bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide association analysis identifies quantitative trait loci for growth and fatness in Diannan small-ear (DSE) pigs
Authors: Liu Mei , Lan Qun , Yang Long , Deng Qiuchun , Wei Taiyun , Zhao Heng , Peng Peiya , Lin Xiaoding , Chen Yuhan , Ma Haiming , Wei Hongjiang , Yin Yulong 
Published: November 2022

Abstract
Background: In the livestock industry, the growth and fatness traits are directly related to production efficiency and economic profits. As for Diannan small-ear (DSE) pigs, a unique indigenous breed, the genetic architecture of growth and fatness traits are still elusive. The aim of this study was to search the genetic loci and candidate genes associated with phenotypic traits in DSE pigs using GWAS based on the Geneseek Porcine 50K SNP Chip data.
Results: A total of 30,648 single nucleotide polymorphisms (SNPs) were detected in 265 DSE pigs. After filtering, 22,146 SNPs were used for Genome-wide association studies (GWAS) analysis. The significant phenotypic correlations among eight important growth traits (body weight, back-fat thickness, and six body measurement traits) were observed. Seven SNPs surpassing the suggestively significant threshold for back height, backfat thickness, chest circumference and cannon bone circumference. Based on gene annotation results, these seven SNPs were mapped to the following candidate genes, VIPR2, SLC10A2, NUCKS1, MCT1, CHCHD3, SMOX and GPR1, which are mainly involved with adipocyte differentiation, lipid metabolism, skeletal muscle development, and average daily weight gain.
Conclusions: Our work offers novel insights into the genetic architecture of swine important economic traits and may play an important role in molecular markers breeding for DSE pig.
Feasibility of applying hyperspectral imaging as a rapid method for estimating potassium content across different plant species datasets
Authors: Baranowski Piotr , Siedliska Anna , Krzyszczak Jaromir , Banach Artur , Siłuch Marcin , Bartmiński Piotr , Wolińska Agnieszka , Tkaczyk Przemysław 
Published: November 2022

Abstract
Purpose The accurate and frequent estimation of the leaf plant potassium concentration enabled by hyperspectral imaging techniques has allowed growers to optimize fertilizer applications and reduce the negative impact on the environment. In this study, we examined the feasibility of using leaf spectral data to accurately estimate the potassium content in sugar beet and celery plants.
Methods Leaf images in the visible and near infrared region (VNIR: 400–1000 nm) and short-wavelength infrared region (SWIR: 1000-2500 nm) were captured by a hyperspectral camera. The potassium content was measured by ordinary destructive laboratory methods. The correlation-based feature selection (CFS) algorithm was implemented to select important wavelengths that carried the most useful information for predicting the potassium content in plant leaves. Four multivariate regression methods were tested to find a model with strong predictive performance.
Results The experimental results showed that the Random Forest (RF) model using 12 bands (425, 443, 479, 599, 631, 662, 798, 863, 897, 921, 1978 and 2053 nm) had the highest accuracy for predicting potassium content in sugar beet, celery and both plant datasets (Rp2 = 0.85, Rp2 = 0.79, and Rp2 = 0.81, respectively).
Conclusion The results confirm the universality of the described method. Although further validation studies involving other plant species are needed, it appears that the spectral reflectance technique could be a promising tool for the rapid, noninvasive and cost-effective estimation of K content in plant leaves, contributing to a significant step forward in precision fertilization management.
MechRetro is a chemical-mechanism-driven graph learning framework for interpretable retrosynthesis prediction and pathway planning
Authors: Wang Yu , Pang Chao , Wang Yuzhe , Jiang Yi , Jin Junru , Liang Sirui , Zou Quan , Wei Leyi 
Published: November 2022

Abstract
Leveraging artificial intelligence for automatic retrosynthesis speeds up organic pathway planning in digital laboratories. However, existing deep learning approaches are unexplainable, like "black box" with few insights, notably limiting their applications in real retrosynthesis scenarios. Here, we propose MechRetro, a chemical-mechanism-driven graph learning framework for interpretable retrosynthetic prediction and pathway planning, which learns several retrosynthetic actions to simulate a reverse reaction via elaborate self-adaptive joint learning. By integrating chemical knowledge as prior information, we design a novel Graph Transformer architecture to adaptively learn discriminative and chemically meaningful molecule representations, highlighting the strong capacity in molecule feature representation learning. We demonstrate that MechRetro outperforms the state-of-the-art approaches for retrosynthetic prediction with a large margin on large-scale benchmark datasets. Extending MechRetro to the multi-step retrosynthesis analysis, we identify efficient synthetic routes via an interpretable reasoning mechanism, leading to a better understanding in the realm of knowledgeable synthetic chemists. We also showcase that MechRetro discovers a novel pathway for protokylol, along with energy scores for uncertainty assessment, broadening the applicability for practical scenarios. Overall, we expect MechRetro to provide meaningful insights for high-throughput automated organic synthesis in drug discovery.
Leaf nutrient resorption and response to soil nutrient availability of different life-form urban garden trees
Authors: Hu Ruyuan , Liu Tairui , Zheng Rongrong , Zhang Yunxiang , Guo Jinping 
Published: November 2022

Abstract
Typical garden tree species are very representative in studying material cycle of urban ecosystem. To study the response of nutrient storage and resorption strategies of different life-form garden tree species to soil nutrients is the key to the sustainability of the urban garden ecosystem. In this research, 9 sample trees out of every 40 garden tree species, which were classified into 2 life forms, were selected for repeated sampling. Nitrogen (N) and phosphorus (P) concentrations in green and senesced leaves and soil nutrient concentrations were investigated, respectively. By comparing nutrient concentrations and resorption of different life-form tree species, the utilization strategies of soil nutrients by different life-form tree species were further analysed. N concentration was substantially higher in deciduous plants with green and senesced leaves than in evergreen ones. Green leaves of deciduous plants had much greater P concentrations than those of evergreen plants, although the difference between the two was not statistically significant. Leaf N:P between different life forms was less than 14, showing a tendency to N limitation. Nitrogen resorption efficiency (NRE) and phosphorous resorption efficiency (PRE) in deciduous plants were significantly higher than in evergreen plants. NRE in deciduous plants was significantly positively correlated with PRE, but not significant in evergreen plants. NuRE of evergreen plants increased as soil N and P concentrations increased, but NuRE of deciduous plants dropped as soil N and P concentrations increased. Compared with deciduous plants, evergreen plants were more sensitive to soil N and P concentrations. These findings have important implications for urban garden trees management practices in this region.
Multiple cystic germinomas presenting as focal dystonia of fingers: a case report
Authors: Han Seungju , Cho Hwa Jin , Lee Bo Lyun , Lee Keun Soo 
Published: November 2022

Abstract
Intracranial germinomas predominantly develop on or near the midline structure in children and young adults and are diagnosed by brain imaging and biopsy. However, if brain imaging and pathology show unusual findings, it becomes difficult to make an accurate diagnosis. Herein, wereport the case of a 14-year-old boy who presented with focal dystonia of the fingers as an initial symptom. Magnetic resonance imaging of the brain showed multifocal heterogeneous lesions with solid and cystic components involving the right frontal lobe, hypothalamus, corpus callosum, left basal ganglia, and left corona radiata. A stereotactic biopsy of the right frontal lesion revealed several granulomatous areas with abundant inflammatory cells. After immunohistochemical staining, the patient was diagnosed with germinoma and treated with chemoradiotherapy according to the Korean Society for Pediatric Neuro-Oncology protocol. The patient has been in complete remission for five years. Germinomas can develop in intracranial off-midline structures, with unusual clinical, radiological, and pathological presentations. It is important to include intracranial germinomas in the differential diagnosis of infiltrative parenchymal tumors, especially in children.
Autophagy limits inflammatory gene expression through targeting of nuclear p65/RelA by LC3 and p62 for lysosomal degradation
Authors: Brischetto Cristina , Mucka Patrick , Kaergel Eva , Scheidereit Claus 
Published: November 2022

Abstract
The interplay between NF-κB signaling and autophagy regulates inflammatory signaling in different cellular contexts and in response to different stimuli. The impairment of this crosstalk may play a role in chronic inflammation and in tumorigenesis. However, the molecular mechanism by which these two pathways interact to regulate the inflammatory response remains elusive. By using biochemical analysis and imaging techniques, we characterized the interaction of the endogenous autophagic marker LC3 and NF-κB/p65 in response to different stress conditions. Following irradiation or TNFα stimulation, nuclear accumulation of LC3 strongly co-localized with p65, suggesting that nuclear p65 is targeted for autophagic degradation. Mechanistically, we showed that the nuclear p65-LC3 interaction is mediated by ubiquitination of the same p65, which is recognized by the cargo receptor p62, resulting in its cytoplasmic export and lysosomal proteolysis. Accordingly, autophagy inhibition by depletion of the essential autophagy gene ATG16L1 selectively stabilizes nuclear p65, in turn enhancing NF-κB gene expression of pro-inflammatory cytokine. Our results revealed a novel molecular mechanism that modulates the NF-κB inflammatory response through nuclear sequestration of the NF-κB/p65 subunit by autophagy proteins. These findings are of importance for developing novel therapeutic strategies against chronic inflammatory diseases displaying defective autophagy and constitutive NF-κB activity.
Targeting cancer-associated fibroblast autophagy renders pancreatic cancer eradicable with immunochemotherapy by inhibiting adaptive immune resistance
Authors: Zhang Xiaozhen , Lao Mengyi , Yang Hanshen , Sun Kang , He Lihong , Li Muchun , Ying Honggang , Chen Yan , Bai Xueli , Liang Tingbo 
Published: November 2022

Abstract

Background
Accumulating evidence suggests that cancer-associated fibroblast (CAF) autophagy is crucial in tumor development and may be a therapeutic target for pancreatic ductal adenocarcinoma (PDAC). However, the role of CAFs autophagy during immune surveillance and cancer immunotherapy is unclear.
Methods
In vivo efficacy and mechanistic studies, using ATG5f/f α-SMAcreERT2 mice, KPC-genetically engineered mouse model (GEMM) mice, C57BL/6 mice and nude mice with KPC cell‑derived orthotopic tumors, employed immune checkpoint blockades (ICBs) and gemcitabine. Mass cytometry (CyTOF), immunohistochemistry (IHC), and flow cytometry analyzed local and systemic alterations in the immunophenotype. The regulatory effects of CAFs autophagy on tumour PD-L1 and its downstream signaling were analyzed by RNA-seq, 4D mass spectrometer (MS), IP-MS, western blotting, GST-pulldown, immunofluorescence (IF), IHC, and flow cytometry.
Results
The present study revealed that the inhibition of CAF autophagy suppresses in vivo tumor development in immune-deficient xenografts. This deletion compromises anti-tumor immunity and anti-tumor efficacy both in vitro and in vivo by upregulating PD-L1 levels in an immune-competent mouse model. A deletion in CAF autophagy reduced the production of interleukin 6, disrupting high desmoplastic TME and decreasing USP14 expression at the transcription level in pancreatic cancer cells. We further identify USP14 as the post-translational factor responsible for downregulating PD-L1 expression by removing K63 linked-ubiquitination at the K280 residue. Finally, chloroquine diphosphate-loaded mesenchymal stem cell (MSC)-liposome, by accurately targeting CAFs, inhibited CAF autophagy, improving the efficacy of immunochemotherapy to combat pancreatic cancer.
Conclusions
Targeting CAFs autophagy disrupt the desmoplastic and immunosuppressive TME to enhance the efficacy of immunochemotherapy by inhibiting adaptive immune resistance.
Easily missed diagnosis of testicular choriocarcinoma with a large retroperitoneal mass as the primary symptom: a case report
Authors: Zhong Bin , Zhang Tao , Dong Yi , Yin Wei , Zhang Jian-Xin , Jin Wei-Dong 
Published: November 2022

Abstract
Testicular choriocarcinoma is a relatively rare malignancy with a highly aggressive nature. Timely diagnosis and treatment can help prolong the survival of patients and even cure them. This case reports a 29-year-old male who presented to the clinic for a month with epigastric pain without complaints of discomfort in the reproductive system. On examination, only a massive mass of approximately 9*10 cm could be palpated in the upper abdomen. When asked about his previous history, the patient only described a history of a right inguinal hernia that had been repaired 12 years earlier without knowing that a testicular descending fixation had been performed at the same time (we only found out afterward by asking his parents). The admission diagnosis was considered the retroperitoneal tumor, which was found to have metastasized to the liver and lungs after the completion of relevant tests. We then performed a CT-guided puncture biopsy of the lung tissue. The biopsy pathology suggested only a tiny heterotypic cell mass, and metastatic cancer was considered. As the symptoms of tumor compression gradually worsened, we nevertheless performed surgical treatment (retroperitoneal tumor resection + partial duodenal resection + enteroanastomosis). The postoperative pathology was choriocarcinoma. It was at this point that we pursued the patient's medical history in detail and, at the same time, performed a testicular ultrasound which revealed a substantial occupation of the right testicle. The diagnosis of testicular choriocarcinoma was finally considered (without pathological confirmation). We wanted to start salvage chemotherapy as soon as possible after surgery. However, the patient's postoperative condition was poor, with rapid progression of hepatopulmonary metastases and gradually increased thyrotoxicosis, and we started salvage chemotherapy (EP regimen: etoposide and cisplatin) on postoperative day 12. However, the patient was forced to stop due to a severe chemotherapy reaction and eventually died of respiratory and cardiac arrest in hospital. For men presenting with a large retroperitoneal mass without reproductive system-related complaints, a detailed history of the inguinal testicle should still be inquired with a detailed physical examination. Meanwhile, laboratory and image tests should be performed to rule out the possibility of a genital tumor to avoid a missed diagnosis that could lead to delayed treatment.
Effect of long-term different land use on soil quality in an Entic Chromoxerert
Authors: Acar Mert , Çelik İsmail , Budak Mesut , Acir Nurullah 
Published: November 2022

Abstract
The differences in land use can potentially affect soil quality. In this respect, this study sought to assess the long-term effect of horticulture and arable lands on the soil quality of the clayey Arıklı soils (Entic Chromoxerert). Physical, chemical, biological and fertility indicators of the soil were analyzed to determine the soil quality index (SQI) using the Fuzzy Analytical Hierarchy Process (FAHP) and Geographical Information System (GIS) for a 225 ha area of the Arıklı soil series. The physical quality received the highest weight in the study. The highest weights in physical, chemical, biological and fertility quality were obtained in AWC, pH, OC and P indicators, respectively. SQI in arable lands ranged from 38.60 to 68.91%, with a mean of 51.77%. Compared to arable, SQI in horticulture varied within a narrower range and had a higher mean SQI (59.87%). In this study, 74.2% of the area had a low SQI and 25.8% had medium SQI. Conventional soil tillage and burning of stubble residues in the arable lands had a statistically negative effect on SQI. Compared to arable, in horticulture BD, OC, AWC, MBC, BGEA and K had better scores thus improving SQI. The results concluded that conventional soil tillage practice should be abandoned and reduced or no-till practices should be adopted.
An enriched environment improves maternal sleep deprivation- induced cognitive deficits via hippocampal histone acetylation
Authors: Zhang Yue-Ming , Wei Ru-Meng , Ni Ming-Zhu , Wu Qi-Tao , Li Yun , Ge Yi-Jun , Kong Xiao-Yi , Li Xue-Yan , Chen Gui-Hai 
Published: November 2022

Abstract
Growing evidence clearly demonstrates that maternal rodents exposure to sleep deprivation during late pregnancy impairs learning and memory in their offspring. Epigenetic mechanisms, particularly histone acetylation, are known to be involved in synaptic plasticity, learning, and memory. We investigated whether cognitive decline induced by sleep deprivation during late-pregnancy is associated with histone acetylation dysfunction and whether this effect could be reversed by an enriched environment (EE). In the present study, pregnant CD-1 mice were exposed to sleep deprivation during the third trimester of pregnancy. After weaning, all offspring were randomly assigned to two subgroups in either a standard environment or an EE. When offspring were three months old, the Morris water maze was used to evaluate hippocampal-dependent learning and memory ability. Molecular biological techniques, including western blot and real-time fluorescence quantitative polymerase chain reaction, were used to examine histone acetylation pathway and synaptic plasticity markers in the hippocampus of offspring. Our results showed that the following were all reversed by EE treatment: maternal sleep deprivation (MSD)-induced cognitive deficits including spatial learning and memory; histone acetylation dysfunction including increased histone deacetylase 2 (HDAC2) and decreased histone acetyltransferase (CBP), and the acetylation levels of H3K9 and H4K12; synaptic plasticity dysfunction including decreased brain-derived neurotrophic factor (BDNF) and postsynaptic density protein-95 (PSD-95). The results suggested that MSD could damage learning ability and memory in offspring via the histone acetylation pathway. This effect could be reversed by EE treatment.
Higher Risk of Car Accidents in Older Patients with Toxoplasma gondii in Yazd Province, Central Iran: A Cohort Study
Authors: Ghasemirad Hamidreza , Aalazade Maryam Sadat , Shariatpanahi Marjan , Owliaey Hamid , Kargar Meraj , Ghasemirad Mohammadreza , Chehrazad Mozhgan , Zare Mahdie 
Published: November 2022

Abstract
Background: Toxoplasmosis appears to be not only an infectious disease with observable symptoms but also one that can affect the social and behavioral aspects of both animals and humans. These social issues, particularly memory dysfunction, may result in dangerous occurrences such as traffic accidents. The purpose of this study was to investigate and compare the rate of traffic accidents among individuals with positive and negative Toxoplasma gondii (T. gondii) serology.
Materials and Methods: This was a retrospective cohort study conducted in the province of Yazd, central Iran, from 2018 to 2021 based on the statistics available in the province’s laboratories. We analyzed the results of the IgG test against Toxoplasma gondii collected in the laboratories of Yazd, Iran, from a total of 360 individuals with valid driver’s licenses who were divided into two groups. One group was Toxoplasma gondii-seropositive, while the other was negative. The traffic police system recorded the statistical analysis of traffic accidents from 2018 to 2021.
Results: The age of the toxoplasmosis group was slightly greater than that of the control group (36.2 and 34.08, respectively; p-value = 0.03). There was no significant difference between the toxoplasmosis group and the control group regarding driving time (p-value = 0.06). The incidence of accidents was greater in the toxoplasmosis group (36.7% vs. 20.6%; p < 0.001). This rate was significantly higher in people aged 35-69 than younger people (40% vs. 32.9%, respectively; p-value = 0.01).
Conclusion: Individuals with latent toxoplasmosis had a significantly higher risk of car accidents than those with negative serology, with the risk increasing with age. Due to contradictory findings regarding the effect of toxoplasmosis on traffic accidents and the higher incidence of toxoplasmosis in Persian cats, these findings should be considered when developing public health strategies.