth. Findings of the robustness checks reveal that the effect of both financial market openness and stock market returns on economic growth differs across countries. Full article

Unmanned aerial vehicles (UAVs) have garnered more attention across various industries in recent years, leading to significant development in their design and application globally. Due to the high coupling between UAV states, model uncertainties, and various disturbances, precise longitudinal control of UAVs remains a significant research challenge. Oriented for the speed and altitude control of an electrical-powered fixed-wing UAV, this paper introduces a new control strategy based on the fuzzy guaranteed cost control (F-GCC) technique, which results in a nonlinear longitudinal state feedback control law with strict stability criterion, effectively addressing the issue of state coupling. Moreover, the strategy also includes a thrust estimation model of the electrical propulsion system to significantly reduce the nonlinearity, simplifying the controller design while effectively preserving tracking control performance. Through numerical validation, the UAV longitudinal nonlinear controller designed using the F-GCC technique offers better transient response and stronger robustness than the traditional linear and ADRC controllers. Full article

Appropriate growth curves can reflect more sophisticated growth patterns of animals than body weight, and thus, the identification of genes and variants related to the growth curve parameter traits contributes to revealing the fine growth and development characteristics of livestock. However, the ability of single genome-wide association analysis (GWAS) and transcriptome analyses to identify valuable genes and variants is limited. In this study, based on genome and transcriptome data, the growth curve parameter traits of hybrid pigs were analyzed, and a set of genes and variants were identified. The Gompertz–Laird growth curve model was optimized to reveal the growth pattern of F₂ individuals of Duroc × Erhualian pigs over four time points. Five growth parameters were estimated, including initial body weight ${(W}_0)$, instantaneous growth rate per day (L), coefficient of relative growth or maturing index (k), body weight at inflection point ${(W}_i)$, and average growth rate (GR). These five parameters were subjected to a genome-wide association study, differential gene expression analysis, and weighted gene co-expression network analysis (WGCNA). In the study, 336 pigs were genotyped, and 39,494 SNP markers were used for each pig in the analysis. Thirty of these pigs were also included in the transcriptomics analysis. Based on genome and transcriptome data, the integrated analyses identified five putative SNPs (including INRA0056566 on chromosome X, DRGA0004151 on chromosome 3, INRA0056460 on chromosome X, H3GA0049324 on chromosome 17, and H3GA0037747 on chromosome 13) and 15 candidate genes (PDGFA, VEGFD, CSPP1, EFHC1, PIK3C3, ZZZ3, GCC2, MAPK14, ZPR1, ISG15, ANG, CEBPD, ZHX3, CTBP2, and MYNN). The functional analysis indicated that these candidate genes played important roles in cell division and differentiation, development and aging, and skeletal muscle and fat formation. Our results provide insight into the genetic mechanisms underlying the growth and development of hybrid pigs and offer a theoretical basis for genomic breeding. Full article

Respiratory syncytial virus (RSV) is a serious human respiratory pathogen that commonly affects children, older adults, and immunocompromised individuals. At present, the design of licensed vaccines focuses on the incorporation of the pre-fusion protein (PreF protein) of RSV, as this protein has the ability to induce antibodies that offer a high level of protection. Moreover, the G protein contains the CX3C motif that binds the chemokine receptor CX3CR1 in respiratory epithelial cells, which plays an essential role in viral infection. Therefore, incorporating the G antigen into vaccine design may prove more advantageous for RSV prevention. In this study, we developed a human adenoviral vector-based RSV vaccine containing highly neutralizing immunogens, a modified full-length PreF protein fused with the central conserved peptides of the G protein (Gcc) from both RSV subgroups trimerized via a C-terminal foldon, and evaluated its immune response in mice through intranasal (i.n.) immunization. Our results showed that immunization with Ad5-PreF-Qa-Gcc elicited a balanced Th1/Th2 immune response and robust mucosal immunity with higher neutralizing antibody titers against RSV Long and RSV B1. Importantly, immunization with Ad5-PreF-Qa-Gcc enhanced CD4⁺ CD25⁺ FoxP3⁺ Treg cell response and protected the mice against RSV infection. Our data demonstrate that the combination of Gcc and the PreF antigen is a viable strategy for developing effective RSV vaccines. Full article

Quercus is a valuable genus ecologically, economically, and culturally. They are keystone species in many ecosystems. Species delimitation and phylogenetic studies of this genus are difficult owing to frequent hybridization. With an increasing number of genetic resources, we will gain a deeper understanding of this genus. In the present study, we collected four Quercus section Cyclobalanopsis species (Q. poilanei, Q. helferiana, Q. camusiae, and Q. semiserrata) distributed in Southeast Asia and sequenced their complete genomes. Following analysis, we compared the results with those of other species in the genus Quercus. These four chloroplast genomes ranged from 160,784 bp (Q. poilanei) to 161,632 bp (Q. camusiae) in length, with an overall guanine and cytosine (GC) content of 36.9%. Their chloroplast genomic organization and order, as well as their GC content, were similar to those of other Quercus species. We identified seven regions with relatively high variability (rps16, ndhk, accD, ycf1, psbZ—trnG-GCC, rbcL—accD, and rpl32—trnL-UAG) which could potentially serve as plastid markers for further taxonomic and phylogenetic studies within Quercus. Our phylogenetic tree supported the idea that the genus Quercus forms two well-differentiated lineages (corresponding to the subgenera Quercus and Cerris). Of the three sections in the subgenus Cerris, the section Ilex was split into two clusters, each nested in the other two sections. Moreover, Q. camusiae and Q. semiserrata detected in this study diverged first in the section Cyclobalanopsis and mixed with Q. engleriana in the section Ilex. In particular, 11 protein coding genes (atpF, ndhA, ndhD, ndhF, ndhK, petB, petD, rbcL, rpl22, ycf1, and ycf3) were subjected to positive selection pressure. Overall, this study enriches the chloroplast genome resources of Quercus, which will facilitate further analyses of phylogenetic relationships in this ecologically important tree genus. Full article

Estimating crop coefficients and evapotranspiration (ET) accurately is crucial for optimizing irrigation. Remote sensing techniques using green canopy cover, leaf area index (LAI), and normalized difference vegetation index (NDVI) have been applied to estimate basal crop coefficients (Kcb) and ET for different crops. However, analysis of the potential of these techniques to improve water management in irrigated potato (Solanum tuberosum L.) is still lacking. This study aimed to assess the modified nonlinear relationship between LAI, Kcb and NDVI in estimating crop coefficients (Kc) and ET of potato. Moreover, Kc and ET were derived from the measured fraction of green canopy cover (FGCC) and the FAO-56 approach. ET estimated from the FAO-56, FGCC and NDVI approaches were compared with the ET simulated using the LINTUL-Potato model. The results showed that the Kc values based on FGCC and NDVI were on average 0.16 lower than values based on FAO-56 Kc during the mid-season growing stage. ET estimated from FAO-56, FGCC and NDVI compared well with ET calculated by the LINTUL-Potato model, with RMSE values of 0.83, 0.79, and 0.78 mm day⁻¹, respectively. These results indicate that dynamic crop coefficients and potato ET can be estimated from canopy cover and NDVI. The outcomes of this study will assist potato growers in determining crop water requirements using real-time ETo, canopy state variables and NDVI data from satellite images. Full article

Knowledge about the spectral response of camelina under different regimes of nitrogen (N) fertilization is very scarce. Therefore, 2-year open-field trials were carried out in the 2021 and 2022 growing seasons with the aim of evaluating the spectral response of spring camelina to four different N fertilization regimes by using remote (UAV) and proximal (leaf-clip Dualex) sensing techniques. The tested treatments were: (i) control: no N application (T0); (ii) top dressing: 60 kg N ha⁻¹ before stem elongation (T1); basal dressing: 60 kg N ha⁻¹ at sowing (T2); basal + top dressing combination: 60 kg N ha⁻¹ at sowing + 60 kg N ha⁻¹ before stem elongation (T3). Camelina seed yield and N use efficiency were strongly affected by fertilization regimes, with the best results obtained at T2. A reduction in plant development and seed yield was detected in 2022, probably due to the rise in air temperatures. A significant effect of both growing season and N fertilization was observed on the photosynthetic pigments content with the T1 highest values in 2022. The highest seed oil content was achieved at T1, while the protein content increased with increasing N, with the best values at T3. Positive and significant correlations were observed among several vegetation indices obtained through UAV flights (NDVI, MRS705, FGCC) and seed yield, as well as between FGCC and leaf N concentration. Overall, these findings demonstrate the feasibility of utilizing remote sensing techniques from UAVs for predicting seed yield in camelina. Full article

Blepharoglossum is a rare orchid genus of the Malaxidinae primarily distributed in tropical Pacific islands, with several species occurring in the Taiwan and Hainan Islands of China. Currently, the monophyletic status of Blepharoglossum has been challenged, and the phylogenetic relationships among its allied groups have remained unresolved with traditional DNA markers. In this study, we initially sequenced and annotated the chloroplast (cp) genomes of two Blepharoglossum species, Blepharoglossum elegans (Lindl.) L. Li and Blepharoglossum grossum (Rchb.f.) L. Li. These cp genomes of Blepharoglossum share the typical quadripartite and circular structure. Each of the genomes encodes a total of 133 functional genes, including 87 protein-coding genes (CDS), 38 tRNA genes and 8 rRNA genes. By comparing the sequence differences between these two cp genomes, it was found that they are relatively conserved in terms of overall gene content and gene arrangement. However, a total of 684 SNPs and 2664 indels were still identified, with ycf1, clpP, and trnK-UUU protein-coding genes having the highest number of SNPs and indels. In further comparative analyses among the six cp genomes in Malaxidinae, significant sequence divergences were identified in the intergenic regions, namely rps16–trnQ-UUG, trnS-GCU–trnG-GCC, rpoB–trnC-GCA, trnE-UUC–trnT-GGU, trnF-GAA–trnV-UAC, atpB–rbcL, petA–psbJ, psbE–petL, psbB–psbT, trnN-GUU–rpl32, trnV-GAC–rps7, and rps7–trnL-CAA, and five coding regions, including matK, and rpoC2, ycf1, and two ycf2 genes. Phylogenetic analysis indicated that Blepharoglossum and Oberonia form a highly supported sister group relationship. Our results are consistent with previous studies and present increased resolution among major clades. Full article

The camellia flower is a famous woody plant with a long-cultivated history and high ornamental value. It is extensively planted and utilized around the world and owns a massive germplasm resource. Camellia ‘Xiari Qixin’ belongs to one of the typical cultivars in the four seasons camellia hybrids series. Due to its long flowering period, this kind of cultivar is identified as a precious resource of camellia flowers. In this study, the complete chloroplast genome sequence of C. ‘Xiari Qixin’ was first reported. Its whole chloroplast genome is 157,039 bp in length with an overall GC content of 37.30%, composed of a large single copy region (LSC, 86,674 bp), a small single copy region (SSC, 18,281 bp), and a pair of inverted repeat regions (IRs, 26,042 bp each). A total of 134 genes were predicted in this genome, including 8 ribosomal RNA genes, 37 transfer RNA genes, and 89 protein-coding genes. In addition, 50 simple sequence repeats (SSRs) and 36 long repeat sequences were detected. By comparing C. ‘Xiari Qixin’ and seven Camellia species on the chloroplast genome, seven mutation hotspot regions were identified, including psbK, trnS (GCU)-trnG(GCC), trnG(GCC), petN-psbM, trnF(GAA)-ndhJ, trnP(UGG)-psaJ, and ycf1. Phylogenetic analysis of 30 chloroplast genomes showed that the genetic relationship between C. ‘Xiari Qixin’ and Camellia azalea is quite close in evolution. These results could not only provide a valuable database for determining the maternal origin of Camellia cultivars, but also contribute to the exploration of the phylogenetic relationship and utilization of germplasm resources for Camellia. Full article

Wheat powdery mildew (Blumeria graminis f. sp. tritici, Bgt, recently clarified as B. graminis s. str.), is one of the most destructive diseases of wheat. Pm60 is a nucleotide-binding leucine-rich repeat (NLR) gene that confers race-specific resistance to Bgt. Allelic variants (Pm60, Pm60a, and Pm60b) were found in Triticum urartu and T. dicoccoides, the wild progenitors of wheat. In the present study, we studied the diversity of the Pm60 locus in a large set of wheat germplasm and found 20 tetraploid wheats harboring the Pm60 alleles, which correspond to three novel haplotypes (HapI–HapIII). HapI (Pm60 allele) and HapII (Pm60a allele) were present in domesticated tetraploid wheats, whereas HapIII (Pm60a allele) was identified in wild tetraploid T. araraticum. A sequence comparison of HapII and HapIII revealed that they differed by three SNPs and a GCC deletion. Results of the phylogenetic analysis revealed that HapII was more closely related to the functional haplotype MlIW172. Infection tests showed that HapII-carrying lines display a partial resistance response to Bgt#GH, while HapI was susceptible. Our results provide insights into the genetic evolution of the Pm60 locus and potential valuable alleles for powdery mildew resistance breeding. Full article

To systematically determine their phylogenetic relationships and develop molecular markers for species discrimination of Salvia bowleyana, S. splendens, and S. officinalis, we sequenced their chloroplast genomes using the Illumina Hiseq 2500 platform. The chloroplast genomes length of S. bowleyana, S. splendens, and S. officinalis were 151,387 bp, 150,604 bp, and 151,163 bp, respectively. The six genes ndhB, rpl2, rpl23, rps7, rps12, and ycf2 were present in the IR regions. The chloroplast genomes of S. bowleyana, S. splendens, and S. officinalis contain 29 tandem repeats; 35, 29, 24 simple-sequence repeats, and 47, 49, 40 interspersed repeats, respectively. The three specific intergenic sequences (IGS) of rps16-trnQ-UUG, trnL-UAA-trnF-GAA, and trnM-CAU-atpE were found to discriminate the 23 Salvia species. A total of 91 intergenic spacer sequences were identified through genetic distance analysis. The two specific IGS regions (trnG-GCC-trnM-CAU and ycf3-trnS-GGA) have the highest K2p value identified in the three studied Salvia species. Furthermore, the phylogenetic tree showed that the 23 Salvia species formed a monophyletic group. Two pairs of genus-specific DNA barcode primers were found. The results will provide a solid foundation to understand the phylogenetic classification of the three Salvia species. Moreover, the specific intergenic regions can provide the probability to discriminate the Salvia species between the phenotype and the distinction of gene fragments. Full article

Background: The aim of the study was to perform a functional and structural evaluation of the anterior visual pathway in patients with Graves’ Orbitopathy (GO) using electrophysiological tests and OCT, as well as to identify potential parameters that could be useful in detecting early optic nerve damage. Methods: 47 GO patients were enrolled in the study and divided into three groups, depending on their disease severity: Group 1 with mild GO, Group 2 with moderate-to-severe GO, and Group 3 with dysthyroid optic neuropathy (DON). Pattern visual evoked potential (PVEP), flash visual evoked potential (fVEP), pattern electroretinogram (pERG), and optical coherence tomography (OCT) findings were compared between the groups. Results: In the DON Group (Group 3), N75, P100, and P2 latencies were significantly extended, whereas P100, P50, and N95 amplitudes were significantly reduced as compared to the non-DON group (Groups 1 and 2). Group 3 also had significantly thinner peripapillary retinal nerve fiber layer (RNFL) and macular ganglion cell complex (GCC). In Group 2, as compared to Group 1, P100 amplitudes were significantly reduced for all check sizes, while P100 latency was elongated for the check size of 0.9°. Group 2 also had a significantly thinner average GCC and GCC in the superior quadrant. Conclusions: Electrophysiological examinations may be of use in diagnosis of DON. OCT findings and electrophysiological responses vary in patients with different GO severity. Including regular electrophysiological evaluation and OCT in the examination of patients with GO could be of benefit. However, more research is needed to establish the true significance of pVEP, fVEP, pERG, and OCT in monitoring patients with GO. Full article

Euonymus maackii Rupr. is a small deciduous tree belonging to family Celastraceae. It is an important ornamental tree and a potential medicinal plant resource. Here, we assembled and annotated the chloroplast (cp) genome of E. maackii. By combining this genome with seven available cp genomes from Euonymus species, we performed plastome variation analysis of E. maackii and Euonymus. Furthermore, we reconstructed a phylogenetic tree and estimated the differentiation time of E. maackii. The newly assembled cp genome of E. maackii was 157,551 bp in size and had a typical quadripartite structure, which consisted of one large single-copy (LSC 86,524 bp) region, one small single-copy (SSC 18,337 bp) region, and a pair of inverted repeat regions (26,345 bp). A total of 652 single nucleotide polymorphisms (SNPs) and 65 insertions/deletions (indels) were detected between the two cp genomes of E. maackii, with overall genetic variation of 4.1 SNPs per kb or a π value of 0.00443, reflecting a high level of intraspecific variation. Some coding and noncoding regions with higher variation were identified, including trnV-UAC, petN, ycf1-ndhF, trnM^-CAU-atpE, rpl2-rpl23, psbZ-trnG^-GCC, trnY^-GUA-trnE^-UUC, trnW^-CCA-trnP^-UGG, rps16-trnQ^-UUG, and psbC-trnS^-UGA. The hypervariable coding and noncoding regions in E. maackii were not the same as those in Euonymus. The phylogenetic tree and divergence time based on the whole cp genomes showed that the seven Euonymus species formed a clade, which was sister to that formed with Catha edulis and Maytenus guangxiensis, and they separated 24.74 million years ago. E. maackii and E. hamiltonianus were most closely related, having separated from each other only approximately 2.68 million years ago. Our study provides important genetic information for further studies of E. maackii, such as studies on its phylogeography, population genetics and molecular ecology, and provides new insights into the evolution of the cp genome in Euonymus. Full article

Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C₄ Stipagrostis and C₃ Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae. Full article