bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fatty acid dysregulation in the anterior cingulate cortex of depressed suicides with a history of child abuse
Authors: Perlman Kelly , Chouinard-Watkins Raphaël , Tanti Arnaud , Cisbani Giulia , Orri Massimiliano , Turecki Gustavo , Bazinet Richard P. , Mechawar Naguib 
Published: October 2021

AbstractChild abuse (CA) strongly increases the lifetime risk of suffering from major depression and predicts an unfavorable course for the illness. Severe CA has been associated with a specific dysregulation of oligodendrocyte function and thinner myelin sheaths in the human anterior cingulate cortex (ACC) white matter. Given that myelin is extremely lipid-rich, it is plausible that these findings may be accompanied by a disruption of the lipid profile that composes the myelin sheath. This is important to explore since the composition of fatty acids (FA) in myelin phospholipids can influence its stability, permeability, and compactness. Therefore, the objective of this study was to quantify and compare FA concentrations in postmortem ACC white matter in the choline glycerophospholipid pool (ChoGpl), a key myelin phospholipid pool, between adult depressed suicides with a history of CA (DS-CA) matched depressed suicides without CA (DS) and healthy non-psychiatric controls (CTRL). Total lipids were extracted from 101 subjects according to the Folch method and separated into respective classes using thin-layer chromatography. FA methyl esters from the ChoGpl fraction were quantified using gas chromatography. Our analysis revealed specific effects of CA in FAs from the arachidonic acid synthesis pathway, which was further validated with RNA-sequencing data. Furthermore, the concentration of most FAs was found to decrease with age. By extending the previous molecular level findings linking CA with altered myelination in the ACC, these results provide further insights regarding white matter alterations associated with early-life adversity.
SARS-CoV-2 promotes RIPK1 activation to facilitate viral propagation
Authors: Xu Gang , Li Ying , Zhang Shengyuan , Peng Haoran , Wang Yunyun , Li Dekang , Jin Taijie , He Zhuohao , Tong Yilun , Qi Chunting , Wu Guowei , Dong Kangyun , Gou Jizhou , Liu Yang , Xiao Tongyang , Qu Jing , Li Liang , Liu Liang , Zhao Ping , Zhang Zheng , Yuan Junying 
Published: October 2021

AbstractCoronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the ongoing global pandemic that poses substantial challenges to public health worldwide. A subset of COVID-19 patients experience systemic inflammatory response, known as cytokine storm, which may lead to death. Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is an important mediator of inflammation and cell death. Here, we examined the interaction of RIPK1-mediated innate immunity with SARS-CoV-2 infection. We found evidence of RIPK1 activation in human COVID-19 lung pathological samples, and cultured human lung organoids and ACE2 transgenic mice infected by SARS-CoV-2. Inhibition of RIPK1 using multiple small-molecule inhibitors reduced the viral load of SARS-CoV-2 in human lung organoids. Furthermore, therapeutic dosing of the RIPK1 inhibitor Nec-1s reduced mortality and lung viral load, and blocked the CNS manifestation of SARS-CoV-2 in ACE2 transgenic mice. Mechanistically, we found that the RNA-dependent RNA polymerase of SARS-CoV-2, NSP12, a highly conserved central component of coronaviral replication and transcription machinery, promoted the activation of RIPK1. Furthermore, NSP12 323L variant, encoded by the SARS-CoV-2 C14408T variant first detected in Lombardy, Italy, that carries a Pro323Leu amino acid substitution in NSP12, showed increased ability to activate RIPK1. Inhibition of RIPK1 downregulated the transcriptional induction of proinflammatory cytokines and host factors including ACE2 and EGFR that promote viral entry into cells. Our results suggest that SARS-CoV-2 may have an unexpected and unusual ability to hijack the RIPK1-mediated host defense response to promote its own propagation and that inhibition of RIPK1 may provide a therapeutic option for the treatment of COVID-19.
A novel mathematical modeling with solution for movement of fluid through ciliary caused metachronal waves in a channel
Authors: Khan Wasim Ullah , Imran Ali , Raja Muhammad Asif Zahoor , Shoaib Muhammad , Awan Saeed Ehsan , Kausar Khadija , He Yigang 
Published: October 2021

AbstractIn the present research, a novel mathematical model for the motion of cilia using non-linear rheological fluid in a symmetric channel is developed. The strength of analytical perturbation technique is employed for the solution of proposed physical process using mectachoronal rhythm based on Cilia induced flow for pseudo plastic nano fluid model by considering the low Reynolds number and long wave length approximation phenomena. The role of ciliary motion for the fluid transport in various animals is explained. Analytical expressions are gathered for stream function, concentration, temperature profiles, axial velocity, and pressure gradient. Whereas, transverse velocity, pressure rise per wave length, and frictional force on the wall of the tubule are investigated with aid of numerical computations and their outcomes are demonstrated graphically. A comprehensive analysis for comparison of Perturb and numerical solution is done. This analysis validates the analytical solution.
Arabidopsis thaliana PrimPol is a primase and lesion bypass DNA polymerase with the biochemical characteristics to cope with DNA damage in the nucleus, mitochondria, and chloroplast
Authors: García-Medel Paola L. , Peralta-Castro Antolín , Baruch-Torres Noe , Fuentes-Pascacio Alma , Pedroza-García José A. , Cruz-Ramirez Alfredo , Brieba Luis G. 
Published: October 2021

AbstractPrimPol is a novel Primase–Polymerase that synthesizes RNA and DNA primers de novo and extents from these primers as a DNA polymerase. Animal PrimPol is involved in nuclear and mitochondrial DNA replication by virtue of its translesion DNA synthesis (TLS) and repriming activities. Here we report that the plant model Arabidopsis thaliana encodes a functional PrimPol (AtPrimPol). AtPrimPol is a low fidelity and a TLS polymerase capable to bypass DNA lesions, like thymine glycol and abasic sites, by incorporating directly across these lesions or by skipping them. AtPrimPol is also an efficient primase that preferentially recognizes the single-stranded 3′-GTCG-5′ DNA sequence, where the 3′-G is cryptic. AtPrimPol is the first DNA polymerase that localizes in three cellular compartments: nucleus, mitochondria, and chloroplast. In vitro, AtPrimPol synthesizes primers that are extended by the plant organellar DNA polymerases and this reaction is regulated by organellar single-stranded binding proteins. Given the constant exposure of plants to endogenous and exogenous DNA-damaging agents and the enzymatic capabilities of lesion bypass and re-priming of AtPrimPol, we postulate a predominant role of this enzyme in avoiding replication fork collapse in all three plant genomes, both as a primase and as a TLS polymerase.
The dialysis facility levels and sizes are associated with outcomes of incident hemodialysis patients
Authors: Kuo George , Lee Tao-Han , Chen Jia-Jin , Yen Chieh-Li , Fan Pei-Chun , Lee Cheng-Chia , Chang Chih-Hsiang 
Published: October 2021

AbstractThe outcomes of patients with incident kidney failure who start hemodialysis are influenced by several factors. Whether hemodialysis facility characteristics are associated with patient outcomes is unclear. We included adults diagnosed as having kidney failure requiring hemodialysis during January 1, 2001 to December 31, 2013 from the Taiwan National Health Insurance Research Database to perform this retrospective cohort study. The exposures included different sizes and levels of hemodialysis facilities. The outcomes were all-cause mortality, cardiovascular death, infection-related death, hospitalization, and kidney transplantation. During 2001–2013, we identified 74,406 patients and divided them in to three groups according to the facilities where they receive hemodialysis: medical center (n = 8263), non-center hospital (n = 40,008), and clinic (n = 26,135). The multivariable Cox model demonstrated that a larger facility size was associated with a low mortality risk (hazard ratio [HR] 0.991, 95% confidence interval [95% CI] 0.984–0.998; every 20 beds per facility). Compared with medical centers, patients in non-center hospitals and clinics had higher mortality risks (HR 1.13, 95% CI 1.09–1.17 and HR 1.11, 95% CI 1.06–1.15, respectively). Patients in medical centers and non-center hospitals had higher risk of hospitalization (subdistribution HR [SHR] 1.11, 95% CI 1.10–1.12 and SHR 1.22, 95% CI 1.21–1.23, respectively). Patients in medical centers had the highest rate of kidney transplantation among the three groups. In patients with incident kidney failure, a larger hemodialysis facility size was associated with lower mortality. Overall, medical center patients had a lower mortality rate and higher transplantation rate, whereas clinic patients had a lower hospitalization risk.
Effect of formaldehyde exposure on bacterial communities in simulating indoor environments
Authors: Guo Jianguo , Xiong Yi , Kang Taisheng , Zhu Hua , Yang Qiwen , Qin Chuan 
Published: October 2021

AbstractIndoor formaldehyde (CH2O) exceeding the recommended level is a severe threat to human health. Few studies have investigated its effect on indoor surface bacterial communities, affecting habitants' health. This study used 20-L glass containers to mimic the indoor environment with bacterial inputs from human oral respiration. The behavior of bacterial communities responding to CH2O varied among the different CH2O levels. The bacterial community structure significantly changed over time in the 0.054 mg·m−3 CH2O group, which varied from the 0.1 mg·m−3 and 0.25 mg·m−3 CH2O groups. The Chao1 and Shannon index significantly increased in the 0.054 mg·m−3 CH2O group at 6 week, while they remained unchanged in the 0.25 mg·m−3 CH2O group. At 12 week, the Chao1 significantly increased in the 0.25 mg·m−3 CH2O group, while it remained unchanged in the 0.054 mg·m−3 CH2O group. Only a few Operational Taxonomic Units (OTUs) significantly correlated with the CH2O concentration. CH2O-induced OTUs mainly belong to the Proteobacteria and Firmicutes. Furthermore, bacterial communities formed at 6 or 12 weeks differed significantly among different CH2O levels. Functional analysis of bacterial communities showed that inferred genes related to chemical degradation and diseases were the highest in the 0.25 mg·m−3 CH2O group at 12 weeks. The development of nematodes fed with bacteria collected at 12 weeks was applied to evaluate the bacterial community's hazards. This showed significantly impaired growth in the 0.1 mg·m−3 and 0.25 mg·m−3 CH2O groups. These findings confirmed that CH2O concentration and exposure time could affect the indoor bacterial community and formed bacterial communities with a possibly more significant hazard to human health after long-term exposure to high CH2O levels.
Profile of esophageal squamous cell carcinoma mutations in Brazilian patients
Authors: Munari Fernanda Franco , dos Santos Wellington , Evangelista Adriane Feijó , Carvalho Ana Carolina , Pastrez Paula Aguiar , Bugatti Diego , Wohnrath Durval R. , Scapulatempo-Neto Cristovam , Guimarães Denise Peixoto , Longatto-Filho Adhemar , Reis Rui Manuel 
Published: October 2021

AbstractEsophageal cancer is an aggressive tumor that has a high rate of incidence and mortality worldwide. It is the 10th most frequent type in Brazil, being squamous cell carcinoma (ESCC) the predominant subtype. There is currently an incessant search to identify the frequently altered genes associated with esophageal squamous cell carcinoma biology that could be druggable. This study aimed to analyze the somatic mutation profile of a large panel of cancer-related genes in Brazilian ESCC. In a series of 46 ESCC diagnoses at Barretos Cancer Hospital, DNA isolated from paired fresh-frozen and blood tissue, a panel of 150 cancer-related genes was analyzed by next-generation sequencing. The genes with the highest frequency of mutations were TP53 (39/46, 84.8%), followed by NOTCH1 (7/46, 15.2%), NFE2L2 (5/46, 10.8%), RB1 (3/46, 6.5%), PTEN (3/46, 6.5%), CDKN2A (3/46, 6.5%), PTCH1 (2/46, 4.3%) and PIK3CA (2/46, 4.3%). There was no significant association between molecular and patients’ clinicopathological features. Applying an evolutionary action score of p53 (EAp53), we observed that 14 (35.9%) TP53 mutations were classified as high-risk, yet no association with overall survival was observed. Concluding, this the largest mutation profile of Brazilian ESCC patients, which helps in the elucidation of the major cancer-related genes in this population.
DNA barcoding allows identification of undescribed crab megalopas from the open sea
Authors: Marco-Herrero Elena , Cuesta Jose A. , González-Gordillo J. Ignacio 
Published: October 2021

AbstractMegalopas of 15 brachyuran crab species collected in the open sea plankton, and unknown until now, were identified using DNA barcodes (COI and 16S rRNA). Specimens belonging to the families Portunidae, Pseudorhombilidae and Xanthidae (Crustacea, Decapoda, Brachyura), and corresponding to the species Achelous floridanus, Arenaeus mexicanus, Callinectes amnicola, C. arcuatus, C. ornatus, C. toxones, Charybdis (Charybdis) hellerii, Portunus hastatus, Thalamita admete, Scopolius nuttingi, Etisus odhneri, Liomera cinctimanus, Neoliomera cerasinus, Pseudoliomera variolosa, and Williamstimpsonia stimpsoni, are described and illustrated, and compared with other congeneric species previously described. We also provide a new geographical record for N. cerasinus and the most remarkable features for each species.
Deregulation of hsa_circ_0001971/miR-186 and hsa_circ_0001874/miR-296 signaling pathways promotes the proliferation of oral squamous carcinoma cells by synergistically activating SHP2/PLK1 signals
Authors: Jun Wang , Shaobo Ouyang , Xianhua Zhang , Siyu Zhao , Mingyang Cheng , Xin Fan , Ying Cai , Lan Liao 
Published: October 2021

AbstractIt has been demonstrated that circ_0001874 and circ_0001971 are potential biomarkers for the diagnosis of oral squamous carcinoma (OSCC). MiR-186 was reported to serve as a tumor suppressor in OSCC, and the down-regulation of miR-186 was reported to lead to higher expression of oncogenic factor SHP2 and the activation of growth promoting signaling. In this study, we aimed to explore the possible molecular role of circ_0001874 and circ_0001971 signaling in the pathogenesis of OSCC. RT-qPCR, Western blot, online bioinformatics tools and luciferase assay were utilized to study the molecular signaling pathways of circ_0001874 and circ_0001971. MTT assay and FCM assay were performed to investigate the synergistic effect of circ_0001971 and circ_0001874 on cell proliferation and apoptosis. By observing the effect of different miRNAs on the levels of circ_0001847 and circ_0001971, it was identified that circ_0001847 and circ_0001971 respectively sponged the expression of miR-296 and miR-186 via binding to these miRNAs. Also, SHP2 mRNA and PLK1 mRNA were respectively targeted by miR-186 and miR-296-5p. We also established two signaling pathways, i.e., circ_0001971/miR-186/SHP2 and circ_0001874/miR-296-5p/PLK1, and validated the synergistic effect of circ_0001971 and circ_0001874 via observing their positive effect on cell proliferation and negative effect on cell apoptosis. The expression of miR-186 and miR-296-5p was generally lower in saliva of OSCC patients compared with that in OLK patients, while the expression of miR-186 and miR-296-5p was specifically up-regulated in saliva of OSCC patients. In conclusion, the finding of this study demonstrated that the relative level of hsa_circ_0001971 and hsa_circ_0001874 were different in the saliva of OSCC patients and could be used as predictive biomarkers for the development of OSCC. Furthermore, oncogenic effects of hsa_circ_0001971 and hsa_circ_0001874 in the development of OSCC might be, at least partially, mediated by its downstream signaling pathways including hsa_circ_0001971/microRNA-186/SHP2 and hsa_circ_0001874/microRNA-297/PLK1.
Comparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders
Authors: Rowlands Charlie , Thomas Huw B. , Lord Jenny , Wai Htoo A. , Arno Gavin , Beaman Glenda , Sergouniotis Panagiotis , Gomes-Silva Beatriz , Campbell Christopher , Gossan Nicole , Hardcastle Claire , Webb Kevin , O’Callaghan Christopher , Hirst Robert A. , Ramsden Simon , Jones Elizabeth , Clayton-Smith Jill , Webster Andrew R. ,   Genomics England Research Consortium, Ambrose J. C. , Arumugam P. , Bevers R. , Bleda M. , Boardman-Pretty F. , Boustred C. R. , Brittain H. , Caulfield M. J. , Chan G. C. , Fowler T. , Giess A. , Hamblin A. , Henderson S. , Hubbard T. J. P. , Jackson R. , Jones L. J. , Kasperaviciute D. , Kayikci M. , Kousathanas A. , Lahnstein L. , Leigh S. E. A. , Leong I. U. S. , Lopez F. J. , Maleady-Crowe F. , McEntagart M. , Minneci F. , Moutsianas L. , Mueller M. , Murugaesu N. , Need A. C. , O’Donovan P. , Odhams C. A. , Patch C. , Perez-Gil D. , Pereira M. B. , Pullinger J. , Rahim T. , Rendon A. , Rogers T. , Savage K. , Sawant K. , Scott R. H. , Siddiq A. , Sieghart A. , Smith S. C. , Sosinsky A. , Stuckey A. , Tanguy M. , Taylor Tavares A. L. , Thomas E. R. A. , Thompson S. R. , Tucci A. , Welland M. J. , Williams E. , Witkowsa K. , Wood S. M. , Douglas Andrew G. L. , O’Keefe Raymond T. , Newman William G. , Baralle Diana , Black Graeme C. M. , Ellingford Jamie M. 
Published: October 2021

AbstractThe development of computational methods to assess pathogenicity of pre-messenger RNA splicing variants is critical for diagnosis of human disease. We assessed the capability of eight algorithms, and a consensus approach, to prioritize 249 variants of uncertain significance (VUSs) that underwent splicing functional analyses. The capability of algorithms to differentiate VUSs away from the immediate splice site as being ‘pathogenic’ or ‘benign’ is likely to have substantial impact on diagnostic testing. We show that SpliceAI is the best single strategy in this regard, but that combined usage of tools using a weighted approach can increase accuracy further. We incorporated prioritization strategies alongside diagnostic testing for rare disorders. We show that 15% of 2783 referred individuals carry rare variants expected to impact splicing that were not initially identified as ‘pathogenic’ or ‘likely pathogenic’; one in five of these cases could lead to new or refined diagnoses.
Identification and analyses of the chemical composition of a naturally occurring albino mutant chanterelle
Authors: Thorn R. Greg , Banwell Alicia , Pham Thu Huong , Vidal Natalia P. , Manful Charles Felix , Nadeem Muhammad , Ivanov Alexander G. , Szyszka Mroz Beth , Bonneville Michael B. , Hüner Norman Peter Andrew , Piercey-Normore Michele D. , Thomas Raymond 
Published: October 2021

AbstractWhite chanterelles (Basidiomycota), lacking the orange pigments and apricot-like odour of typical chanterelles, were found recently in the Canadian provinces of Québec (QC) and Newfoundland & Labrador (NL). Our phylogenetic analyses confirmed the identification of all white chanterelles from NL and QC asCantharellus enelensis; we name these formaacolodorus. We characterized carotenoid pigments, lipids, phenolics, and volatile compounds in these and related chanterelles. White mutants ofC. enelensislacked detectable β-carotene, confirmed to be the primary pigment of wild-type, golden-orange individuals, and could also be distinguished by their profiles of fatty acids and phenolic acids, and by the ketone and terpene composition of their volatiles. We detected single base substitutions in the phytoene desaturase (Al-1) and phytoene synthase (Al-2) genes of the white mutant, which are predicted to result in altered amino acids in their gene products and may be responsible for the loss of β-carotene synthesis in that form.
Dialyzer surface area is a significant predictor of mortality in patients on hemodialysis: a 3-year nationwide cohort study
Authors: Abe Masanori , Masakane Ikuto , Wada Atsushi , Nakai Shigeru , Nitta Kosaku , Nakamoto Hidetomo 
Published: October 2021

AbstractA target Kt/V of > 1.4 and use of a high-flux dialyzer are recommended for patients on hemodialysis. However, there is little information on the relationship between the dialyzer surface area and mortality in these patients. In this nationwide cohort study, we aimed to clarify this relationship by analyzing data from the Japanese Society for Dialysis Therapy for 2010–2013. We enrolled 234,638 patients on hemodialysis who were divided according to quartile for dialyzer surface area into the S group (small, < 1.5 m2), M group (medium, 1.5 m2), L group (large, 1.6 to < 2.0 m2), or XL group (extra-large, ≥ 2.0 m2). We assessed the association of each group with 3-year mortality using Cox proportional hazards models and performed propensity score matching analysis. By the end of 2013, a total of 53,836 patients on dialysis (22.9%) had died. There was a significant decrease in mortality with larger dialyzer surface areas. The hazard ratio (95% confidence interval) was significantly higher in the S group (1.15 [1.12–1.19], P < 0.0001) and significantly lower in the L group (0.89 [0.87–0.92] P < 0.0001) and XL group (0.75 [0.72–0.78], P < 0.0001) than in the M group as a reference after adjustment for all confounders. Findings were robust in several sensitivity analyses. Furthermore, the findings remained significant after propensity score matching. Hemodialysis using dialyzers, especially super high-flux dialyzers with a larger surface area might reduce mortality rates, and a surface area of ≥ 2.0 m2 is superior, even with the same Kt/V.
The influence of the grass mixture composition on the quality and suitability for football pitches
Authors: Wolski Karol , Markowska Joanna , Radkowski Adam , Brennensthul Marek , Sobol Łukasz , Pęczkowski Grzegorz , Bujak Henryk , Grzebieniarz Wiktoria , Radkowska Iwona , Khachatryan Karen 
Published: October 2021

AbstractThe selection of grass mixtures with appropriate visual and functional parameters for sowing football fields is a key element in shaping the sports infrastructure, ensuring the spectacularity of a match and comfort for players. The aim of the research was to investigate the properties of lawn grass mixtures and their suitability for football pitches. The experiment was conducted at the Toya Golf & Country Club (51° 20′ E, 17° 07′ N), Wrocław, Poland, between 2007 and 2009. 12 grass mixtures were selected, mainly based on red fescue, Kentucky bluegrass, and perennial ryegrass. The assessment was carried out using a nine-point scale, according to the Plant Variety Office methodology for crops and turf grass. Six features of sports turf were studied: appearance, density, colour, leaf fineness, overwintering, and susceptibility to disease and they significantly varied, depending on the grass mixture and the year of research. Our study showed that mixtures based on the dominance of meadow grass were characterized by higher values of the general visual aspect, colour and slenderness of the leaf blade and these based on the dominance of perennial ryegrass and co-dominance of perennial ryegrass and meadow grass were the most useful in terms of wintering, resistance to diseases and sodding.