bluuebunny/crossref_metadata_2025 huggingface dataset:
Pyrimidine metabolism regulator-mediated molecular subtypes display tumor microenvironmental hallmarks and assist precision treatment in bladder cancer
Authors: Wu Zixuan , Li Xiaohuan , Gu Zhenchang , Xia Xinhua , Yang Jing
Published: August 2023

Background

Bladder cancer (BLCA) is a common urinary system malignancy with a significant morbidity and death rate worldwide. Non-muscle invasive BLCA accounts for over 75% of all BLCA cases. The imbalance of tumor metabolic pathways is associated with tumor formation and proliferation. Pyrimidine metabolism (PyM) is a complex enzyme network that incorporates nucleoside salvage, de novo nucleotide synthesis, and catalytic pyrimidine degradation. Metabolic reprogramming is linked to clinical prognosis in several types of cancer. However, the role of pyrimidine metabolism Genes (PyMGs) in the BLCA-fighting process remains poorly understood.

Methods

Predictive PyMGs were quantified in BLCA samples from the TCGA and GEO datasets. TCGA and GEO provided information on stemness indices (mRNAsi), gene mutations, CNV, TMB, and corresponding clinical features. The prediction model was built using Lasso regression. Co-expression analysis was conducted to investigate the relationship between gene expression and PyM.

Results

PyMGs were overexpressed in the high-risk sample in the absence of other clinical symptoms, demonstrating their predictive potential for BLCA outcome. Immunological and tumor-related pathways were identified in the high-risk group by GSWA. Immune function and m6a gene expression varied significantly between the risk groups. In BLCA patients, DSG1, C6orf15, SOST, SPRR2A, SERPINB7, MYBPH, and KRT1 may participate in the oncology process. Immunological function and m6a gene expression differed significantly between the two groups. The prognostic model, CNVs, single nucleotide polymorphism (SNP), and drug sensitivity all showed significant gene connections.

Conclusions

BLCA-associated PyMGs are available to provide guidance in the prognostic and immunological setting and give evidence for the formulation of PyM-related molecularly targeted treatments. PyMGs and their interactions with immune cells in BLCA may serve as therapeutic targets.
Causal association between serum 25-Hydroxyvitamin D levels and cutaneous melanoma: a two-sample Mendelian randomization study
Authors: Cai Beichen , Lin Qian , Ke Ruonan , Shan Xiuying , Yu Jiaqi , Ni Xuejun , Lin Xinjian , Wang Biao
Published: August 2023

Background

Despite numerous observational studies on the association between serum 25-Hydroxyvitamin D levels and cutaneous melanoma, causal inferences remain ambiguous due to confounding and reverse causality. This study aimed to elucidate the causal relationship between serum 25-Hydroxyvitamin D levels and melanoma incidence using Mendelian randomization (MR).

Methods

A two-sample MR was conducted using genetic variants associated with serum 25-Hydroxyvitamin D levels as instrumental variables. Summary statistics for these variants were derived from genome-wide association studies, and those for melanoma risk were obtained from a comprehensive melanoma case-control study. Robustness of the results was assessed through sensitivity analyses, including the “leave-one-out” approach and tests for potential pleiotropy.

Results

The MR analysis provided substantial evidence of a positive causal relationship between serum 25-Hydroxyvitamin D levels and the incidence of cutaneous melanoma, suggesting that each unit increase in serum 25-Hydroxyvitamin D levels corresponds with an increased risk of melanoma. Tests for pleiotropy showed minimal effects, and the sensitivity analysis confirmed no disproportionate influence by any individual single nucleotide polymorphism (SNP).

Conclusion

The findings indicated a potentially causal positive association between serum 25-Hydroxyvitamin D levels and melanoma risk, challenging traditional beliefs about vitamin D’s role in melanoma. This emphasizes the need for a balanced and personalized approach to vitamin D supplementation and sun exposure, particularly in high-risk populations. These results should be interpreted with caution due to potential unrecognized pleiotropy and confounding factors. Future research should focus on validating these findings in diverse populations and exploring underlying biological mechanisms.
ICOS and OX40 tandem co-stimulation enhances CAR T-cell cytotoxicity and promotes T-cell persistence phenotype
Authors: Moreno-Cortes Eider , Franco-Fuquen Pedro , Garcia-Robledo Juan E. , Forero Jose , Booth Natalie , Castro Januario E.
Published: August 2023

Chimeric Antigen Receptor (CAR) T-cell therapies have emerged as an effective and potentially curative immunotherapy for patients with relapsed or refractory malignancies. Treatment with CD19 CAR T-cells has shown unprecedented results in hematological malignancies, including heavily refractory leukemia, lymphoma, and myeloma cases. Despite these encouraging results, CAR T-cell therapy faces limitations, including the lack of long-term responses in nearly 50-70% of the treated patients and low efficacy in solid tumors. Among other reasons, these restrictions are related to the lack of targetable tumor-associated antigens, limitations on the CAR design and interactions with the tumor microenvironment (TME), as well as short-term CAR T-cell persistence. Because of these reasons, we developed and tested a chimeric antigen receptor (CAR) construct with an anti-ROR1 single-chain variable-fragment cassette connected to CD3ζ by second and third-generation intracellular signaling domains including 4-1BB, CD28/4-1BB, ICOS/4-1BB or ICOS/OX40. We observed that after several successive tumor-cell in vitro challenges, ROR1.ICOS.OX40ζ continued to proliferate, produce pro-inflammatory cytokines, and induce cytotoxicity against ROR1+ cell lines in vitro with enhanced potency. Additionally, in vivo ROR1.ICOS.OX40ζ T-cells showed anti-lymphoma activity, a long-lasting central memory phenotype, improved overall survival, and evidence of long-term CAR T-cell persistence. We conclude that anti-ROR1 CAR T-cells that are activated by ICOS.OX40 tandem co-stimulation show in vitro and in vivo enhanced targeted cytotoxicity associated with a phenotype that promotes T-cell persistence.
Comparison analysis of PD-1/PD-L1 inhibitors plus lenvatinib or gemcitabine/cisplatin as first-line treatment for patients with advanced intrahepatic cholangiocarcinoma
Authors: Huang Jia-Xin , Liu Bo , Li Yu , Li Xi , Ding Li-Juan , Wang Nan-Ya
Published: August 2023

Background

Intrahepatic cholangiocarcinoma (ICC) is a highly aggressive primary liver cancer, with increasing incidence worldwide. Effective first-line treatments for advanced ICC patients are currently limited. Therefore, our study aimed to assess the efficacy and safety of programmed death-1 (PD-1)/programmed death-ligand 1 (PD-L1) inhibitors in combination with gemcitabine/cisplatin (GC) and lenvatinib as first-line treatment in advanced ICC patients.

Methods

This retrospective cohort study included 51 advanced ICC patients, among whom 25 patients were administered with PD-1/PD-L1 plus lenvatinib and 26 patients were administered with PD-1/PD-L1 plus GC. Baseline characteristics including demographic information, medical history, clinical characteristics, laboratory data, and imaging examination were collected. The primary endpoints were progression-free survival (PFS) and sixth- and ninth-month overall survival (OS) rate. Survival curve was plotted by the Kaplan–Meier method. A Cox proportion risk model was performed to investigate independent risk factors of PFS and OS. The secondary outcomes were objective response rate (ORR), disease control rate (DCR), and adverse events.

Results

The median age of advanced ICC patients in our study was 58.0 (95% confidence interval [95% CI] = 48.0–72.4) years, with 33 male and 18 female patients. Patients in the PD-1/PD-L1 inhibitors plus lenvatinib group were more likely to be in ECOG grade above 1, develop ascites, and have an elevated level of ALT. The ORR was 16.0% in the PD-1/PD-L1 inhibitors plus lenvatinib group and 23.1% in the GC group (p = 0.777). The DCR was 52.0% in the lenvatinib group and 46.2% in the GC group (p = 0.676). The combination treatment of PD-1/PD-L1 inhibitors plus lenvatinib was associated with longer PFS than the GC group; however, it was not statistically significant (lenvatinib: 9.5 months, GC: 5.1 months, p = 0.454). The sixth-month and ninth-month OS rates were 82.0% and 76.9% in the lenvatinib group and 87.4% and 71.5% in the GC group. After adjusting for confounders, multivariate Cox regression analysis showed that ECOG grade above 1 was an independent risk factor for PFS (hazard ratio [HR] = 3.388, 95% CI = 1.312–8.746, p = 0.012) and OS (HR = 4.220, 95% CI = 1.131–15.742, p = 0.032).

Conclusion

PD-1/PD-L1 inhibitors in combination with lenvatinib or GC all demonstrated significant efficacy and safety as first-line treatment in patients with advanced ICC. As for patients who refuse or are intolerant to chemotherapy, PD-1/PD-L1 plus lenvatinib would be recommended.
Landscape of germline BRCA1/BRCA2 variants in breast and ovarian cancer in Peru
Authors: Ferreyra Yomali , Rosas Gina , Cock-Rada Alicia M. , Araujo Jhajaira , Bravo Leny , Doimi Franco , Casas Jhoysi , Clavo María de los Ángeles , Pinto Joseph A. , Belmar-López Carolina
Published: August 2023

Background

There is an increasing amount of data from Latin America on the characterization of BRCA variants; however, there is limited information from Peru. We conducted a retrospective study to describe germline pathogenic/likely pathogenic(P/LP) variants and variants of uncertain/unknown significance (VUS) in the BRCA1 and BRCA2 genes in Peru, in patients with breast and ovarian cancer, candidates for treatment with poly (adenosine diphosphate–ribose) polymerase (PARP) inhibitors.

Methods

The patients were evaluated during the period 2019-2021. Genomic DNA was isolated from peripheral blood samples and targeted sequencing was performed using the Ampliseq BRCA panel. Genetic variant interpretation was carried out in accordance with the recommendations of the American College of Medical Genetics and ClinVar. During this period, 525 patients (143 with breast cancer and 382 with ovarian cancer) were studied.

Results

We found that 14.7% (21/143) of breast cancer patients and 20.7% (79/382) of ovarian cancer patients were carriers of P/LP variants in BRCA1/2. The most frequent pathogenic variants detected in BRCA1 were c.2105dupT (BIC: 2224insT, n=12, 18.75%), c.68_69delAG (BIC: 185delAG, n=6, 9.38%), c.140G>T and c.815_824dupAGCCATGTGG (n=5, 7.81%), while in BRCA2 were c.8023A>G (n=6, 16.67%), c.6024dupG (BIC: 6252insG, n=4, 11.11%), and c.9235delG (BIC: 9463delG, n=3, 8.33%). Regarding VUS, we found that 6.99% (10/143) of breast cancer patients and 7.33% (28/382) of ovarian cancer patients were carriers of a VUS in BRCA1/2. For BRCA1, the most frequent VUS was c.93C>G (n=2), and for BRCA2, c.5465A>T (n=4), c.3101T>C (n=3), c.205C>A and c.437T>C (n=2).

Conclusion

We found a frequency of 14.7% germline mutations in breast cancer patients and 20.7% in ovarian cancer patients. The most recurrent mutations were BRCA1 c.2105dupT and BRCA2 c.8023A>G. We found that BRCA2 c.8023A>G, c.6024dupG, and c.9235delG were not previously reported in Peruvian patients. BRCA1 c.2344dupA is a novel mutation that has not been previously reported in any database. The frequency of VUS in our cohort was 7.2%.
A systematic review of progress on hepatocellular carcinoma research over the past 30 years: a machine-learning-based bibliometric analysis
Authors: Lee Kiseong , Hwang Ji Woong , Sohn Hee Ju , Suh Sanggyun , Kim Sun-Whe
Published: August 2023

Introduction

Research on hepatocellular carcinoma (HCC) has grown significantly, and researchers cannot access the vast amount of literature. This study aimed to explore the research progress in studying HCC over the past 30 years using a machine learning-based bibliometric analysis and to suggest future research directions.

Methods

Comprehensive research was conducted between 1991 and 2020 in the public version of the PubMed database using the MeSH term “hepatocellular carcinoma.” The complete records of the collected results were downloaded in Extensible Markup Language format, and the metadata of each publication, such as the publication year, the type of research, the corresponding author’s country, the title, the abstract, and the MeSH terms, were analyzed. We adopted a latent Dirichlet allocation topic modeling method on the Python platform to analyze the research topics of the scientific publications.

Results

In the last 30 years, there has been significant and constant growth in the annual publications about HCC (annual percentage growth rate: 7.34%). Overall, 62,856 articles related to HCC from the past 30 years were searched and finally included in this study. Among the diagnosis-related terms, “Liver Cirrhosis” was the most studied. However, in the 2010s, “Biomarkers, Tumor” began to outpace “Liver Cirrhosis.” Regarding the treatment-related MeSH terms, “Hepatectomy” was the most studied; however, recent studies related to “Antineoplastic Agents” showed a tendency to supersede hepatectomy. Regarding basic research, the study of “Cell Lines, Tumors,’’ appeared after 2000 and has been the most studied among these terms.

Conclusion

This was the first machine learning-based bibliometric study to analyze more than 60,000 publications about HCC over the past 30 years. Despite significant efforts in analyzing the literature on basic research, its connection with the clinical field is still lacking. Therefore, more efforts are needed to convert and apply basic research results to clinical treatment. Additionally, it was found that microRNAs have potential as diagnostic and therapeutic targets for HCC.
Baseline whole-lung CT features deriving from deep learning and radiomics: prediction of benign and malignant pulmonary ground-glass nodules
Authors: Huang Wenjun , Deng Heng , Li Zhaobin , Xiong Zhanda , Zhou Taohu , Ge Yanming , Zhang Jing , Jing Wenbin , Geng Yayuan , Wang Xiang , Tu Wenting , Dong Peng , Liu Shiyuan , Fan Li
Published: August 2023

Objective

To develop and validate the model for predicting benign and malignant ground-glass nodules (GGNs) based on the whole-lung baseline CT features deriving from deep learning and radiomics.

Methods

This retrospective study included 385 GGNs from 3 hospitals, confirmed by pathology. We used 239 GGNs from Hospital 1 as the training and internal validation set; 115 and 31 GGNs from Hospital 2 and Hospital 3 as the external test sets 1 and 2, respectively. An additional 32 stable GGNs from Hospital 3 with more than five years of follow-up were used as the external test set 3. We evaluated clinical and morphological features of GGNs at baseline chest CT and extracted the whole-lung radiomics features simultaneously. Besides, baseline whole-lung CT image features are further assisted and extracted using the convolutional neural network. We used the back-propagation neural network to construct five prediction models based on different collocations of the features used for training. The area under the receiver operator characteristic curve (AUC) was used to compare the prediction performance among the five models. The Delong test was used to compare the differences in AUC between models pairwise.

Results

The model integrated clinical-morphological features, whole-lung radiomic features, and whole-lung image features (CMRI) performed best among the five models, and achieved the highest AUC in the internal validation set, external test set 1, and external test set 2, which were 0.886 (95% CI: 0.841-0.921), 0.830 (95%CI: 0.749-0.893) and 0.879 (95%CI: 0.712-0.968), respectively. In the above three sets, the differences in AUC between the CMRI model and other models were significant (all P < 0.05). Moreover, the accuracy of the CMRI model in the external test set 3 was 96.88%.

Conclusion

The baseline whole-lung CT features were feasible to predict the benign and malignant of GGNs, which is helpful for more refined management of GGNs.
A real-world pharmacovigilance analysis of FDA adverse event reporting system database for upadacitinib
Authors: Wu Yan , Wei Meihao , Zhang Jing
Published: August 2023

Objective: To mine the adverse drug event (ADE) signals of upadacitinib based on the Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) database to provide a reference for the safe clinical use of the drug.

Methods: The ADE data for upadacitinib from Q1 2004 to Q1 2023 in the FAERS database were retrieved, and data mining was performed using the reporting odds ratio and proportional reporting ratio.

Results: A total of 21,213 ADE reports for the primary suspect drug upadacitinib were obtained, involving 444 ADEs. Patients aged ≥60 years (21.48%) and female (70.11%) patients were at a higher risk of ADEs with upadacitinib. After data cleaning, 182 ADE signals from 19 system organ classes (SOCs) were obtained. Six of these SOCs that occurred more frequently and were not mentioned in the drug labeling information included renal and urinary system (1.09%), reproductive and breast diseases (1.14%), ear and labyrinth disorders (0.57%), psychiatric disease (0.57%), blood and lymphatic system disorders (0.57%), and endocrine disorders (0.57%). The top ten most frequent ADE signals reported for upadacitinib were mainly related to: infections and infestations (7), investigations (2), and skin and subcutaneous tissue disorders (1). The top 10 ADEs in signal intensity ranking were lip neoplasm, ureteral neoplasm, eczema herpeticum, vulvar dysplasia, mediastinum neoplasm, eosinopenia, herpes zoster cutaneous disseminated, eye ulcer, acne cystic, and Moraxella infection. The top 10 high-frequency events leading to serious adverse events were urinary tract infection (2.74%), herpes zoster (1.63%), diverticulitis (1.19%), bronchitis (0.68%), nasopharyngitis (0.68%), localised infection (0.66%), nephrolithiasis (0.66%), pulmonary thrombosis (0.66%), blood cholesterol increased (0.55%), and Pneumocystis jirovecii pneumonia (0.53%).

Conclusion: Clinicians should be vigilant to upadacitinib-induced events in systems not covered in the drug labeling information and to new and highly signaled ADEs to ensure the safe and effective use of upadacitinib.
A novel role of the splenic volume in Crohn’s disease: evaluating the efficacy of infliximab
Authors: Shi Xuan , Wang Jia-Hui , Rao Sheng-Xiang , Liu Tao-Tao , Wu Hao
Published: August 2023

Background: A number of patients with Crohn’s disease (CD) suffer from loss of response to infliximab (IFX) therapy. Splenic volume is reported to be enlarged in patients with CD compared to normal individuals. The association between splenic volume and IFX efficacy in CD remains unclear.

Methods: We performed a retrospective study of patients with CD who received regular IFX treatment at Zhongshan Hospital, Fudan University, between August 2015 and December 2021. We collected baseline characteristics and clinical features from medical records in the CD database of Zhongshan Hospital. We accurately measured the splenic volume using semi-auto spleen segmentation software, followed by the analysis of splenic volume and IFX efficacy.

Results: We included 49 patients with CD receiving IFX treatment, of whom 41 responded to IFX and 8 failed to respond to IFX. Splenic volume, as well as volume adjusted for body mass index (SV/BMI) and body weight (SV/W), was significantly decreased after IFX treatment in responders but increased in non-responders compared to the volume before the treatment. Accordingly, the levels of leukocyte count, platelet count, C-reactive protein (CRP), and erythrocyte sedimentation rate (ESR) were decreased after IFX treatment in responders. Contrarily, the levels of hemoglobin, albumin, and tumor necrosis factor (TNF)-α were elevated in responders. Moreover, both CRP and TNF-α levels were significantly positively correlated with SV/BMI in all patients.

Conclusion: Splenic volume, especially SV/BMI and SV/W, was reduced after IFX treatment in CD patients responsive to IFX. SV/BMI was positively correlated with disease activity. Splenic volume is a promising indicator to evaluate IFX efficacy in CD.
Carnitine metabolites and cognitive improvement in patients with schizophrenia treated with olanzapine: a prospective longitudinal study
Authors: Zhao Lei , Liu Hua , Wang Wenjuan , Wang Youping , Xiu Meihong , Li Shuyun
Published: August 2023

Objective: Cognitive impairment is one of the core symptoms of schizophrenia, which is stable and lifelong. L-carnitine has been shown to improve cognitive function and decrease the rate of cognitive deterioration in patients with Alzheimer’s disease. However, it remains unclear regarding the role of L-carnitine and its metabolites in cognitive functions in schizophrenia after treatment with olanzapine. The purpose of this study was to evaluate the relationship between changes in plasma levels of L-carnitine metabolites and cognitive improvement after olanzapine treatment.

Methods: This was a prospective longitudinal study. In this study, we recruited 25 female patients with first episode schizophrenia (FES) who were drug naïve at baseline and received 4 weeks of olanzapine monotherapy. Cognitive function was assessed at baseline and 4-week follow-up using the RBANS. Plasma L-carnitine metabolite levels were determined by a metabolomics technology based on untargeted ultra-performance liquid chromatography-mass spectrometry (UPLC-MS).

Results: We found that the immediate memory index, delayed memory index and RBANS composite score were significantly increased at the 4-week follow-up after treatment. A total of 7 differential L-carnitine metabolites were identified in FES patients after olanzapine monotherapy. In addition, we found that changes in butyrylcarnitine were positively correlated with improvements in language index and RBANS composite score. Further regression analyses confirmed the association between reduced butyrylcarnitine levels and cognitive improvement after olanzapine monotherapy in FES patients.

Conclusion: Our study shows that cognitive improvement after olanzapine treatment was associated with changes in L-carnitine metabolite levels in patients with FES, suggesting a key role of L-carnitine in cognition in schizophrenia.
Highlighting of the interactions of MYD88 and NFKB1 SNPs in rats resistant to decompression sickness: toward an autoimmune response
Authors: Vallée Nicolas , Dugrenot Emmanuel , Desruelle Anne-Virginie , Richard Simone , Coupé Stéphane , Ramdani Céline , Guieu Régis , Risso Jean-Jacques , Gaillard Sandrine , Guerrero François
Published: August 2023

Decompression sickness (DCS) with neurological disorders includes an inappropriate inflammatory response which degenerates slowly, even after the disappearance of the bubbles. There is high inter-individual variability in terms of the occurrence of DCS that could have been mastered by the selection and then the breeding of DCS-resistant rats. We hypothesized the selection of single-nucleotide polymorphisms (SNPs) linked to autoimmunity operated upon a generation of a DCS-resistant strain of rats. We used the candidate gene approach and targeted SNPs linked to the signaling cascade that directly regulates inflammation of innate immunity transiting by the Toll-like receptors. Twenty candidate SNPs were investigated in 36 standard rats and 33 DCS-resistant rats. For the first time, we identify a diplotype (i.e., with matched haplotypes)—when coinherited—that strengthens protection against DCS, which is not strictly homozygous and suggests that a certain tolerance may be considered. We deduced an ideal haplotype of six variants from it (MyD88_50-T, _49-A, _97-C coupled to NFKB_85-T, _69-T, _45-T) linked to the resistant phenotype. Four among the six identified variants are located in pre- and/or post-transcriptional areas regulating MyD88 or NFKB1 expression. Because of missense mutations, the other two variants induce a structural change in the NFKB1 protein complex including one damage alteration according to the Missense3D algorithm. In addition to the MyD88/NFKB1 haplotype providing rats with a strong resistance to DCS, this also highlights the importance that the immune response, here linked to the genetic heritage, can have in the development of DCS and offer a new perspective for therapeutic strategies.
A systematic in silico report on iron and zinc proteome of Zea mays
Authors: Sharma Ankita , Sharma Dixit , Verma Shailender Kumar
Published: August 2023

Zea mays is an essential staple food crop across the globe. Maize contains macro and micronutrients but is limited in essential mineral micronutrients such as Fe and Zn. Worldwide, serious health concerns have risen due to the deficiencies of essential nutrients in human diets, which rigorously jeopardizes economic development. In the present study, the systematic in silico approach has been used to predict Fe and Zn binding proteins from the whole proteome of maize. A total of 356 and 546 putative proteins have been predicted, which contain sequence and structural motifs for Fe and Zn ions, respectively. Furthermore, the functional annotation of these predicted proteins, based on their domains, subcellular localization, gene ontology, and literature support, showed their roles in distinct cellular and biological processes, such as metabolism, gene expression and regulation, transport, stress response, protein folding, and proteolysis. The versatile roles of these shortlisted putative Fe and Zn binding proteins of maize could be used to manipulate many facets of maize physiology. Moreover, in the future, the predicted Fe and Zn binding proteins may act as relevant, novel, and economical markers for various crop improvement programs.
ALAD-YOLO:an lightweight and accurate detector for apple leaf diseases
Authors: Xu Weishi , Wang Runjie
Published: August 2023

Suffering from various apple leaf diseases, timely preventive measures are necessary to take. Currently, manual disease discrimination has high workloads, while automated disease detection algorithms face the trade-off between detection accuracy and speed. Therefore, an accurate and lightweight model for apple leaf disease detection based on YOLO-V5s (ALAD-YOLO) is proposed in this paper. An apple leaf disease detection dataset is collected, containing 2,748 images of diseased apple leaves under a complex environment, such as from different shooting angles, during different spans of the day, and under different weather conditions. Moreover, various data augmentation algorithms are applied to improve the model generalization. The model size is compressed by introducing the Mobilenet-V3s basic block, which integrates the coordinate attention (CA) mechanism in the backbone network and replacing the ordinary convolution with group convolution in the Spatial Pyramid Pooling Cross Stage Partial Conv (SPPCSPC) module, depth-wise convolution, and Ghost module in the C3 module in the neck network, while maintaining a high detection accuracy. Experimental results show that ALAD-YOLO balances detection speed and accuracy well, achieving an accuracy of 90.2% (an improvement of 7.9% compared with yolov5s) on the test set and reducing the floating point of operations (FLOPs) to 6.1 G (a decrease of 9.7 G compared with yolov5s). In summary, this paper provides an accurate and efficient detection method for apple leaf disease detection and other related fields.
Iron-modified biochar improves plant physiology, soil nutritional status and mitigates Pb and Cd-hazard in wheat (Triticum aestivum L.)
Authors: Algethami Jari S. , Irshad Muhammad Kashif , Javed Wasim , Alhamami Mohsen A. M. , Ibrahim Muhammad
Published: August 2023

Environmental quality and food safety is threatened by contamination of lead (Pb) and cadmium (Cd) heavy metals in agricultural soils. Therefore, it is necessary to develop effective techniques for remediation of such soils. In this study, we prepared iron-modified biochar (Fe-BC) which combines the unique characteristics of pristine biochar (BC) and iron. The current study investigated the effect of pristine and iron modified biochar (Fe-BC) on the nutritional values of soil and on the reduction of Pb and Cd toxicity in wheat plants (Triticum aestivum L.). The findings of present study exhibited that 2% Fe-BC treatments significantly increased the dry weights of roots, shoots, husk and grains by 148.2, 53.2, 64.2 and 148%, respectively compared to control plants. The 2% Fe-BC treatment also enhanced photosynthesis rate, transpiration rate, stomatal conductance, intercellular CO2, chlorophyll a and b contents, by 43.2, 88.4, 24.9, 32.5, 21.4, and 26.7%, respectively. Moreover, 2% Fe-BC treatment suppressed the oxidative stress in wheat plants by increasing superoxide dismutase (SOD) and catalase (CAT) by 62.4 and 69.2%, respectively. The results showed that 2% Fe-BC treatment significantly lowered Cd levels in wheat roots, shoots, husk, and grains by 23.7, 44.5, 33.2, and 76.3%. Whereas, Pb concentrations in wheat roots, shoots, husk, and grains decreased by 46.4, 49.4, 53.6, and 68.3%, respectively. Post-harvest soil analysis showed that soil treatment with 2% Fe-BC increased soil urease, CAT and acid phosphatase enzyme activities by 48.4, 74.4 and 117.3%, respectively. Similarly, 2% Fe-BC treatment significantly improved nutrients availability in the soil as the available N, P, K, and Fe contents increased by 22, 25, 7.3, and 13.3%, respectively. Fe-BC is a viable solution for the remediation of hazardous Cd and Pb contaminated soils, and improvement of soil fertility status.
Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives
Authors: Liu Huihui , Hou Zhuangwei , Xu Lei , Ma Qing , Wei Min , Tembrock Luke R. , Zhang Shuo , Wu Zhiqiang
Published: August 2023

Chrysanthemum indicum, a species native to Eastern Asia is well known as one of the progenitor species of the cultivated Chrysanthemum which is grown for its ornamental and medicinal value. Previous genomic studies on Chrysanthemum have largely ignored the dynamics of plastid genome (plastome) and mitochondria genome (mitogenome) evolution when analyzing this plant lineage. In this study, we sequenced and assembled the plastomes and mitogenomes of diploid and tetraploid C. indicum as well as the morphologically divergent variety C. indicum var. aromaticum. We used published data from 27 species with both plastome and mitogenome complete sequences to explore differences in sequence evolution between the organellar genomes. The size and structure of organellar genome between diploid and tetraploid C. indicum were generally similar but the tetraploid C. indicum and C. indicum var. aromaticum were found to contain unique sequences in the mitogenomes which also contained previously undescribed open reading frames (ORFs). Across Chrysanthemum mitogenome structure varied greatly but sequences transferred from plastomes in to the mitogenomes were conserved. Finally, differences observed between mitogenome and plastome gene trees may be the result of the difference in the rate of sequence evolution between genes in these two genomes. In total the findings presented here greatly expand the resources for studying Chrysanthemum organellar genome evolution with possible applications to conservation, breeding, and gene banking in the future.
Farmland boundary extraction based on the AttMobile-DeeplabV3+ network and least squares fitting of straight lines
Authors: Lu Hao , Wang Hao , Ma Zhifeng , Ren Yaxin , Fu Weiqiang , Shan Yongchao , Hu Shupeng , Zhang Guangqiang , Meng Zhijun
Published: August 2023

The rapid extraction of farmland boundaries is key to implementing autonomous operation of agricultural machinery. This study addresses the issue of incomplete farmland boundary segmentation in existing methods, proposing a method for obtaining farmland boundaries based on unmanned aerial vehicle (UAV) remote sensing images. The method is divided into two steps: boundary image acquisition and boundary line fitting. To acquire the boundary image, an improved semantic segmentation network, AttMobile-DeeplabV3+, is designed. Subsequently, a boundary tracing function is used to track the boundaries of the binary image. Lastly, the least squares method is used to obtain the fitted boundary line. The paper validates the method through experiments on both crop-covered and non-crop-covered farmland. Experimental results show that on crop-covered and non-crop-covered farmland, the network’s intersection over union (IoU) is 93.25% and 93.14%, respectively; the pixel accuracy (PA) for crop-covered farmland is 96.62%. The average vertical error and average angular error of the extracted boundary line are 0.039 and 1.473°, respectively. This research provides substantial and accurate data support, offering technical assistance for the positioning and path planning of autonomous agricultural machinery.
Effect of varying UAV height on the precise estimation of potato crop growth
Authors: Njane Stephen Njehia , Tsuda Shogo , van Marrewijk Bart M. , Polder Gerrit , Katayama Kenji , Tsuji Hiroyuki
Published: August 2023

A phenotyping pipeline utilising DeepLab was developed for precisely estimating the height, volume, coverage and vegetation indices of European and Japanese varieties. Using this pipeline, the effect of varying UAV height on the precise estimation of potato crop growth properties was evaluated. A UAV fitted with a multispectral camera was flown at a height of 15 m and 30 m in an experimental field where various varieties of potatoes were grown. The properties of plant height, volume and NDVI were evaluated and compared with the manually obtained parameters. Strong linear correlations with R2 of 0.803 and 0.745 were obtained between the UAV obtained plant heights and manually estimated plant height when the UAV was flown at 15 m and 30 m respectively. Furthermore, high linear correlations with an R2 of 0.839 and 0.754 were obtained between the UAV-estimated volume and manually estimated volume when the UAV was flown at 15 m and 30 m respectively. For the vegetation indices, there were no observable differences in the NDVI values obtained from the UAV flown at the two heights. Furthermore, high linear correlations with R2 of 0.930 and 0.931 were obtained between UAV-estimated and manually measured NDVI at 15 m and 30 m respectively. It was found that UAV flown at the lower height had a higher ground sampling distance thus increased resolution leading to more precise estimation of both the height and volume of crops. For vegetation indices, flying the UAV at a higher height had no effect on the precision of NDVI estimates.
RAB7 GTPases as coordinators of plant endomembrane traffic
Authors: Rodriguez-Furlan Cecilia , Borna Rita , Betz Oliver
Published: August 2023

The ras gene from rat brain (RAB) family of small GTPases is highly conserved among eukaryotes and regulates endomembrane trafficking pathways. RAB7, in particular, has been linked to various processes involved in regulating endocytic and autophagic pathways. Plants have several copies of RAB7 proteins that reflect the intricacy of their endomembrane transport systems. RAB7 activity regulates different pathways of endomembrane trafficking in plants: (1) endocytic traffic to the vacuole; (2) biosynthetic traffic to the vacuole; and (3) recycling from the late endosome to the secretory pathway. During certain developmental and stress related processes another pathway becomes activated (4) autophagic trafficking towards the vacuole that is also regulated by RAB7. RAB7s carry out these functions by interacting with various effector proteins. Current research reveals many unexplored RAB7 functions in connection with stress responses. Thus, this review describes a comprehensive summary of current knowledge of plant RAB7’s functions, discusses unresolved challenges, and recommends prospective future research directions.
Low soil available phosphorus level reduces cotton fiber length via osmoregulation
Authors: Sun Miao , Zheng Cangsong , Feng Weina , Shao Jingjing , Pang Chaoyou , Li Pengcheng , Dong Helin
Published: August 2023

Introduction

Phosphorus (P) deficiency hinders cotton (Gossypium hirustum L.) growth and development, seriously affecting lint yield and fiber quality. However, it is still unclear how P fertilizer affects fiber length.

Methods

Therefore, a two-year (2019-2020) pool-culture experiment was conducted using the split-plot design, with two cotton cultivars (CCRI-79; low-P tolerant and SCRC-28; low-P sensitive) as the main plot. Three soil available phosphorus (AP) contents (P0: 3 ± 0.5, P1: 6 ± 0.5, and P2 (control) with 15 ± 0.5 mg kg−1) were applied to the plots, as the subplot, to investigate the impact of soil AP content on cotton fiber elongation and length.

Results

Low soil AP (P0 and P1) decreased the contents of the osmotically active solutes in the cotton fibers, including potassium ions (K+), malate, soluble sugar, and sucrose, by 2.2–10.2%, 14.4–47.3%, 8.7–24.5%, and 10.1–23.4%, respectively, inhibiting the vacuoles from facilitating fiber elongation through osmoregulation. Moreover, soil AP deficiency also reduced the activities of enzymes participated in fiber elongation (plasma membrane H+-ATPase (PM-H+-ATPase), vacuole membrane H+-ATPase (V-H+-ATPase), vacuole membrane H+-translocating inorganic pyrophosphatase (V-H+-PPase), and phosphoenolpyruvate carboxylase (PEPC)). The PM-H+-ATPase, V-H+-ATPase, V-H+-PPase, and PEPC were reduced by 8.4–33.0%, 7.0–33.8%, 14.1–38.4%, and 16.9–40.2%, respectively, inhibiting the transmembrane transport of the osmotically active solutes and acidified conditions for fiber cell wall, thus limiting the fiber elongation. Similarly, soil AP deficiency reduced the fiber length by 0.6–3.0 mm, mainly due to the 3.8–16.3% reduction of the maximum velocity of fiber elongation (VLmax). Additionally, the upper fruiting branch positions (FB10–11) had higher VLmax and longer fiber lengths under low soil AP.

Discussion

Cotton fibers with higher malate content and V-H+-ATPase and V-H+-PPase activities yielded longer fibers. And the malate and soluble sugar contents and V-H+-ATPase and PEPC activities in the SCRC-28's fiber were more sensitive to soil AP deficiency in contrast to those of CCRI-79, possibly explaining the SCRC-28 fiber length sensitivity to low soil AP.
The role of orthographic and phonological processing during reading Chinese sentences: Evidence from eye movements
Authors: Lijuan Zhang , Yingying Zhang , Zhiwei Liu , Lin Li , Sha Li , Jingxin Wang
Published: August 2023

The role of phonological and orthographic processing and their time course during lexical processing and sentence reading remain controversial. By adopting a misspelled-characters disruption paradigm and eye-tracking technique, we manipulated the writing for the first characters of two-character target words to investigate the relative role of orthographic and phonological processing on word recognition in Chinese reading. There are four conditions: (a) correct character, (b) misspelled character with a stroke missing, (c) misspelled homographic character, and (d) misspelled homophonic character. The results showed that homophonic errors caused more disruptions than other conditions in the early (first-pass reading times) and later (total reading time) stages of lexical processing during Chinese reading. Homographic errors and omitted stroke errors lead to equal disruptions at the early stage of word recognition, but homographic errors cause more disruptions at the later stage. These results suggest that orthography plays a dominant role in word recognition during Chinese reading, whereas phonology plays a weaker and more limited role. The direct access and dual-rote hypothesis may well explain the mechanism of lexical processing in Chinese reading.
Conceptualizing the peer contribution in Open Dialogue practice
Authors: Hendy Corrine , Tew Jerry , Carr Sarah
Published: August 2023

In English mental health services, people with their own experience of mental distress have trained as Open Dialogue practitioners and have been employed as peer practitioners, co-working as equals alongside workers with professional backgrounds in Network Meetings. The conceptual underpinnings of the peer practitioner role have been drawn from the principles and relational approach of Intentional Peer Support. These have significant similarities with Open Dialogue, in terms of philosophical and theoretical orientations, with a particular focus on what happens in the “between” of a relational encounter. However, there are also significant differences in how practice principles are conceptualized, particularly around areas such as mutuality and self-disclosure. This article offers an analysis of this conceptual territory drawing on the relevant literature. This is then taken forward with the teasing out of specific practice principles that capture the unique contribution that peer practitioners can bring to Open Dialogue practice. These are derived through discussions that took place in an Action Learning Set for peer practitioners who have been involved in delivering Open Dialogue services in mainstream mental health service settings. This was part of a wider research study entitled Open Dialogue: Development and Evaluation of a Social Network Intervention for Severe Mental Illness (ODDESSI). The principles address how peer practitioners may be particularly well-placed to offer attunement, validation, connection and mutuality, and self-disclosure – and hence how they may be able to contribute an additional dimension to dialogical practice.
Perception of rigidity in three- and four-dimensional spaces
Authors: He Dongcheng , Nguyen Dat-Thanh , Ogmen Haluk , Nishina Shigeaki , Yazdanbakhsh Arash
Published: August 2023

Our brain employs mechanisms to adapt to changing visual conditions. In addition to natural changes in our physiology and those in the environment, our brain is also capable of adapting to “unnatural” changes, such as inverted visual-inputs generated by inverting prisms. In this study, we examined the brain’s capability to adapt to hyperspaces. We generated four spatial-dimensional stimuli in virtual reality and tested the ability to distinguish between rigid and non-rigid motion. We found that observers are able to differentiate rigid and non-rigid motion of hypercubes (4D) with a performance comparable to that obtained using cubes (3D). Moreover, observers’ performance improved when they were provided with more immersive 3D experience but remained robust against increasing shape variations. At this juncture, we characterize our findings as “3 1/2 D perception” since, while we show the ability to extract and use 4D information, we do not have yet evidence of a complete phenomenal 4D experience.
The significance of feeling safe for resilience of adolescents in sub-Saharan Africa
Authors: Bandeira Monica , Graham Marien A. , Ebersöhn Liesel
Published: August 2023

Introduction

Adolescents in sub-Saharan Africa (SSA) are exposed to several challenges and risk factors, linked to historical legacies. Sub-Saharan Africa has one of the highest rates of poverty and inequality in the world, is one of the regions most negatively affected by climate change, performs poorly on many health measures, and has high rates of different forms of violence, especially gender-based violence. These contextual challenges impact adolescent mental health outcomes, preventing them to access resilience-enabling pathways that support positive outcomes despite adversity. This study aimed to contribute to knowledge generation on resilience of young people in the understudied SSA region by investigating which variables directly (or indirectly) affect the resilience of adolescents.

Methods

Purposive sampling was used to collect quantitative survey data from 3,312 adolescents (females = 1,818; males = 1,494) between the ages of 12 and 20 years, participating in interventions implemented by a non-governmental organization, the Regional Psychosocial Support Initiative. Data were collected in Angola (385, 11.6%), Eswatini (128, 3.9%), Kenya (390, 11.8%), Lesotho (349, 10.5%), Mozambique (478, 14.4%), Namibia (296, 8.9%), South Africa (771, 23.3%), Uganda (201, 6.1%), and Zambia (314, 9.5%). The survey collected data on socio-demographic status, resilience (CYRM-R), depression (PHQ-9), self-esteem (Rosenberg Self-Esteem Scale) and feelings of safety (self-developed scale). Mental health was defined as lower levels of depression, higher levels of self-esteem and higher levels of feeling safe. A mediation analysis was conducted to investigate the relationship between the predictors (the socio-demographic variables) and the output (resilience), with the mediators being depression, self-esteem and feeling safe (which all link to mental health).

Results

This study contributes to a gap in knowledge on country-level comparative evidence on significant predictors that impact resilience outcomes (directly or indirectly) for adolescents in sub-Saharan African countries. The results indicate that, when considering all countries collectively, feeling safe is the only predictor that has a significant direct effect on overall resilience and personal resilience, but not on caregiver resilience. When considering each country separately, feeling safe has a direct effect on overall, personal and caregiver resilience for all countries; but not for South Africa and Mozambique.

Discussion

The results provide evidence on which to craft youth development interventions by measuring mediators (depression, self-esteem and feeling safe) and resilience for adolescents in sub-Saharan Africa. The overall results of the present paper point toward a contextually relevant pathway to supporting their resilience, namely, the need to systemically target the creation and/or strengthening of structures that enable adolescents to feel safe.
Early triadic interactions in the first year of life: a systematic review on object-mediated shared encounters
Authors: Mendoza-García Ana , Moreno-Núñez Ana
Published: August 2023

Infants’ early interactions with adults and everyday objects are key to socio-communicative development, but their emergence and development are still under debate. Aiming at describing the diversity of theoretical and methodological approaches on triadicity during the first year of life, we conducted a systematic and qualitative review of recent literature. Following PRISMA 2020 guidelines, we explored the scientific production of recent decades on triadic interactions up to 12 months of age. We initially screened 1943 items from which we obtained a final sample of 51 publications. Studies are usually conducted in laboratory settings, while ecological research is becoming increasingly common, especially in home settings. According to a thematic analysis of the data, we discussed the different perspectives on the origin and conceptualization of triadic interactions, and how they contribute to structuring and facilitating other developmental phenomena, such as the children’s communicative gestures and uses of objects. Prior to the origin of intentional communication, adults facilitate early forms of triadicity based on fostering opportunities for infants’ communication and engagement with both adults and materiality. However, there is a need for further research that explore the potential of early triadic interactions for parenting and early childhood education practises.