bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maturation and specialization of group 2 innate lymphoid cells through the lung-gut axis
Authors: Zhao Min , Shao Fei , Yu Dou , Zhang Jiaqi , Liu Zhen , Ma Jiangwen , Xia Pengyan , Wang Shuo 
Published: December 2022

AbstractInnate lymphoid cells (ILC) are abundant in mucosal tissues. They serve critical functions in anti-pathogen response and tissue homeostasis. However, the heterogenous composition of ILCs in mucosal sites and their various maturation trajectories are less well known. In this study, we characterize ILC types and functions from both the lung and the small intestine, and identify their tissue-specific markers. We find that ILC2s residing in the lung express CCR2, whereas intestinal ILC2s express CCR4. Through the use of CCR2 and CCR4 reporter mice, we show that ILC2s undergo translocation via the lung-gut axis upon IL-33 treatment. This trajectory of ILC2s is also observed at the postnatal stage. Allergen-induced activation of lung ILC2s affects the homeostasis of gut ILC2s. Together, our findings implicate that ILCs display tissue-specific features in both the lung and gut, and ILC2s mature along the lung-gut axis in particular homeostatic and inflammatory conditions.
Parvalbumin basket cell myelination accumulates axonal mitochondria to internodes
Authors: Kole Koen , Voesenek Bas J. B. , Brinia Maria E. , Petersen Naomi , Kole Maarten H. P. 
Published: December 2022

AbstractParvalbumin-expressing (PV+) basket cells are fast-spiking inhibitory interneurons that exert critical control over local circuit activity and oscillations. PV+ axons are often myelinated, but the electrical and metabolic roles of interneuron myelination remain poorly understood. Here, we developed viral constructs allowing cell type-specific investigation of mitochondria with genetically encoded fluorescent probes. Single-cell reconstructions revealed that mitochondria selectively cluster to myelinated segments of PV+ basket cells, confirmed by analyses of a high-resolution electron microscopy dataset. In contrast to the increased mitochondrial densities in excitatory axons cuprizone-induced demyelination abolished mitochondrial clustering in PV+ axons. Furthermore, with genetic deletion of myelin basic protein the mitochondrial clustering was still observed at internodes wrapped by noncompacted myelin, indicating that compaction is dispensable. Finally, two-photon imaging of action potential-evoked calcium (Ca2+) responses showed that interneuron myelination attenuates both the cytosolic and mitochondrial Ca2+ transients. These findings suggest that oligodendrocyte ensheathment of PV+ axons assembles mitochondria to branch selectively fine-tune metabolic demands.
A self-healing electrocatalytic system via electrohydrodynamics induced evolution in liquid metal
Authors: Hou Yifeng , Wang Fengyan , Qin Chichu , Wu Shining , Cao Mengyang , Yang Pengkun , Huang Lu , Wu Yingpeng 
Published: December 2022

AbstractCatalytic deterioration during electrocatalytic processes is inevitable for conventional composite electrodes, which are prepared by depositing catalysts onto a rigid current collector. In contrast, metals that are liquid at near room temperature, liquid metals (LMs), are potential electrodes that are uniquely flexible and maneuverable, and whose fluidity may allow them to be more adaptive than rigid substrates. Here we demonstrate a self-healing electrocatalytic system for CO2electroreduction using bismuth-containing Ga-based LM electrodes. Bi2O3dispersed in the LM matrix experiences a series of electrohydrodynamic-induced structural changes when exposed to a tunable potential and finally transforms into catalytic bismuth, whose morphology can be controlled by the applied potential. The electrohydrodynamically-induced evolved electrode shows considerable electrocatalytic activity for CO2reduction to formate. After deterioration of the electrocatalytic performance, the catalyst can be healed via simple mechanical stirring followed by in situ regeneration by applying a reducing potential. With this procedure, the electrode’s original structure and catalytic activity are both recovered.
Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence
Authors: Tu Xiaoyu , Ren Sibo , Shen Wei , Li Jianjian , Li Yuxiang , Li Chuanshun , Li Yangmeihui , Zong Zhanxiang , Xie Weibo , Grierson Donald , Fei Zhangjun , Giovannoni Jim , Li Pinghua , Zhong Silin 
Published: December 2022

AbstractNon-coding cis-regulatory variants in animal genomes are an important driving force in the evolution of transcription regulation and phenotype diversity. However, cistrome dynamics in plants remain largely underexplored. Here, we compare the binding of GOLDEN2-LIKE (GLK) transcription factors in tomato, tobacco, Arabidopsis, maize and rice. Although the function of GLKs is conserved, most of their binding sites are species-specific. Conserved binding sites are often found near photosynthetic genes dependent on GLK for expression, but sites near non-differentially expressed genes in the glk mutant are nevertheless under purifying selection. The binding sites’ regulatory potential can be predicted by machine learning model using quantitative genome features and TF co-binding information. Our study show that genome cis-variation caused wide-spread TF binding divergence, and most of the TF binding sites are genetically redundant. This poses a major challenge for interpreting the effect of individual sites and highlights the importance of quantitatively measuring TF occupancy.
Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage
Authors: Wang Ling , Liu Wan , Liang Jieliang , Zhao Linna , Li Qiang , Zhou Chenfen , Cen Hui , Weng Qingbei , Zhang Guoqing 
Published: December 2022

AbstractAcid mine drainage (AMD) is usually acidic (pH < 4) and contains high concentrations of dissolved metals and metalloids, making AMD a typical representative of extreme environments. Recent studies have shown that microbes play a key role in AMD bioremediation, and secondary metabolite biosynthetic gene clusters (smBGCs) from AMD microbes are important resources for the synthesis of antibacterial and anticancer drugs. Here, 179 samples from 13 mineral types were used to analyze the putative novel microorganisms and secondary metabolites in AMD environments. Among 7,007 qualified metagenome-assembled genomes (MAGs) mined from these datasets, 6,340 MAGs could not be assigned to any GTDB species representative. Overall, 11,856 smBGCs in eight categories were obtained from 7,007 qualified MAGs, and 10,899 smBGCs were identified as putative novel smBGCs. We anticipate that these datasets will accelerate research in the field of AMD bioremediation, aid in the discovery of novel secondary metabolites, and facilitate investigation into gene functions, metabolic pathways, and CNPS cycles in AMD.
Long-term prognostic impact of paravalvular leakage on coronary artery disease requires patient-specific quantification of hemodynamics
Authors: Khodaei Seyedvahid , Garber Louis , Bauer Julia , Emadi Ali , Keshavarz-Motamed Zahra 
Published: December 2022

AbstractTranscatheter aortic valve replacement (TAVR) is a frequently used minimally invasive intervention for patient with aortic stenosis across a broad risk spectrum. While coronary artery disease (CAD) is present in approximately half of TAVR candidates, correlation of post-TAVR complications such as paravalvular leakage (PVL) or misalignment with CAD are not fully understood. For this purpose, we developed a multiscale computational framework based on a patient-specific lumped-parameter algorithm and a 3-D strongly-coupled fluid–structure interaction model to quantify metrics of global circulatory function, metrics of global cardiac function and local cardiac fluid dynamics in 6 patients. Based on our findings, PVL limits the benefits of TAVR and restricts coronary perfusion due to the lack of sufficient coronary blood flow during diastole phase (e.g., maximum coronary flow rate reduced by 21.73%, 21.43% and 21.43% in the left anterior descending (LAD), left circumflex (LCX) and right coronary artery (RCA) respectively (N = 6)). Moreover, PVL may increase the LV load (e.g., LV load increased by 17.57% (N = 6)) and decrease the coronary wall shear stress (e.g., maximum wall shear stress reduced by 20.62%, 21.92%, 22.28% and 25.66% in the left main coronary artery (LMCA), left anterior descending (LAD), left circumflex (LCX) and right coronary artery (RCA) respectively (N = 6)), which could promote atherosclerosis development through loss of the physiological flow-oriented alignment of endothelial cells. This study demonstrated that a rigorously developed personalized image-based computational framework can provide vital insights into underlying mechanics of TAVR and CAD interactions and assist in treatment planning and patient risk stratification in patients.
MKL-1-induced PINK1-AS overexpression contributes to the malignant progression of hepatocellular carcinoma via ALDOA-mediated glycolysis
Authors: Wang Jun , Zhang Hui-Min , Dai Zhou-Tong , Huang You , Liu Hui , Chen Zhen , Wu Yuan , Liao Xing-Hua 
Published: December 2022

AbstractAldolase A (ALDOA), an important metabolic enzyme in the glycolytic pathway, plays an important role in regulating tumour metabolism. In this study, we investigated the expression pattern of ALDOA in hepatocellular carcinoma (HCC) and its biological role in tumour progression. Bioinformatics analysis, western blot (WB) and RT-qPCR were performed to detect the relative expression of ALDOA in HCC tissues and cell lines. A loss-of-function approach was used to investigate the biological function of ALDOA. The role of ALDOA on glycolysis was assessed by WB, glucose and lactate assay kits and a nude mouse xenograft model. Luciferase reporter experiment, chromatin immunoprecipitation and WB were performed to elucidate the underlying molecular. The expression level of ALODA was up-regulated in HCC tissues and cell lines. High ALDOA levels were associated with poorer patient overall survival. Mechanistic studies suggest that ALDOA is a direct target of miR-34a-5p, which can inhibit glycolysis in hepatocellular carcinoma cells by targeting the 3′UTR of ALDOA. PINK1 antisense RNA (PINK1-AS) competitively sponged miR-34a-5p to increase ALDOA expression by antagonizing miR-34a-5p-mediated ALDOA inhibition. MKL-1 acted as a transcription factor to promote the expression of PINK1-AS and ALDOA, thus promoting the deterioration of HCC cells. This study shows that high expression of ALDOA contributes to the development and poor prognosis of hepatocellular carcinoma and will be a target and potential prognostic biomarker for the treatment of HCC.
Unlocking the organic residues preserved in the corrosion from the Pewsey Hoard vessels
Authors: Carvalho Luciana da Costa , Henry Richard , McCullagh James S. O. , Pollard A. Mark 
Published: December 2022

AbstractThe characterization of archaeological metal corrosion has traditionally been limited to the identification of inorganic compounds usually by X-ray diffraction (XRD), thought to result from the interaction between the metal object and the deposition environment. The discovery of a hoard of Late Roman copper-alloy vessels in Wiltshire, UK presented an unique opportunity to adopt a multi-analytical approach to characterize corrosion combining XRD with Fourier-transform infrared (FTIR) and gas chromatography with quadrupole time-of-flight mass spectrometry using a thermal separation probe (GC-QTOF-MS with TSP). This approach revealed organic compounds potentially historical preserved within crystalline inorganic matrices. It has been known for some time that ceramics can harbour organic residues, which provide crucial evidence about the use of these vessels in the past. Our results confirms that similar residues appear to survive in metal corrosion thus extending the potential for identification of biomaterials used in the past.
Ecological study of ambient air pollution exposure and mortality of cardiovascular diseases in elderly
Authors: Dehghani Samaneh , Vali Mohebat , Jafarian Arian , Oskoei Vahide , Maleki Zahra , Hoseini Mohammad 
Published: December 2022

AbstractAs an independent risk factor, ambient air pollution can assume a considerable part in mortality and worsening of cardiovascular disease. We sought to investigate the association between long-term exposure to ambient air pollution and cardiovascular disease mortality and their risk factors in Iranian's elderly population. This inquiry was conducted ecologically utilizing recorded data on cardiovascular disease mortality from 1990 to 2019 for males and females aged 50 years or more from the Global Burden of Disease dataset. Data was interned into Joinpoint software 4.9.0.0 to present Annual Percent Change (APC), Average Annual Percent Change (AAPC), and its confidence intervals. The relationship between recorded data on ambient air pollution and cardiovascular disease' mortality, the prevalence of high systolic blood pressure, high LDL cholesterol levels, high body mass index, and diabetes mellitus type2 was investigated using the Spearman correlation test in R 3.5.0 software. Our finding demonstrated that cardiovascular diseases in elderly males and females in Iran had a general decreasing trend (AAPC = −0.77% and −0.65%, respectively). The results showed a positive correlation between exposure to ambient ozone pollution (p ≤ 0.001, r = 0.94) ambient particulate and air pollution (p < 0.001, r = 0.99) and mortality of cardiovascular disease. Also, ambient air pollution was positively correlated with high systolic blood pressure (p < 0.001, r = 0.98), high LDL cholesterol levels (p < 0.001, r = 0.97), high body mass index (p < 0.001, r = 0.91), diabetes mellitus type2 (p < 0.001, r = 0.77). Evidence from this study indicated that ambient air pollution, directly and indirectly, affects cardiovascular disease mortality in two ways by increasing the prevalence of some traditional cardiovascular disease risk factors. Evidence-based clinical and public health methodologies are necessary to decrease the burden of death and disability associated with cardiovascular disease.
Association of polymorphisms in TGFB1, XRCC1, XRCC3 genes and CD8 T-lymphocyte apoptosis with adverse effect of radiotherapy for prostate cancer
Authors: Mališić Emina , Petrović Nina , Brengues Muriel , Azria David , Matić Ivana Z. , Srbljak Ćuk Ivana , Kopčalić Katarina , Stanojković Tatjana , Nikitović Marina 
Published: December 2022

AbstractThe genetic background of each person might affect the severity of radiotherapy (RT)-induced normal tissue toxicity. The aim of study was to evaluate the influence of TGFB1 C-509T and Leu10Pro, XRCC1 Arg280His and XRCC3 Thr241Met polymorphisms as well as the level of radiation-induced CD8 T-lymphocyte apoptosis (RILA) on adverse effects of RT for prostate cancer (PCa). The study included 88 patients with localized or locally advanced PCa who were treated with RT. The polymorphisms were determined by PCR–RFLP analysis on DNA from peripheral blood mononuclear cells. RILA values were measured by flow cytometry. We found that CT genotype of TGFB1 C-509T could be protective biomarker for acute genitourinary (GU) and gastrointestinal (GI) radiotoxicity, while Thr variant of XRCC3 Thr241Met could predict the risk for acute GU radiotoxicity. Correlation between RILA values and toxicity was not detected. Univariate logistic regression analysis showed that Gleason score and risk group were risk factors for late GU, while for late GI radiotoxicity it was diabetes mellitus type 2. However, in multivariate model those were not proven to be significant and independent risk factors. Identification of assays combination predicting individual radiosensitivity is a crucial step towards personalized RT approach.
Estimation and feasibility of correction modelling for mother-reported child height and weight at 2 years using data from the Australian CHAT trial
Authors: Cheng Yan , Xu Huilan , Rissel Chris , Phongsavan Philayrath , Buchanan Limin , Taki Sarah , Hayes Alison , Baur Louise A. , Wen Li Ming 
Published: December 2022

AbstractCorrection modelling using reported BMI values has been employed in adolescent and adult populations to improve the accuracy of self-reporting. This study aimed to evaluate the feasibility of establishing correction modelling for mother-reported child height and weight at 2 years using data from an Australian trial in 2019. Correction modelling for BMI was conducted using mother-reported and objectively measured height and weight of 2-year-olds. Mother-reported height, weight and BMI values of 2-year-old children were adjusted based on objectively measured anthropometric data using linear regression models. ‘Direct’ and ‘indirect’ corrections were applied to the correction of BMI values. We defined the direct collection as using corrected BMI values that were predicted directly by the model and indirect correction as using corrected weight and height values to calculate corrected BMI values. Corrected BMI values via the indirect correction showed higher sensitivity or similar specificity in predicting overweight status, compared to the direct correction, and also showed higher agreement with measured values compared to the mother-reported measures. Corrected self-reported measures via an indirect correction had a better accuracy and agreement with the objectively measured data in the BMI values and classification of overweight, compared to the mother-reported values.
Inflammatory bowel disease and COVID-19 outcomes: a meta-analysis
Authors: Abdulla Maheeba , Mohammed Nafeesa , AlQamish Jehad , Mosli Mahmoud 
Published: December 2022

AbstractThere is conflicting evidence concerning the effect of inflammatory bowel disease (IBD) on COVID-19 incidence and outcome. Hence, we aimed to evaluate the published evidence through a systematic review process and perform a meta-analysis to assess the association between IBD and COVID-19. A compressive literature search was performed in PubMed/Medline, Scopus, Embase, and Cochrane Library from inception to July 2021. A snowball search in Google, Google Scholar, Research Gate, and MedRxiv; and bibliographic research were also performed to identify any other relevant articles. Quantitative observational studies such as cohort, cross-sectional, and case–control studies that assessed the incidence, risk, and outcomes of COVID-19 among the adult IBD patients published in the English language, were considered for this review. The incidence and risk of COVID-19, COVID-19 hospitalization, the severity of COVID-19, and mortality were considered as the outcomes of interest. The Joanna Briggs Institute critical appraisal checklist was used for quality assessment. A subgroup and sensitivity analysis were performed to explore the heterogeneity and robustness of the results, respectively. A total of 86 studies out of 2828 non-duplicate records were considered for this meta-analysis. The studies were single or multicentric internationally from settings such as IBD centres, medical colleges, hospitals, or from the general public. Most of the studies were observed to be of good quality with an acceptable risk of bias. The pooled prevalence of COVID-19, COVID-19 hospitalization, severe COVID-19, and mortality in the IBD population were 6.10%, 10.63%, 40.43%, and 1.94%, respectively. IBD was not significantly (p > 0.05) associated with the risk of COVID-19, COVID-19 hospitalization, severe COVID-19, and mortality. In contrast, ulcerative colitis was significantly associated with a higher risk of COVID-19 (OR 1.37; p = 0.01), COVID-19 hospitalization (OR 1.28; p < 0.00001), and severe COVID-19 (OR 2.45; p < 0.0007). Crohn’s disease was significantly associated with a lesser risk of severe COVID-19 (OR 0.48; p = 0.02). Type of IBD was a potential factor that might have contributed to the higher level of heterogeneity. There was a significant association between ulcerative colitis and increased risk of COVID-19, COVID-19 hospitalization, and severe COVID-19 infection. This association was not observed in patients with Crohns' disease or in those diagnosed non-specifically as IBD.
Soluble immune checkpoint molecules in patients with antineutrophil cytoplasmic antibody-associated vasculitis
Authors: Pyo Jung Yoon , Yoon Taejun , Ahn Sung Soo , Song Jason Jungsik , Park Yong-Beom , Lee Sang-Won 
Published: December 2022

AbstractImmune checkpoint molecules balance immune effector responses with regulatory reactions. We speculated that soluble immune checkpoint molecules are involved in dysregulation of the immune response and autoimmunity. We evaluated the association between soluble immune checkpoint molecules and antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). A total of 56 patients with AAV from a prospective observational cohort and 40 healthy controls (HCs) were analyzed. Soluble PD-1, PD-L1, PD-L2, CTLA-4, CD28, CD80, CD86, ICOS, TIM-3, BTLA, CD40, LAG-3, TLR-2, and CD27 were measured in stored sera using the Milliplex MAP assay. Paired analyses were performed before and after the treatment. AAV-specific indices, including Birmingham vasculitis activity score, five factor score , vasculitis damage index, and blood samples, were collected. Patients with AAV had higher levels of sPD-L1, sCD28, sCD80, sCD86, sICOS, sTIM-3, sLAG-3, sTLR-2, and sCD27 and lower level of sCTLA-4 than HCs (p < 0.05). Patients with AAV had higher serum sCD28, sCD80, sTIM-3, and sCD27 levels than HCs at baseline and decreased after treatment. Furthermore, the serum levels of sCD28 and sTIM-3 were significantly correlated with disease activity. This study demonstrated altered concentrations of serum soluble immune checkpoint molecules in patients with AAV. In particular, sCD28 and sTIM-3 may act as surrogate markers of AAV disease activity.
An integrated approach for the restoration of Australian temperate grasslands invaded by Nassella trichotoma
Authors: Humphries Talia , Turville Christopher , Sinclair Steven , Florentine Singarayer 
Published: December 2022

AbstractInvasive plants are considered to be one of the biggest threats to environmental assets, and once established, they can be immensely difficult to control. Nassella trichotoma is an aggressive, perennial grass species, and is considered to be one of the most economically damaging weeds to grazing systems due to its unpalatability, as well as being one of the leading causes of biodiversity loss in grassland communities. This species produces high density seedbanks that rapidly respond to disturbance events. Despite control programs being developing in Australia since the 1930s, this species is still widespread throughout south-east Australia, indicating that a new management approach is critical to control this Weed of National Significance at the landscape scale. The present study explored the effect of 12 different combinations of herbicide, fire, a second application of herbicide, grazing exclusion, tillage and broadcasting seeds in order to reduce the above and below-ground density of N. trichotoma. A control treatment was also included. The results were assessed using a Hierarchy analysis, whereby treatments of increasing complexity were compared for their efficacy in reducing N. trichotoma cover and seedbank density, while simultaneously increasing the establishment of the broadcast species. Whilst all integrated treatments effectively reduced N. trichotoma’s seedbank, the treatments that included fire performed significantly better at simultaneously reducing N. trichotoma and increasing the establishment of broadcasted seeds. Overall, the integration of herbicide, fire and broadcasting native seeds was observed to provide the most economically feasible management strategy for the landscape scale restoration of a degraded temperate grassland dominated by N. trichotoma.