bluuebunny/crossref_metadata_2025_split huggingface dataset:
HNRNPA1-mediated exosomal sorting of miR-483-5p out of renal tubular epithelial cells promotes the progression of diabetic nephropathy-induced renal interstitial fibrosis
Authors: Liu DongWei , Liu FengXun , Li ZhengYong , Pan ShaoKang , Xie JunWei , Zhao ZiHao , Liu ZhenJie , Zhang JiaHui , Liu ZhangSuo 
Published: March 2021

AbstractDiabetic nephropathy (DN) is a serious complication in type 1 and type 2 diabetes, and renal interstitial fibrosis plays a key role in DN progression. Here, we aimed to probe into the role and potential mechanism of miR-483-5p in DN-induced renal interstitial fibrosis. In this study, we corroborated that miR-483-5p expression was lessened in type 1 and type 2 diabetic mice kidney tissues and high glucose (HG)-stimulated tubular epithelial cells (TECs), and raised in the exosomes derived from renal tissues in type 1 and type 2 diabetic mice. miR-483-5p restrained the expressions of fibrosis-related genes in vitro and renal interstitial fibrosis in vivo. Mechanistically, miR-483-5p bound both TIMP2 and MAPK1, and TIMP2 and MAPK1 were bound up with the regulation of miR-483-5p on renal TECs under HG conditions. Importantly, HNRNPA1-mediated exosomal sorting transported cellular miR-483-5p out of TECs into the urine. Our results expounded that HNRNPA1-mediated exosomal sorting transported cellular miR-483-5p out of TECs into the urine, thus lessening the restraint of cellular miR-483-5p on MAPK1 and TIMP2 mRNAs, and ultimately boosting extracellular matrix deposition and the progression of DN-induced renal interstitial fibrosis.
Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication
Authors: Zhang Le , Zhao Jingtian , Bi Hao , Yang Xiangyu , Zhang Zhiyang , Su Yutao , Li Zhenghao , Zhang Lei , Sanderson Brian J. , Liu Jianquan , Ma Tao 
Published: March 2021

AbstractThe nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.
Measuring human capital using global learning data
Authors: Angrist Noam , Djankov Simeon , Goldberg Pinelopi K. , Patrinos Harry A. 
Published: March 2021

AbstractHuman capital—that is, resources associated with the knowledge and skills of individuals—is a critical component of economic development1,2. Learning metrics that are comparable for countries globally are necessary to understand and track the formation of human capital. The increasing use of international achievement tests is an important step in this direction3. However, such tests are administered primarily in developed countries4, limiting our ability to analyse learning patterns in developing countries that may have the most to gain from the formation of human capital. Here we bridge this gap by constructing a globally comparable database of 164 countries from 2000 to 2017. The data represent 98% of the global population and developing economies comprise two-thirds of the included countries. Using this dataset, we show that global progress in learning—a priority Sustainable Development Goal—has been limited, despite increasing enrolment in primary and secondary education. Using an accounting exercise that includes a direct measure of schooling quality, we estimate that the role of human capital in explaining income differences across countries ranges from a fifth to half; this result has an intermediate position in the wide range of estimates provided in earlier papers in the literature5–13. Moreover, we show that average estimates mask considerable heterogeneity associated with income grouping across countries and regions. This heterogeneity highlights the importance of including countries at various stages of economic development when analysing the role of human capital in economic development. Finally, we show that our database provides a measure of human capital that is more closely associated with economic growth than current measures that are included in the Penn world tables version 9.014 and the human development index of the United Nations15.
Differential expression analysis and profiling of hepatic miRNA and isomiRNA in dengue hemorrhagic fever
Authors: de Oliveira Layanna Freitas , de Andrade Amanda Araújo Serrão , Pagliari Carla , de Carvalho Leda Viegas , Silveira Taiana S. , Cardoso Jedson Ferreira , Silva André Luiz Teles e , de Vasconcelos Janaina Mota , Moreira-Nunes Caroline Aquino , Burbano Rommel Mario Rodríguez , Nunes Márcio Roberto Teixeira , dos Santos Eduardo José Melo , Júnior João Lídio da Silva Gonçalves Viane 
Published: March 2021

AbstractDengue virus causes dengue hemorrhagic fever (DHF) and has been associated to fatal cases worldwide. The liver is one of the most important target tissues in severe cases, due to its intense viral replication and metabolic role. microRNAs role during infection is crucial to understand the regulatory mechanisms of DENV infection and can help in diagnostic and anti-viral therapies development. We sequenced the miRNome of six fatal cases and compared to five controls, to characterize the human microRNAs expression profile in the liver tissue during DHF. Eight microRNAs were differentially expressed, including miR-126-5p, a regulatory molecule of endothelial cells, miR-122-5p, a liver specific homeostasis regulator, and miR-146a-5p, an interferon-regulator. Enrichment analysis with predicted target genes of microRNAs revealed regulatory pathways of apoptosis, involving MAPK, RAS, CDK and FAS. Immune response pathways were related to NF- kB, CC and CX families, IL and TLR. This is the first description of the human microRNA and isomicroRNA profile in liver tissues from DHF cases. The results demonstrated the association of miR-126-5p, miR-122-5p and miR-146a-5p with DHF liver pathogenesis, involving endothelial repair and vascular permeability regulation, control of homeostasis and expression of inflammatory cytokines.
Exploratory study of the long-term footprint of deep brain stimulation on brain metabolism and neuroplasticity in an animal model of obesity
Authors: Casquero-Veiga Marta , Bueno-Fernandez Clara , Romero-Miguel Diego , Lamanna-Rama Nicolás , Nacher Juan , Desco Manuel , Soto-Montenegro María Luisa 
Published: March 2021

AbstractDeep brain stimulation (DBS) is a powerful neurostimulation therapy proposed for the treatment of several neuropsychiatric disorders. However, DBS mechanism of action remains unclear, being its effects on brain dynamics of particular interest. Specifically, DBS reversibility is a major point of debate. Preclinical studies in obesity showed that the stimulation of the lateral hypothalamus (LH) and nucleus accumbens (NAcc), brain centers involved in satiety and reward circuits, are able to modulate the activity of brain structures impaired in this pathology. Nevertheless, the long-term persistence of this modulation after DBS withdrawal was unexplored. Here we examine the in vivo presence of such changes 1 month after LH- and NAcc-DBS, along with differences in synaptic plasticity, following an exploratory approach. Thus, both stimulated and non-stimulated animals with electrodes in the NAcc showed a common pattern of brain metabolism modulation, presumably derived from the electrodes’ presence. In contrast, animals stimulated in the LH showed a relative metabolic invariance, and a reduction of neuroplasticity molecules, evidencing long-lasting neural changes. Our findings suggest that the reversibility or persistence of DBS modulation in the long-term depends on the selected DBS target. Therefore, the DBS footprint would be influenced by the stability achieved in the neural network involved during the stimulation.
A theorized new class of polyhedral hydrocarbons of molecular formula CnHn and their bottom-up scaffold expansions into hyperstructures
Authors: Machado Camila M. B. , Lima Nathalia B. D. , Lins Sóstenes L. S. , Simas Alfredo M. 
Published: March 2021

AbstractWe address the use of Euler's theorem and topological algorithms to design 18 polyhedral hydrocarbons of general formula CnHn that exist up to 28 vertexes containing four- and six-membered rings only; compounds we call “nuggets”. Subsequently, we evaluated their energies to verify the likelihood of their chemical existence. Among these compounds, 13 are novel systems, of which 3 exhibit chirality. Further, the ability of all nuggets to perform fusion reactions either through their square faces, or through their hexagonal faces was evaluated. Indeed, they are potentially able to form bottom-up derived molecular hyperstructures with great potential for several applications. By considering these fusion abilities, the growth of the nuggets into 1D, 2D, and 3D-scaffolds was studied. The results indicate that nugget24a (C24H24) is predicted to be capable of carrying out fusion reactions. From nugget24a, we then designed 1D, 2D, and 3D-scaffolds that are predicted to be formed by favorable fusion reactions. Finally, a 3D-scaffold generated from nugget24a exhibited potential to be employed as a voxel with a chemical structure remarkably similar to that of MOF ZIF-8. And, such a voxel, could in principle be employed to generate any 3D sculpture with nugget24a as its level of finest granularity.
MicroRNAs modulate ethylene induced retrograde signal for rice endosperm starch biosynthesis by default expression of transcriptome
Authors: Panigrahi Sonam , Panigrahy Madhusmita , Kariali Ekamber , Dash Sushanta Kumar , Sahu Binod Bihari , Sahu Sushil Kumar , Mohapatra Pravat Kumar , Panigrahi Kishore Chandra Sekhar 
Published: March 2021

AbstractControl of stage specific spike in ethylene production at anthesis has been a vauable route to potentially enhance genetic ceiling for grain filling of rice spikelet. A number of genes controlling ethylene homeostasis and starch synthesis have been identified so long, but lack of credible information on master modulation of gene expression by miRNAs and their target genes associated with hormonal dynamics obfuscate mechanisms controlling genotype difference in quantum of grain filling. The confusion accounts for consequent shrinkage of options for yield manipulation. In a two by two factorial design, miRNA regulation of spikelet specific grain development in low against high sterile recombinant inbred lines of riceOryza sativaL. namely CR 3856-62-11-3-1-1-1-1-1-1 (SR 157) and CR 3856-63-1-1-1-1-1-1-1 (SR 159) respectively, and inferior verses superior spikelets were compared during first 10 days after anthesis. Grain filling was poorer in SR159 than SR157 and inferior spikelets in the former were most vulnerable. Between the cultivars, overall expression of unique miRNAs with targets on ethylene pathway genes was higher in SR159 than SR157 and the situation was opposite for auxin pathway genes. Precision analysis in psTarget server database identified up-regulation of MIR2877 and MIR530-5p having Os11t0141000-02 and Os07t0239400-01 (PP2A regulatory subunit-like protein and ethylene-responsive small GTP-binding proteins) and MIR396h having Os01t0643300-02 (an auxin efflux carrier protein) and Os01t0643300-01 (a PIN1-like auxin transport protein), as targets with highest probability at anthesis and 5 days after anthesis respectively, in the inferior spikelet and the fold change values of DGE matched with pattern of gene expression (relative transcript level) in the qRT-PCR studies conducted for relevant miRNAs and protein factors for ethylene and auxin signalling. In conclusion, epigenetic regulation of both auxin and ethylene homeostasis control grain filling of rice spikelet was established, but evidences were more robust for the latter.
Neutralization of SARS-CoV-2 with IgG from COVID-19-convalescent plasma
Authors: Maeda Kenji , Higashi-Kuwata Nobuyo , Kinoshita Noriko , Kutsuna Satoshi , Tsuchiya Kiyoto , Hattori Shin-ichiro , Matsuda Kouki , Takamatsu Yuki , Gatanaga Hiroyuki , Oka Shinichi , Sugiyama Haruhito , Ohmagari Norio , Mitsuya Hiroaki 
Published: March 2021

AbstractWhile there are various attempts to administer COVID-19-convalescent plasmas to SARS-CoV-2-infected patients, neither appropriate approach nor clinical utility has been established. We examined the presence and temporal changes of the neutralizing activity of IgG fractions from 43 COVID-19-convalescent plasmas using cell-based assays with multiple endpoints. IgG fractions from 27 cases (62.8%) had significant neutralizing activity and moderately to potently inhibited SARS-CoV-2 infection in cell-based assays; however, no detectable neutralizing activity was found in 16 cases (37.2%). Approximately half of the patients (~ 41%), who had significant neutralizing activity, lost the neutralization activity within ~ 1 month. Despite the rapid decline of neutralizing activity in plasmas, good amounts of SARS-CoV-2-S1-binding antibodies were persistently seen. The longer exposure of COVID-19 patients to greater amounts of SARS-CoV-2 elicits potent immune response to SARS-CoV-2, producing greater neutralization activity and SARS-CoV-2-S1-binding antibody amounts. The dilution of highly-neutralizing plasmas with poorly-neutralizing plasmas relatively readily reduced neutralizing activity. The presence of good amounts of SARS-CoV-2-S1-binding antibodies does not serve as a surrogate ensuring the presence of good neutralizing activity. In selecting good COVID-19-convalescent plasmas, quantification of neutralizing activity in each plasma sample before collection and use is required.
Quantitative dual contrast photon-counting computed tomography for assessment of articular cartilage health
Authors: Paakkari Petri , Inkinen Satu I. , Honkanen Miitu K. M. , Prakash Mithilesh , Shaikh Rubina , Nieminen Miika T. , Grinstaff Mark W. , Mäkelä Janne T. A. , Töyräs Juha , Honkanen Juuso T. J. 
Published: March 2021

AbstractPhoton-counting detector computed tomography (PCD-CT) is a modern spectral imaging technique utilizing photon-counting detectors (PCDs). PCDs detect individual photons and classify them into fixed energy bins, thus enabling energy selective imaging, contrary to energy integrating detectors that detects and sums the total energy from all photons during acquisition. The structure and composition of the articular cartilage cannot be detected with native CT imaging but can be assessed using contrast-enhancement. Spectral imaging allows simultaneous decomposition of multiple contrast agents, which can be used to target and highlight discrete cartilage properties. Here we report, for the first time, the use of PCD-CT to quantify a cationic iodinated CA4+ (targeting proteoglycans) and a non-ionic gadolinium-based gadoteridol (reflecting water content) contrast agents inside human osteochondral tissue (n = 53). We performed PCD-CT scanning at diffusion equilibrium and compared the results against reference data of biomechanical and optical density measurements, and Mankin scoring. PCD-CT enables simultaneous quantification of the two contrast agent concentrations inside cartilage and the results correlate with the structural and functional reference parameters. With improved soft tissue contrast and assessment of proteoglycan and water contents, PCD-CT with the dual contrast agent method is of potential use for the detection and monitoring of osteoarthritis.
The effects of exercise training on lipid profile in patients with sarcoidosis
Authors: Jastrzebski Dariusz , Toczylowska Beata , Zieminska Elzbieta , Zebrowska Aleksandra , Kostorz-Nosal Sabina , Swietochowska Elzbieta , Di Giulio Camillo , Ziora Dariusz 
Published: March 2021

AbstractThis study aimed to determine the use of lipid profiling to assess the effects of moderate intensity exercise training (ET) on patients with sarcoidosis. Fourteen patients with sarcoidosis (mean age, 46.0 ± 9.6 years) were examined before and after 3-week of ET programme in hospital settings. Symptoms (fatigue: FAS, dyspnoea: MRC), lung function tests and physical function tests (6 MWT, muscle force) were measured before and after ET. Proton nuclear magnetic resonance (NMR) spectroscopy combined with orthogonal partial least squares-discriminant analysis (OPLS-DA) was used to determine lipid profile before and after ET. Twenty-five NMR signals from lipid compounds were selected for further analysis as well as serum lipid and inflammatory markers. Three weeks of ET results in improvement of symptoms (FAS: 27.5 vs. 21.0; p < 0.001, MRC: 0.86 vs. 0.14; p = 0.002) and physical function (6MWT: 508.43 vs. 547.29; p = 0.039). OPLS-DA analysis of the lipid profiles of patients with sarcoidosis revealed differences among the samples before and after ET, including decreases in fatty acids (p < 0.017), triglycerides (p < 0.022) and total cholesterol (p < 0.020). Other changes included shifts in fatty acids oxidation products and triacylglycerol esters. A short-time, in-hospital exercise training benefits patients with sarcoidosis by enhancing their physical function. Additionally, positive effect on lipid profile was observed also in this study. It is suggested that lipid profiling could become a new prognostic method to assess effects of pulmonary rehabilitation in patients with sarcoidosis.
Cost-effectiveness of percutaneous coronary intervention versus medical therapy in patients with acute myocardial infarction: real-world and lifetime-horizon data from Taiwan
Authors: Liao Chia-Te , Hsieh Tung-Han , Shih Chia-Yin , Liu Ping-Yen , Wang Jung-Der 
Published: March 2021

AbstractAlthough some studies have assessed the cost-effectiveness of percutaneous coronary intervention (PCI) in acute myocardial infarction (AMI), there has been a lack of nationwide real-world studies estimating life expectancy (LE), loss-of-LE, life-years saved, and lifetime medical costs. We evaluated the cost-effectiveness of PCI versus non-PCI therapy by integrating a survival function and mean-cost function over a lifelong horizon to obtain the estimations for AMI patients without major comorbidities. We constructed a longitudinal AMI cohort based on the claim database of Taiwan's National Health Insurance during 1999–2015. Taiwan's National Mortality Registry Database was linked to derive a survival function to estimate LE, loss-of-LE, life-years saved, and lifetime medical costs in both therapies. This study enrolled a total of 38,441 AMI patients; AMI patients receiving PCI showed a fewer loss-of-LE (3.6 versus 5.2 years), and more lifetime medical costs (US$ 49,112 versus US$ 43,532). The incremental cost-effectiveness ratio (ICER) was US$ 3488 per life-year saved. After stratification by age, the AMI patients aged 50–59 years receiving PCI was shown to be cost-saving. From the perspective of Taiwan's National Health Insurance, PCI is cost-effective in AMI patients without major comorbidities. Notably, for patients aged 50–59 years, PCI is cost-saving.
The Y chromosome of autochthonous Basque populations and the Bronze Age replacement
Authors: Luis Javier Rodriguez , Palencia-Madrid Leire , Mendoza Vivian C. , Garcia-Bertrand Ralph , de Pancorbo Marian M. , Herrera Rene J. 
Published: March 2021

AbstractHere we report on the Y haplogroup and Y-STR diversity of the three autochthonous Basque populations of Alava (n = 54), Guipuzcoa (n = 30) and Vizcaya (n = 61). The same samples genotyped for Y-chromosome SNPs were typed for 17 Y-STR loci (DYS19, DYS385a/b, DYS398I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA H4) using the AmpFlSTR Yfiler system. Six major haplogroups (R, I, E, J, G, and DE) were detected, being R-S116 (P312) haplogroup the most abundant at 75.0% in Alava, 86.7% in Guipuzcoa and 87.3% in Vizcaya. Age estimates for the R-S116 mutation in the Basque Country are 3975 ± 303, 3680 ± 345 and 4553 ± 285 years for Alava, Guipuzcoa and Vizcaya, respectively. Pairwise Rst genetic distances demonstrated close Y-chromosome affinities among the three autochthonous Basque populations and between them and the male population of Ireland and Gascony. In a MDS plot, the population of Ireland segregates within the Basque cluster and closest to the population of Guipuzcoa, which plots closer to Ireland than to any of the other Basque populations. Overall, the results support the notion that during the Bronze Age a dispersal of individuals carrying the R-S116 mutation reached the Basque Country replacing the Paleolithic/Neolithic Y chromosome of the region.
Mutation spectrum of NOD2 reveals recessive inheritance as a main driver of Early Onset Crohn’s Disease
Authors: Horowitz Julie E. , Warner Neil , Staples Jeffrey , Crowley Eileen , Gosalia Nehal , Murchie Ryan , Van Hout Cristopher , Fiedler Karoline , Welch Gabriel , King Alejandra Klauer , Reid Jeffrey G. , Overton John D. , Baras Aris , Shuldiner Alan R. , Griffiths Anne , Gottesman Omri , Muise Aleixo M. , Gonzaga-Jauregui Claudia 
Published: March 2021

AbstractInflammatory bowel disease (IBD), clinically defined as Crohn’s disease (CD), ulcerative colitis (UC), or IBD-unclassified, results in chronic inflammation of the gastrointestinal tract in genetically susceptible hosts. Pediatric onset IBD represents ≥ 25% of all IBD diagnoses and often presents with intestinal stricturing, perianal disease, and failed response to conventional treatments. NOD2 was the first and is the most replicated locus associated with adult IBD, to date. However, its role in pediatric onset IBD is not well understood. We performed whole-exome sequencing on a cohort of 1,183 patients with pediatric onset IBD (ages 0–18.5 years). We identified 92 probands with biallelic rare and low frequency NOD2 variants accounting for approximately 8% of our cohort, suggesting a Mendelian inheritance pattern of disease. Additionally, we investigated the contribution of recessive inheritance of NOD2 alleles in adult IBD patients from a large clinical population cohort. We found that recessive inheritance of NOD2 variants explains ~ 7% of cases in this adult IBD cohort, including ~ 10% of CD cases, confirming the observations from our pediatric IBD cohort. Exploration of EHR data showed that several of these adult IBD patients obtained their initial IBD diagnosis before 18 years of age, consistent with early onset disease. While it has been previously reported that carriers of more than one NOD2 risk alleles have increased susceptibility to Crohn’s Disease (CD), our data formally demonstrate that recessive inheritance of NOD2 alleles is a mechanistic driver of early onset IBD, specifically CD, likely due to loss of NOD2 protein function. Collectively, our findings show that recessive inheritance of rare and low frequency deleterious NOD2 variants account for 7–10% of CD cases and implicate NOD2 as a Mendelian disease gene for early onset Crohn’s Disease.