bluuebunny/crossref_metadata_2025_split huggingface dataset:
Luminescence characteristics of muddy sediments in the turbidity maximum zone of the Yangtze River mouth and implications for the depositional mechanisms
Authors: Niu Wenlei , Nian Xiaomei , Zhao Luo , Zhai Yang , Meadows Michael E , Zhang Wentong , Wang Zhanghua 
Published: August 2022

Muddy sediments are the most prominent constituents of sedimentary successions in tide-dominated river deltas and have highly complex depositional mechanisms. In this study, we performed fine-grained (4–11 μm) quartz optically stimulated luminescence (OSL) dating on two sediment cores collected at a shipwreck site in the turbidity maximum zone (TMZ) of the modern Yangtze River mouth, China, which were compared with previously published dating results including 45–63 um quartz OSL dating, radionuclide dating, porcelain artifacts recovered from the wreck, macro-plastics, and the morphological history recorded in marine charts. We investigate the luminescence characteristics of muddy sediments trapped in the TMZ and discuss the implications of OSL ages in understanding depositional mechanisms in tide-dominated river mouths. The results indicate that most OSL ages of muddy sediments in the delta front setting are overestimated compared with other dating methods. We suggest that OSL age overestimation reflects the trapping of sediments from offshore in the TMZ imported by saltwater intrusions and storm events. The offshore inputs contain high percentages of residual luminescence and are also subjected to incomplete bleaching due to turbid water conditions and near-bed dispersal in the salt-wedge river mouth. We thus suggest that the reduced bleaching efficiency of muddy sediments in delta front settings needs to be accounted for in understanding sedimentary processes and distinguishing between different sedimentary facies in tide-dominated river mouths. Furthermore, we propose that differences in quartz OSL ages of fine- and medium-grained fractions may arise in response to extreme events.
Cuproptosis-related lncRNA: Prediction of prognosis and subtype determination in clear cell renal cell carcinoma
Authors: Huili Youlong , Nie Shiwen , Zhang Liguo , Yao Anliang , Liu Jian , Wang Yong , Wang Lei , Cao Fenghong 
Published: August 2022

Background: Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cell carcinoma, accounting for approximately 70% of all RCC cases. Cuproptosis, a novel mechanism of cell death, may be a potential target for intervention in tumor development.Methods: Cuproptosis-related prognostic lncRNAs were identified by co-expression analysis and univariable Cox regression. Five lncRNA profiles were obtained by LASSO regression analysis, and a model with high accuracy was constructed to assess the prognosis of ccRCC patients based on these cuproptosis-related lncRNAs. Survival analysis and time-dependent ROC curves were performed for the α and β groups, and the results confirmed the high accuracy of the model in predicting the prognosis of ccRCC patients. Immunoassay, principal component analysis (PCA), and drug sensitivity analysis were also performed for different risk categories. Finally, we classified ccRCC patients into two different subtypes by consistent class clustering, and performed immune checkpoint activation, tumor microenvironment analysis, PCA, and drug sensitivity analysis for different subtypes.Results: We developed a prognostic model using five cuproptosis-associated lncRNAs, which was found to be highly accurate in predicting ccRCC patients’ prognosis. Immunotherapy may be more beneficial to the hyper-risk category and the C2 subtype.Conclusion: The results of this study confirm that five cuproptosis-associated lncRNAs can be used as potential prognostic markers for ccRCC.
Comprehensive genome sequence analysis of the devastating tobacco bacterial phytopathogen Ralstonia solanacearum strain FJ1003
Authors: Chen Kun , Zhuang Yuhui , Wang Lihui , Li Huaqi , Lei Taijie , Li Mengke , Gao Meijia , Wei Jiaxian , Dang Hao , Raza Ali , Yang Qiang , Sharif Yasir , Yang Huan , Zhang Chong , Zou Huasong , Zhuang Weijian 
Published: August 2022

Due to its high genetic diversity and broad host range, Ralstonia solanacearum, the causative phytopathogen of the bacterial wilt (BW) disease, is considered a “species complex”. The R. solanacearum strain FJ1003 belonged to phylotype I, and was isolated from the Fuzhou City in Fujian Province of China. The pathogen show host specificity and infects tobacco, especially in the tropical and subtropical regions. To elucidate the pathogenic mechanisms of FJ1003 infecting tobacco, a complete genome sequencing of FJ1003 using single-molecule real-time (SMRT) sequencing technology was performed. The full genome size of FJ1003 was 5.90 Mb (GC%, 67%), containing the chromosome (3.7 Mb), megaplasmid (2.0 Mb), and small plasmid (0.2 Mb). A total of 5133 coding genes (3446 and 1687 genes for chromosome and megaplasmid, respectively) were predicted. A comparative genomic analysis with other strains having the same and different hosts showed that the FJ1003 strain had 90 specific genes, possibly related to the host range of R. solanacearum. Horizontal gene transfer (HGT) was widespread in the genome. A type Ⅲ effector protein (Rs_T3E_Hyp14) was present on both the prophage and genetic island (GI), suggesting that this gene might have been acquired from other bacteria via HGT. The Rs_T3E_Hyp14 was proved to be a virulence factor in the pathogenic process of R. solanacearum through gene knockout strategy, which affects the pathogenicity and colonization ability of R. solanacearum in the host. Therefore, this study will improve our understanding of the virulence of R. solanacearum and provide a theoretical basis for tobacco disease resistance breeding.
Identification and characterization of a novel homozygous splice site variant of PATL2 causing female infertility due to oocyte germinal vesicle arrest
Authors: Sun Liwei , Tong Keya , Liu Weiwei , Tian Yin , Yang Sheng , Zhou Danni , Liu Dongyun , Huang Guoning , Li Jingyu 
Published: August 2022

Background: This study aims to describe clinical and diagnostic phenotype and identify pathogenic variants of a female with unknown causes of infertility.Methods: Clinical assessment was performed for the phenotype diagnosis. Whole-exome sequencing (WES) and the followed cDNA-PCR sequencing were applied to identify the pathogenic variant and investigate the potentially aberrant mRNA splicing event. The pathogenicity of the variant was analysed using multiple in silico prediction tools, including the 3D protein remodelling. Quantitative RT-PCR (qRT-PCR) was performed to measure PATL2 mRNA expression in the peripheral blood leukocytes of the proband and controls.Results: The proband was diagnosed with the female infertility due to oocyte germinal vesicle (GV) arrest. A novel homozygous splice site variant of PATL2 (NM_001145112.2, c.871-1G&gt;A), inherited from her asymptomatic heterozygous parents, was detected by WES. Sequencing of cDNA amplification products demonstrated that this variant resulted in the exon 10 skipping and in-frame loss of 54 nucleotides in the PATL2 transcript. Quantitative RT-PCR suggested that the mutant transcript escape the mRNA degradation.Conclusion: We identified a novel pathogenic homozygous splice site of PATL2 (c.871-1G&gt;A) underlying the oocyte GV arrest phenotype and elucidated its molecular mechanism. This study expands the variant spectrum of PATL2 and benefits our understanding of its genotype-phenotype correlations.
Identification of ISCA1 as novel immunological and prognostic biomarker for bladder cancer
Authors: Zhou Renlong , Peng Naixiong , Li Wei 
Published: August 2022

BackgroundIron-sulfur cluster assembly 1 (ISCA1) has a significant effect on respiratory complexes and energy metabolism. Although there is some evidence that ISCA1 gene expression impacts energy metabolism and consequently has a role in tumorigenesis and cancer metastasis in different types of malignancies, no systematic pan-cancer study of the ISCA1 has been conducted. As a result, we sought to investigate ISCA1’s predictive value in 33 cancer types as well as its possible immunological function.MethodsWe included the pan-cancer expression profile dataset and clinical data from the public database. Firstly, the single-sample Gene Set Enrichment Analysis (ssGSEa) approach was employed for analyzing the immune link in pan-cancer, while the limma package was utilized for analyzing the differential expression in cancer species. Subsequently, ciberport, MCP-counter, TIMER2, quanTIseq, and xCELL were employed for analyzing bladder cancer (BLCA)’s immune infiltration. Least absolute shrinkage and selection operator (Lasso) were employed for choosing the best gene to develop the immune risk scoring model.ResultsISCA1 gene expression was positively related to four immune signatures (chemokine, immunostimulator, MHC, and receptor) in BLCA. Samples of BLCA were sorted into two groups by the best cut-off of ISCA1 expression degree. The group with a high level of ISCA1 expression had a higher risk, suggesting that the ISCA1 gene was a risk factor in BLCA, and its high expression resulted in a poorer prognosis. Additionally, it was noted that ISCA1 was positively linked with these immune checkpoints. Moreover, there was a considerable positive link between ISCA1 and different immune properties in subgroups with different immune checkpoint inhibiting responses. Finally, an immune risk scoring model was made and it showed a better score in comparison to that of TIDE.ConclusionISCA1 can be a prognostic marker for a variety of cancers, particularly BLCA. Its high level of expression has a deleterious impact on the prognosis of BLCA patients. This strongly shows that ISCA1 is a significant prognostic factor for BLCA and that it could be used as a new prognostic detection target and treatment approach.
Experimental diesel spray characterization of the medium-duty injector with single- and multi-hole nozzle configurations under non-reacting, non-vaporizing conditions
Authors: Park Ji-Woong , Jouzdani Shirin , Tzanetakis Tom , Schmidt Henry , Atkinson William , Naber Jeffrey , Pei Yuanjiang , Tao Feng , Garg Rajesh , Langenderfer David , Zhang Yu , Som Sibendu 
Published: August 2022

Characteristics of diesel sprays injected through Cummins medium-duty ISB injectors were studied experimentally in an optically accessible constant-volume combustion vessel. The experiments were performed with ultra-low-sulfur diesel (ULSD) under non-reacting and non-vaporizing conditions, including different ambient gas densities (23–65 kg/m3), injection pressures (500–1,500 bar), and injection duration times (0.5–1.5 ms). The ambient temperature of the vessel was maintained at a room temperature of 313 K for all the tests. A systematic comparison was made between single-hole (SH) and multi-hole (MH) injector configurations. A plume-to-plume variation in spray penetration length was observed for various operating conditions. A substantial deviation was observed for a specific hole against the averaged plume, indicating that arbitrary selection of the plume index may result in inaccurate spray characterization of the MH injector. The penetration length of the MH injector was shorter than that of the SH injector under the same operating conditions, indicating that a spray model calibrated on SH injector data may not accurately predict the transient spray behavior of the MH injector in practical engine simulations. A square-root correlation of the spray penetration length was applied for both the SH and MH injectors. The spray penetration length and dispersion angles of the ISB SH injector were also compared with those of the heavy-duty Cummins ISX SH injector. While the ISX SH injector showed a faster penetration than the ISB SH injector, the dispersion angle was similar. The differences in spray penetration between ISB and ISX injectors followed the expected trend based on their nozzle hole diameters.
Impact of DSA and immunosuppression minimization on rejection, graft, and patient survival after simultaneous liver–kidney transplantation
Authors: Dekeyser Manon , Taupin Jean-Luc , Elias Michelle , Ichaï Philippe , Herr Florence , Boudon Marc , Brunel Melanie , Sa cunha Antonio , Coilly Audrey , Saliba Faouzi , Durrbach Antoine 
Published: August 2022

BackgroundAcute rejection rate is low after simultaneous liver–kidney transplantation (SLKT), leading some groups to minimize immunosuppressive (IS) regimens. However, the impact of preformed (pDSA) or de novo donor-specific antibodies (dnDSA) on the graft remains unclear.MethodsWe performed a retrospective analysis of 102 consecutive SLKT patients to study the impact of anti-HLA antibodies.ResultsAnti-HLA antibodies were detected in 75 recipients (class I 23.8%, both classes I and II 23.8%, and class II 14.3%). In total, 42.8% of the patients had pDSA and 21.7% developed dnDSA. Overall patient survival at 1–3 and 5 years, was respectively 88, 84, and 80%. Acute rejection occurred respectively in 3 (2.9%) liver and 6 kidney (5.9%) recipients. pDSA with titers over 10,000 mean fluorescence intensity (14.3%) was associated with lower patient survival (40 vs. 82%) but not with acute rejection. In a multivariable Cox regression analysis, the risk of death was associated with maleness, the highest titer of pDSA (p &lt; 0.0007) or the sum of pDSA &gt;10,000. Renal function did not differ between patients with class I pDSA (p = 0.631) and those with class II pDSA (p = 0.112) or between patients with and without a positive cross-match (p = 0.842). dnDSA were not associated with acute rejection, graft dysfunction or patient survival. IS minimization was not associated with rejection, graft dysfunction or death.ConclusionIn SLKT, high levels of pDSA &gt;10,000 were associated with lower patient survival, but not rejection or graft survival. Minimization of maintenance immunosuppression regimen was not associated with a poorer outcome.
Retinal microvasculature and imaging markers of brain frailty in normal aging adults
Authors: Tao Wendan , Kwapong William Robert , Xie Jianyang , Wang Zetao , Guo Xiaonan , Liu Junfeng , Ye Chen , Wu Bo , Zhao Yitian , Liu Ming 
Published: August 2022

BackgroundThe retina and brain share a similar embryologic origin, blood barriers, and microvasculature features. Thus, retinal imaging has been of interest in the aging population to help in the early detection of brain disorders. Imaging evaluation of brain frailty, including brain atrophy and markers of cerebral small vessel disease (CSVD), could reflect brain health in normal aging, but is costly and time-consuming. In this study, we aimed to evaluate the retinal microvasculature and its association with radiological indicators of brain frailty in normal aging adults.MethodsSwept-source optical coherence tomography angiography (SS-OCTA) and 3T-MRI brain scanning were performed on normal aging adults (aged ≥ 50 years). Using a deep learning algorithm, microvascular tortuosity (VT) and fractal dimension parameter (Dbox) were used to evaluate the superficial vascular complex (SVC) and deep vascular complex (DVC) of the retina. MRI markers of brain frailty include brain volumetric measures and CSVD markers that were assessed.ResultsOf the 139 normal aging individuals included, the mean age was 59.43 ± 7.31 years, and 64.0% (n = 89) of the participants were females. After adjustment of age, sex, and vascular risk factors, Dbox in the DVC showed a significant association with the presence of lacunes (β = 0.58, p = 0.007), while VT in the SVC significantly correlated with the score of cerebral deep white matter hyperintensity (β = 0.31, p = 0.027). No correlations were found between brain volumes and retinal microvasculature changes (P &gt; 0.05).ConclusionOur report suggests that imaging of the retinal microvasculature may give clues to brain frailty in the aging population.
Association between playing cards/mahjong and risk of incident dementia among the Chinese older adults: a prospective cohort study
Authors: Tian Gang , Shuai Jingliang , Li Rui , Zhou Tong , Shi Yan , Cheng Gang , Yan Yan 
Published: August 2022

Objectives: Studies have shown that the frequent participation of the elderly in cognitive stimulation activities is associated with a reduced risk of dementia, but the prospective evidence of this association is limited.Methods: We used data from a prospective cohort study of the Chinese Longitudinal Healthy Longevity Survey (CLHLS), and included 11,821 community-living Chinese individuals aged 65 years or older at 2008 baseline who were free of dementia, and were followed up every 2–3 years until 2018. Cox proportional hazards models were applied to generate the hazard ratios (HRs) and 95% confidence intervals (CIs) for analyzing the associations between the frequency of playing cards/mahjong and the incidence of dementia.Results: A total of 821 participants were diagnosed with dementia during the 10-year follow-up. The average age of patients with dementia and non dementia were 89 and 90 years old, respectively. Compared with participants who rarely or never played cards/mahjong, participants who played cards/mahjong almost every day had a significantly lower risk of dementia (HR = 0.63; 95%CI, 0.42–0.95) after the multivariable-adjusted model. Similar results were observed in subgroup analyses based on sex (male: HR = 0.52, 0.28–0.96; female: HR = 0.62, 0.36–0.98), age (&lt;85years: HR = 0.55, 0.32–0.89), regularly exercise (yes: HR = 0.44, 0.28–0.87) and MMSE score [above median (25): HR = 0.66, 0.41–0.92].Conclusions: Playing cards/mahjong in the elderly may contribute to reducing the risk of dementia.
Transvenous embolization of hemorrhagic brain arteriovenous malformations: Case reports and literature review
Authors: Chen Xiheng , Zhang Longhui , Zhu Haoyu , Wang Yajie , Fan Liwei , Ni Leying , Dong Linggen , Lv Ming , Liu Peng 
Published: August 2022

IntroductionTransvenous embolization (TVE) has been proven to be safe and feasible as an alternative management of brain arteriovenous malformations (AVMs). We presented four patients with a hemorrhagic brain AVM who underwent TVE and reviewed the relevant literature.MethodsFour patients underwent TVE of a hemorrhagic brain AVM in our center between July 2019 and July 2020. We retrospectively collected and analyzed the clinical and imaging data of these patients and those reported in previously published studies.ResultsFour patients with a hemorrhagic brain AVM were included. Nidus sizes ranged from 0.79 to 2.56 cm. Spetzler-Martin grade ranged from grade II to grade III. The AVM nidus was located in a deep brain region in three patients. One patient underwent TVE alone and three underwent combined transarterial and transvenous approaches. Digital subtraction angiography (DSA) demonstrated complete obliteration of the vascular malformation after embolization in all four patients. Three patients were independent [modified Rankin Scale (mRS) score ≤ 2] at discharge. All four patients were independent at the last follow-up. AVM obliteration was confirmed in all four patients at the last angiographic follow-up.ConclusionTransvenous embolization can be used as an alternative treatment for contemporary management of brain AVMs, appropriate patient selection is essential to achieve a good clinical outcome.
Brainstem evoked auditory potentials in tinnitus: A best-evidence synthesis and meta-analysis
Authors: Jacxsens Laura , De Pauw Joke , Cardon Emilie , van der Wal Annemarie , Jacquemin Laure , Gilles Annick , Michiels Sarah , Van Rompaey Vincent , Lammers Marc J. W. , De Hertogh Willem 
Published: August 2022

IntroductionAccumulating evidence suggests a role of the brainstem in tinnitus generation and modulation. Several studies in chronic tinnitus patients have reported latency and amplitude changes of the different peaks of the auditory brainstem response, possibly reflecting neural changes or altered activity. The aim of the systematic review was to assess if alterations within the brainstem of chronic tinnitus patients are reflected in short- and middle-latency auditory evoked potentials (AEPs).MethodsA systematic review was performed and reported according to the PRISMA guidelines. Studies evaluating short- and middle-latency AEPs in tinnitus patients and controls were included. Two independent reviewers conducted the study selection, data extraction, and risk of bias assessment. Meta-analysis was performed using a multivariate meta-analytic model.ResultsTwenty-seven cross-sectional studies were included. Multivariate meta-analysis revealed that in tinnitus patients with normal hearing, significantly longer latencies of auditory brainstem response (ABR) waves I (SMD = 0.66 ms, p &lt; 0.001), III (SMD = 0.43 ms, p &lt; 0.001), and V (SMD = 0.47 ms, p &lt; 0.01) are present. The results regarding possible changes in middle-latency responses (MLRs) and frequency-following responses (FFRs) were inconclusive.DiscussionThe discovered changes in short-latency AEPs reflect alterations at brainstem level in tinnitus patients. More specifically, the prolonged ABR latencies could possibly be explained by high frequency sensorineural hearing loss, or other modulating factors such as cochlear synaptopathy or somatosensory tinnitus generators. The question whether middle-latency AEP changes, representing subcortical level of the auditory pathway, are present in tinnitus still remains unanswered. Future studies should identify and correctly deal with confounding factors, such as age, gender and the presence of somatosensory tinnitus components.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021243687, PROSPERO [CRD42021243687].