bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multigenerational mistimed feeding drives circadian reprogramming with an impaired unfolded protein response
Authors: Huang Kai , Zhang Tao , Zhang Wenjun , Gu Yue , Yu Pan , Sun Lanqing , Liu Zhiwei , Wang Tao , Xu Ying 
Published: March 2023

Mistimed food intake in relation to the day/night cycle disrupts the synchrony of circadian rhythms in peripheral tissues and increases the risk of metabolic diseases. However, the health effects over generations have seldom been explored. Here, we established a 10-generation mouse model that was continuously fed with daytime-restricted feeding (DRF). We performed RNA-seq analysis of mouse liver samples obtained every 4 h over a 24 h period from F2, F5 and F10 generations exposed to DRF. Multigenerational DRF programs the diurnal rhythmic transcriptome through a gain or loss of diurnal rhythmicity over generations. Gene ontology (GO) analysis of the differential rhythmic transcriptome revealed that adaptation to persistent DRF is accompanied by impaired endoplasmic reticulum (ER) stress. Consistently, a substantially higher level of folding-deficient proinsulin was observed in F10 liver tissues than in F2 and F5 liver tissues following tail vein injection. Subsequently, tunicamycin induced more hepatocyte death in F10 samples than in F2 and F5 samples. These data demonstrate that mistimed food intake could produce cumulative effects over generations on ER stress sensitivity in mice.
The influence of dust aerosols on solar radiation and near-surface temperature during a severe duststorm transport episode
Authors: Huang Guan , Zhou Yaman , Guo Zijia , Liu Xin , Chen Yonghang , Liu Qiong , Ta Zhijie , Wang Pengtao , He Qing , Gao Jiacheng , Zhang Ying 
Published: March 2023

In the west of China, a rarely seen black storm, with a high intensity of dust aerosols and a large area of influence, occurred from April 26–29, 2015, for the first time, after more than 30 years. Based on the regional climate model (RegCM version 4.6), combined with Moderate Resolution Imaging Spectroradiometer (MODIS) satellite retrieval, meteorological, and environmental data, this work presents the pollution situation, weather background, and backward trajectory during the black storm process. In addition, we analyzed the temporal–spatial distribution of aerosol optical depth (AOD) and the impacts of dust aerosols on solar radiation and near-surface temperature under this extreme weather condition. We discovered that this black storm process was caused by the surface cold high pressure and frontal transit under the background of the upper-air circulation of “two troughs and two ridges.” The pollutants primarily from Xinjiang and the Central Asia region, along with the airflow, entered northern Xinjiang almost simultaneously with the southwest airflow, piled up along the Tianshan Mountains, and then crossed the mountains into southern Xinjiang. In addition, the areas with high AOD were mostly in the desert regions and basins, whereas the low-value areas were mountainous areas with relatively high altitudes due to the effect of geographical and climatic conditions. The AOD from RegCM 4.6 was generally lower, unlike the MODIS AOD. Moreover, the dust aerosols from this black storm caused a significant decline in net short-wave radiation (NSR) both at the top of the atmosphere (TOA) and surface. The cooling effect was more significant in the region with high AOD. For the areas where the AOD was higher than 0.7, the net short-wave radiative forcing of dust aerosols (ADRF) at the surface was above −70 W•m−2; on the other hand, the cooling effect at the TOA was not as significant as that at the surface, with the ADRFTOA being only about a quarter of the ADRFSUR. The ADRFSUR could reduce the near-surface temperature, and the region with a large temperature drop corresponded to the high-value areas of ADRFSUR/AOD. During this black storm, the near-surface temperature response to dust aerosols reached 0.40°C–2.9°C with a significant temperature drop because of cold air.
Rhizosphere soil nutrients and bacterial community diversity of four broad-leaved trees planted under Chinese fir stands with different stocking density levels
Authors: Wang Liyan , Sun Yangyang , Li Jing , Tigabu Mulualem , Xu Qingli , Ma Xiangqing , Li Ming 
Published: March 2023

ObjectiveRhizosphere soil nutrients and bacterial diversity of four broad-leaved tree species underplanted in Chinese fir plantation with different stand density levels were analyzed to reveal characteristics of the rhizosphere soil environment and selection of suitable underplanted tree species.MethodsChinese fir plantation with three density levels (900, 1,200, and 1,875 stems ha–1, respectively) were selected and underplanted with Michelia macclurei, Schima superba, Phoebe zhennan, and Tsoongiodendron odorum. The rhizosphere soil nutrients and bacterial community of the broad-leaved tree species were determined after 4 years.ResultsSignificant differences in rhizosphere nutrient content were detected among different tree density levels, where the contents of total K, available K and available P in 900 stems ha–1 stands were significantly higher than the other stocking density levels. There were also significant differences in the contents of total C, total N, total K, available K and available P in the rhizosphere soils of the four trees species, while there were no significant differences in pH and total P. Rhizosphere soil nutrient contents were higher under S. superba and M. macclurei than under P. zhennan and T. odorum. The rhizosphere soil nutrient contents and bacterial diversity decreased with the increase of stand density, and the bacterial diversity showed significant differences in the rhizosphere soils of P. zhennan, T. odorum and S. superba when underplanted in different stand densities. The bacterial diversity was positively correlated with the available P content of rhizosphere soils, suggesting that soil available P content plays an important role in shaping the structure of bacterial community.ConclusionThe nutrient contents and bacterial diversity of rhizosphere soils of underplated broad-leaved species decreased with increasing stand density of Chinese fir plantation. Rhizosphere soils of M. macclurei and S. superba were rich in nutrient contents and bacterial diversity. Thus, low density of Chinese fir plantation (900 stems ha–1) underplanted with M. macclurei and S. superba is suitable for the establishment of mixed forest, which will facilitate better tree growth and maintaining soil fertility to realize sustainable management of forests.
Gene-wide significant association analyses of DNMT1 genetic variants with Parkinson’s disease
Authors: Wang Jian-Yong , Cui Lei , Shi Hong-Yi , Chen Ling-Hao , Jin Ren-Wei , Jiang Xiao-Xia , Chen Zhu-Ling , Zhu Jian-Hong , Zhang Xiong 
Published: March 2023

Background: DNA methylation plays an important role in Parkinson’s disease (PD) pathogenesis. DNA methyltransferase 1 (DNMT1) is critical for maintaining DNA methylation in mammals. The link between DNMT1 polymorphisms and PD remains elusive.Methods: The DNMT1 gene contained a total of 28 single nucleotide polymorphisms (SNPs). Four representing tag-SNPs (rs16999593, rs2162560, rs11880553, and rs9305012) were identified and genotyped in a Han Chinese population comprising 712 PD patients and 696 controls. Association analyses were performed at gene-wide significance (p &lt; 1.8 × 10−3).Results: Rs9305012, but not the other 3 tag-SNPs, was gene-wide significantly associated with PD risk (p = 0.8 × 10−3). The rs9305012/C was a protective allele against PD (p = 1.5 × 10−3, OR 0.786, 95% CI 0.677–0.912). No significant association was observed in individual genders or PD subtypes. Haplotypes of the 4 tag-SNPs showed a significant overall distribution difference between PD patients and controls (p &lt; 1 × 10−4). The 3-allele ACC module in the order of rs2162560, rs11880553, and rs9305012 was the highest-risk haplotype associated with PD (p &lt; 1 × 10−4, OR 2.439, 95% CI 1.563–3.704). Rs9305012 displayed certain probability to affect transcription factor binding and target gene expression based on functional annotation analyses.Conclusion: The DNMT1 variant rs9305012 together with its haplotypes may gene-wide significantly modulate PD susceptibility. Our results support a role of DNMT1 in PD pathogenesis and provide novel insights into the genetic connection in between.
Immune checkpoint inhibitors related respiratory disorders in patients with lung cancer: A meta-analysis of randomized controlled trials
Authors: Liu Han , Luo Sean X. , Jie Jing , Peng Liping , Wang Shuai , Song Lei 
Published: March 2023

BackgroundIn recent years, immune checkpoint inhibitors (ICIs) had extremely rapid growth in anti-cancer and improved outcomes of many malignancies, specifically lung cancer. However, the incidence of ICIs-related adverse events also raised. Using this meta-analysis, ICIs-related respiratory disorders were investigated in lung cancer patients.MethodsUsing Cochrane Library, Embase, and PubMed databases, we performed an integrated search for randomized controlled trials (RCTs) to compare respiratory disorders among different regimens. The data was prepared with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) reporting guideline, and the quality of included studies was evaluated based on the Cochrane manual.ResultsIn total, 22 RCTs were involved in this meta-analysis. Compared with ICIs, chemotherapy reduced the risk of interstitial lung disease (p = 0.03; SMD: 2.81; 95% CI: 1.08, 7.27), pleural effusion (p = 0.002; SMD: 2.12; 95% CI: 1.32, 3.42), and pneumonitis (p &lt; 0.00001; SMD: 9.23; 95% CI: 4.57, 18.64). ICIs plus chemotherapy could provide a higher probability for patients to suffer pneumonitis than chemotherapy (p = 0.01; SMD: 1.96; 95% CI: 1.17, 3.28). In addition, single ICI brought a lower likelihood for patients suffering pneumonitis than double ICIs (p = 0.004; SMD: 2.17; 95% CI: 1.27, 3.69).ConclusionICIs-based treatment, such as ICIs alone, ICIs plus chemotherapy and double ICIs, can raise the incidences of some respiratory disorders in patients with lung cancer. It suggests that ICIs should be conducted based on a comprehensive consideration to prevent ICIs-related respiratory disorders. To a certain degree, this study might be provided to the clinician as a reference for ICIs practice.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022378901, identifier (CRD42022378901).
Hypothermic machine perfusion alleviates ischemia-reperfusion injury of intestinal transplantation in pigs
Authors: Hou Wen , Yang Shuang , Lu Jiansen , Shi Yuan , Chen Jing , Chen Decheng , Wang Fei , Liu Lei 
Published: March 2023

BackgroundIntestinal transplantation (IT) has become an important procedure for the treatment of irreversible intestinal failure. However, IT is extremely vulnerable to ischemia–reperfusion injury (IRI). Due to the limitations of static cold storage (SCS), hypothermic machine perfusion (HMP) is rapidly gaining popularity. In this study, the intestinal HMP system is established and HMP is compared with SCS.MethodsAn intestinal HMP system was built. Ten miniature pigs were randomly divided into the HMP and SCS groups, and their intestines were perfused using the HMP device and SCS, respectively, followed by orthotopic auto-transplantation. Analysis was done on the grafts between the two groups.ResultsOperation success rates of the surgery were 100% in both groups. The 7-day survival rate was 100% in the HMP group, which was significantly higher than that of the SCS group (20%, P&lt; 0.05). The pathological results showed that fewer injuries of grafts were in the HMP group. Endotoxin (ET), IL-1, IL-6, IFN-γ and TNF-α levels in the HMP group were significantly lower than in the SCS group (P&lt;0.05), whereas IL-10 levels were significantly higher (P&lt;0.05).The intestinal expression levels of ZO-1 and Occludin were higher in the HMP group compared to the SCS group, whereas Toll-like receptor 4 (TLR4), nuclear factor kappa B (NFκB), and caspase-3 were lower.ConclusionsIn this study, we established a stable intestinal HMP system and demonstrated that HMP could significantly alleviate intestinal IRI and improve the outcome after IT.
Population genetics of zig-zag eel (Mastacembelus armatus) uncover gene flow between an isolated island and the mainland China
Authors: Yang Yexin , Wang Yuanyuan , Wu Yuli , Liu Yi , Liu Chao , Jiang Zhiyong , Mu Xidong 
Published: March 2023

IntroductionMastacembelus armatus is a commercially valuable fish, normally distributed in southern China and Southeast Asia. The natural population size of M. armatus is shrinking in recent years because of overfishing and habitat loss. In order to clarify the genetic diversity and differentiation of M. armatus populations, we collected 114 samples from eight populations in southern China and Vietnam and analyzed their population structure using nuclear ribosomal DNA sequences, the concatenated 18S and ITS2 regions.MethodsGenomic DNA from the fin clip was extracted and sequenced on an Illumina novaseq 6000 (Illumina, USA) high-throughput sequencing platform in accordance with the manufacturer’s instructions. After assembly and annotation, haplotype diversity, TCS network analysis, AMOVA analysis, population pairwise genetic distances, and UPGMA tree construction were conducted based on the concatenated sequences of 18S and ITS2.Results and discussionIn total, eleven nrDNA haplotypes were detected based on the concatenated sequences of 18S and ITS2. Amongst, three haplotypes were the main haplotypes, as representatives of three corresponding Clusters. There were two major Clusters in China, however, the Cluster in Vietnam was significantly divergent from the other two in China, likely due to the lack of river connection between China and Vietnam. Interestingly, based on low FST value, we found that gene flow occurred between the isolated island, Hainan Province, and the mainland China of Guangxi Province, probably as a result of exposed continental shelf connected them during glacial periods. In general, combing our data and literature data, genetic diversity and differentiation of M. armatus populations are relatively high regardless of spatial scale, although their natural population size is declining. This suggests that it is not too late to adopt measures to protect M. armatus, which benefits not only species itself but also the whole ecosystem.
Class 1 integrons and multiple mobile genetic elements in clinical isolates of the Klebsiella pneumoniae complex from a tertiary hospital in eastern China
Authors: Wang Lan , Zhu Mei , Yan Chunxia , Zhang Yanfang , He Xuying , Wu Lin , Xu Jiefeng , Lu Junwan , Bao Qiyu , Hu Yunliang , Xu Teng , Liang Jialei 
Published: March 2023

BackgroundThe emergence of highly drug-resistant K. pneumoniae, has become a major public health challenge. In this work, we aim to investigate the diversity of species and sequence types (STs) of clinical Klebsiella isolates and to characterize the prevalence and structure of class 1 integrons.MethodsBased on the whole genome sequencing, species identification was performed by 16S rRNA gene homology and average nucleotide identity (ANI) analysis. STs were determined in accordance with the international MLST schemes for K. pneumoniae and K. variicola. Integron characterization and comparative genomic analysis were performed using various bioinformatic tools.ResultsSpecies identification showed that the 167 isolates belonged to four species: K. pneumoniae, K. variicola subsp. variicola, K. quasipneumoniae and K. aerogenes. Thirty-six known and 5 novel STs were identified in K. pneumoniae, and 10 novel STs were identified in K. variicola subsp. variicola. Class 1 integrons were found in 57.49% (96/167) of the isolates, and a total of 169 resistance gene cassettes encoding 19 types of resistance genes, including carbapenem resistance gene (blaIPM-4) and class D β-lactamases gene (blaOXA-1 and blaOXA-10), were identified. Among the 17 complete genomes, 29 class 1 integrons from 12 groups were found, only 1 group was encoded on chromosomes. Interestingly, one plasmid (pKP167-261) carrying two copies of approximately 19-kb IS26-Int1 complex resistance region that contains an integron and a multidrug resistance gene fragment.ConclusionThe results of this work demonstrated that the species and STs of the clinical Klebsiella isolates were more complex by the whole genome sequence analysis than by the traditional laboratory methods. Finding of the new structure of MGEs related to the resistance genes indicates the great importance of deeply exploring the molecular mechanisms of bacterial multidrug resistance.
Altered topological properties of functional brain networks in patients with first episode, late-life depression before and after antidepressant treatment
Authors: Liu Chaomeng , Li Li , Pan Weigang , Zhu Dandi , Lian Siyuan , Liu Yi , Ren Li , Mao Peixian , Ren Yanping , Ma Xin 
Published: March 2023

ObjectivesTo preliminarily explore the functional activity and information integration of the brains under resting state based on graph theory in patients with first-episode, late-life depression (LLD) before and after antidepressant treatment.MethodsA total of 50 patients with first-episode LLD and 40 non-depressed controls (NCs) were recruited for the present research. Participants underwent the RBANS test, the 17-item Hamilton depression rating scale (HAMD-17) test, and resting-state functional MRI scans (rs-fMRI). The RBANS test consists of 12 sub-tests that contribute to a total score and index scores across the five domains: immediate memory, visuospatial/constructional, language, attention, and delayed memory. Escitalopram or sertraline was adopted for treating depression, and the dosage of the drug was adjusted by the experienced psychiatrists. Of the 50 LLD patients, 27 cases who completed 6-month follow-ups and 27 NCs matched with age, sex, and education level were included for the final statistical analysis.ResultsThere were significant differences in RBANS total score, immediate memory, visuospatial/constructional, language, attention, and delayed memory between LLD baseline group and NCs group (P &lt; 0.05). Considering the global attribute indicators, the clustering coefficient of global indicators was lower in the LLD baseline group than in the NCs group, and the small-world attribute of functional brain networks existed in all three groups. The degree centrality and node efficiency of some brains were lower in the LLD baseline group than in the NCs group. After 6 months of antidepressant therapy, the scores of HAMD-17, immediate memory, language, and delayed memory in the LLD follow-up group were higher than those in the LLD baseline group. Compared with the LLD baseline group, the degree centrality and node efficiency of some brains in the cognitive control network were decreased in the LLD follow-up group.ConclusionsThe ability to integrate and divide labor of functional brain networks declines in LLD patients and linked with the depression severity. After the relief of depressive symptoms, the small-world attribute of functional brain networks in LLD patients persists. However, the information transmission efficiency and centrality of some brain regions continue to decline over time, perhaps related to their progressive cognitive impairment.
Novel mutations in the ABCD1 gene caused adrenomyeloneuropathy in the Chinese population
Authors: He Raoli , Zhang Jian , Huang Tianwen , Cai Guoen , Zou Zhangyu , Ye Qinyong 
Published: March 2023

BackgroundAs a rare genetic disease, adrenomyeloneuropathy (AMN) is the most common adult phenotype of X-linked adrenoleukodystrophy (X-ALD). Mutations in the ABCD1 gene have been identified to cause AMN.MethodsWe applied clinical evaluation, laboratory tests, and neuroimaging on three patients with progressive spastic paraparesis. In genetic analysis, we investigated ABCD1 gene mutations by whole-exome sequencing and Sanger sequencing. Bioinformatics tools were used to predict the effects of identified ABCD1 mutations on the protein.ResultsAll three patients were men with adult-onset disease, mainly characterized by progressive spastic paraparesis. Among them, two patients had peripheral neuropathy and one patient had signs of adrenal insufficiency. All three patients showed cerebral involvement on brain MRI, while two patients were found with diffuse cord atrophy on spinal MRI. High-VLCFA levels in plasma, as well as C24:0/C22:0 and C26:0/C22:0 ratios, were found in all three patients. In addition, three different ABCD1 mutations were identified in three unrelated Chinese families, including one known mutation (c.1415_1416delAG) and two novel mutations (c.217C&gt;T and c.160_170delACGCAGGAGGC). Based on the clinical assessment, radiographic, biochemical, and genetic testing, the final diagnosis was AMN in these patients with spastic paraparesis.ConclusionThis study reported three patients with AMN and identified two novel mutations in the ABCD1 in the Chinese population. Our finding emphasized that X-ALD is an important cause of adult-onset spastic paraplegia. Thus, neuroimaging, VLCFA testing, and especially the detection of the ABCD1 gene have important implications for the etiological diagnosis of adult patients with spastic paraplegia.