bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of a conditional transgenic mouse model expressing human Phospholipase A2 Receptor 1
Authors: Jaber Sara , Goehrig Delphine , Bertolino Philippe , Massemin Amélie , Bihl Franck , Chabry Joëlle , Lambeau Gérard , Vindrieux David , Bernard David 
Published: May 2020

AbstractThe Phospholipase A2 Receptor 1 (PLA2R1) was first identified for its ability to bind some secreted PLA2s (sPLA2s). It belongs to the C-type lectin superfamily and it binds different types of proteins. It is likely a multifunctional protein that plays a role i) in inflammation and inflammatory diseases, ii) in cellular senescence, a mechanism participating in aging and age-related diseases including cancer, and iii) in membranous nephropathy (MN), a rare autoimmune kidney disease where PLA2R1 is the major autoantigen. To help study the role of PLA2R1 in these pathophysiological conditions, we have generated a versatile NeoR-hPLA2R1 conditional transgenic mice which will allow the specific expression of human PLA2R1 (hPLA2R1) in relevant organs and cells following Cre recombinase-driven excision of the NeoR-stop cassette flanked by LoxP sites. Proof-of-concept breeding of NeoR-hPLA2R1 mice with the ubiquitous adenoviral EIIa promoter-driven Cre mouse line resulted in the expected excision of the NeoR-stop cassette and the expression of hPLA2R1 in all tested tissues. These Tg-hPLA2R1 animals breed normally, with no reproduction or apparent growth defect. These models, especially the NeoR-hPLA2R1 conditional transgenic mouse line, will facilitate the future investigation of PLA2R1 functions in relevant pathophysiological contexts, including inflammatory diseases, age-related diseases and MN.
Upregulation of follistatin and low apoptotic activity in intraductal oncocytic papillary neoplasm of the pancreatobiliary system
Authors: Nakahodo Jun , Fukumura Yuki , Saito Tsuyoshi , Hirabayashi Kenichi , Doi Reiko , Hayashi Takuo , Yao Takashi 
Published: May 2020

AbstractIntraductal oncocytic papillary neoplasm (IOPN) is a rare intraductal tumor of the pancreatobiliary system. Currently, little is known about its distinct characteristics, unlike intraductal papillary mucinous neoplasms (IPMN) and intraductal papillary neoplasms of the bile duct (IPNB). The present study compared 22 IOPNs (18 pancreatic and 4 biliary) with those of 61 IPMNs/8 IPNBs. IOPNs were classified into pure and combined types, depending on the coexistence of IPMN/IPNB. Multiple gene expression analysis (nCounter system) was performed, and hierarchical clustering analysis separated IOPNs(n = 4) and IPMNs(n = 3)/ IPNBs(n = 3), and pathway score analysis supported the result. Volcano plot identified follistatin (FST) as the most upregulated mRNA in IOPN in comparison to the gastric subtype (log2 fold change of 5.34) and the intestinal subtype (that of 5.81) of IPMN/IPNB. The expression of FST in IOPN was also high in quantitative polymerase chain reaction and immunohistochemical analysis. We also found lower apoptotic activity in IOPN, particularly in pure type, compared to high-grade or invasive IPMN/IPNB using immunohistochemistry for cleaved caspase 3. But, combined type IOPN was more similar to IPMN/IPNB than pure IOPN. In conclusion, we proved that IOPN, particularly pure IOPN, is distinct from IPMN/IPNB in FST mRNA overexpression and exhibits lower apoptotic activity.
A mobile MRI field study of the biochemical cartilage reaction of the knee joint during a 4,486 km transcontinental multistage ultra-marathon using T2* mapping
Authors: Schütz Uwe , Ehrhardt Martin , Göd Sabine , Billich Christian , Beer Meinrad , Trattnig Siegfried 
Published: May 2020

AbstractNearly nothing is known about the consequences of ultra-long-distance running on knee cartilage. In this mobile MRI field study, we analysed the biochemical effects of a 4,486 km transcontinental multistage ultra-marathon on femorotibial joint (FTJ) cartilage. Serial MRI data were acquired from 22 subjects (20 male, 18 finisher) using a 1.5 T MR scanner mounted on a 38-ton trailer, travelling with the participants of the TransEurope FootRace (TEFR) day by day over 64 stages. The statistical analyses focused on intrachondral T2* behaviour during the course of the TEFR as the main outcome variable of interest. T2* mapping (sagittal FLASH T2* weighted gradient echo) is a validated and highly accurate method for quantitative compositional cartilage analysis of specific weightbearing areas of the FTJ. T2* mapping is sensitive to changes in the equilibrium of free intrachondral water, which depends on the content and orientation of collagen and the proteoglycan content in the extracellular cartilage matrix. Within the first 1,100 km, a significant running load-induced T2* increase occurred in all joint regions: 44.0% femoral-lateral, 42.9% tibial-lateral, 34.9% femoral-medial, and 25.1% tibial-medial. Osteochondral lesions showed no relevant changes or new occurrence during the TEFR. The reasons for stopping the race were not associated with knee problems. As no further T2* elevation was found in the second half of the TEFR but a decreasing T2* trend (recovery) was observed after the 3,500 km run, we assume that no further softening of the cartilage occurs with ongoing running burden over ultra-long distances extending 4,500 km. Instead, we assume the ability of the FTJ cartilage matrix to reorganize and adapt to the load.
Regularized selection indices for breeding value prediction using hyper-spectral image data
Authors: Lopez-Cruz Marco , Olson Eric , Rovere Gabriel , Crossa Jose , Dreisigacker Susanne , Mondal Suchismita , Singh Ravi , Campos Gustavo de los 
Published: May 2020

AbstractHigh-throughput phenotyping (HTP) technologies can produce data on thousands of phenotypes per unit being monitored. These data can be used to breed for economically and environmentally relevant traits (e.g., drought tolerance); however, incorporating high-dimensional phenotypes in genetic analyses and in breeding schemes poses important statistical and computational challenges. To address this problem, we developed regularized selection indices; the methodology integrates techniques commonly used in high-dimensional phenotypic regressions (including penalization and rank-reduction approaches) into the selection index (SI) framework. Using extensive data from CIMMYT’s (International Maize and Wheat Improvement Center) wheat breeding program we show that regularized SIs derived from hyper-spectral data offer consistently higher accuracy for grain yield than those achieved by standard SIs, and by vegetation indices commonly used to predict agronomic traits. Regularized SIs offer an effective approach to leverage HTP data that is routinely generated in agriculture; the methodology can also be used to conduct genetic studies using high-dimensional phenotypes that are often collected in humans and model organisms including body images and whole-genome gene expression profiles.
Metagenomic analysis of an urban resistome before and after wastewater treatment
Authors: Lira Felipe , Vaz-Moreira Ivone , Tamames Javier , Manaia Célia M. , Martínez José Luis 
Published: May 2020

AbstractDetermining the effect of wastewater treatment in water resistome is a topic of interest for water quality, mainly under re-use and One-Health perspectives. The resistome, the plasmidome, and the bacterial community composition of samples from influents and treated effluents from a wastewater treatment plant located in Northern Portugal were studied using metagenomic techniques. Wastewater treatment contributed to reduce the abundance of resistance genes and of plasmid replicons, coinciding with a decline in the number of intrinsic resistance genes from Enterobacteriaceae, as well as with a reduction in the relative abundance of Firmicutes and Proteobacteria after treatment. These taxons comprise bacterial pathogens, including those belonging to the ESKAPE group, which encompasses bacteria with the highest risk of acquiring antibiotic resistance, being the most relevant hosts of resistance genes acquired through horizontal gene transfer. Our results support that wastewater treatment efficiently removes the hosts of antibiotic resistance genes and, consequently, the harboured antibiotic resistance genes. Principal component analysis indicates that the resistome and the bacterial composition clustered together in influent samples, while did not cluster in final effluent samples. Our results suggest that wastewater treatment mitigates the environmental dissemination of urban resistome, through the removal of the hosts harbouring mobile resistance genes.
Fibrillar form of α-synuclein-specific scFv antibody inhibits α-synuclein seeds induced aggregation and toxicity
Authors: Gupta Vijay , Salim Safa , Hmila Issam , Vaikath Nishant N. , Sudhakaran Indulekha P. , Ghanem Simona S. , Majbour Nour K. , Abdulla Sara A. , Emara Mohamed M. , Abdesselem Houari B. , Lukacsovich Tamas , Erskine Daniel , El-Agnaf Omar M. A. 
Published: May 2020

AbstractSynucleinopathies including Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA) are characterized by pathological accumulation of α-synuclein (α-syn). Amongst the various approaches attempting to tackle the pathological features of synucleinopathies, antibody-based immunotherapy holds much promise. However, the large size of antibodies and corresponding difficulty in crossing the blood-brain barrier has limited development in this area. To overcome this issue, we engineered single-chain variable fragments (scFvs) against fibrillar α-syn, a putative disease-relevant form of α-syn. The purified scFvs showed specific activity towards α-syn fibrils and oligomers in comparison to monomers and recognized intracellular inclusions in human post-mortem brain tissue of Lewy body disease cases, but not aged controls. In vitro studies indicated scFvs inhibit the seeding of α-syn aggregation in a time-dependent manner, decreased α-syn seed-induced toxicity in a cell model of PD, and reduced the production of insoluble α-syn phosphorylated at Ser-129 (pS129-α-syn). These results suggest that our α-syn fibril-specific scFvs recognize α-syn pathology and can inhibit the aggregation of α-syn in vitro and prevent seeding-dependent toxicity. Therefore, the scFvs described here have considerable potential to be utilized towards immunotherapy in synucleinopathies and may also have applications in ante-mortem imaging modalities.
Circulating lymphocytes and monocytes transcriptomic analysis of patients with type 2 diabetes mellitus, dyslipidemia and periodontitis
Authors: Corbi Sâmia C. T. , de Vasconcellos Jaira F. , Bastos Alliny S. , Bussaneli Diego Girotto , da Silva Bárbara Roque , Santos Raquel Alves , Takahashi Catarina S. , de S. Rocha Cristiane , Carvalho Benilton de Sá , Maurer-Morelli Cláudia V. , Orrico Silvana R. P. , Barros Silvana P. , Scarel-Caminaga Raquel M. 
Published: May 2020

AbstractType 2 diabetes mellitus (T2DM), dyslipidemia and periodontitis are frequently associated pathologies; however, there are no studies showing the peripheral blood transcript profile of these combined diseases. Here we identified the differentially expressed genes (DEGs) of circulating lymphocytes and monocytes to reveal potential biomarkers that may be used as molecular targets for future diagnosis of each combination of these pathologies (compared to healthy patients) and give insights into the underlying molecular mechanisms of these diseases. Study participants (n = 150) were divided into groups: (H) systemically and periodontal healthy (control group); (P) with periodontitis, but systemically healthy; (DL-P) with dyslipidemia and periodontitis; (T2DMwell-DL-P) well-controlled type 2 diabetes mellitus with dyslipidemia and periodontitis; and (T2DMpoorly-DL-P) poorly-controlled type 2 diabetes mellitus with dyslipidemia and periodontitis. We preprocessed the microarray data using the Robust Multichip Average (RMA) strategy, followed by the RankProd method to identify candidates for DEGs. Furthermore, we performed functional enrichment analysis using Ingenuity Pathway Analysis and Gene Set Enrichment Analysis. DEGs were submitted to pairwise comparisons, and selected DEGs were validated by quantitative polymerase chain reaction. Validated DEGs verified from T2DMpoorly-DL-P versus H were: TGFB1I1, VNN1, HLADRB4 and CXCL8; T2DMwell-DL-P versus H: FN1, BPTF and PDE3B; DL-P versus H: DAB2, CD47 and HLADRB4; P versus H: IGHDL-P, ITGB2 and HLADRB4. In conclusion, we identified that circulating lymphocytes and monocytes of individuals simultaneously affected by T2DM, dyslipidemia and periodontitis, showed an altered molecular profile mainly associated to inflammatory response, immune cell trafficking, and infectious disease pathways. Altogether, these results shed light on novel potential targets for future diagnosis, monitoring or development of targeted therapies for patients sharing these conditions.
Optimization of cultivation techniques improves the agronomic behavior of Agaricus subrufescens
Authors: Pardo-Giménez Arturo , Pardo José Emilio , Dias Eustáquio Souza , Rinker Danny Lee , Caitano Cinthia Elen Cardoso , Zied Diego Cunha 
Published: May 2020

AbstractNew species of medicinal mushrooms have emerged over the past several decades, such as the Sun mushroom, Agaricus subrufescens. Horticultural improvements are required to shift its cultivation from small-scale local production to large-scale international production. The research reported here evaluated the agronomic behavior and the chemical characteristics of the Sun mushroom as a function of i) nutritional supplementation ii) ruffling of the casing layer and iii) the temperature management on the primordia induction and reduction of the crop cycle. Supplementation was beneficial for yield, unit mushroom weigh and decrease in time to first harvest. Supplementation improved biological efficiency with Champfood providing a yield increase of 15% over the non-supplemented compost. Among the supplements only Promycel increased the individual mushroom weight. Ruffling overall improved the yield in the 2nd and 4th flush. Already biological efficiency was greater by 21%. The highest yield harvested in any single day in the crop occurred in 3rd flush with the amount of 2.484 kg of mushrooms per m2 for the rapid induction method. Still the biological efficiency was not significantly affected by the mushroom induction temperature method. Only the fat content of the mushrooms was positively affected by the rapid induction of primordia. Champfood supplement promotes a reduction in the value of earliness and an increase of 1st flush yield. The ruffling technique provided an increase in biological efficiency due to the great number of mushrooms harvested. Rapid primordia induction allowed the crop cycle to end 3 days earlier than the slow primordia induction, providing a higher production rate.
A single variant sequencing method for sensitive and quantitative detection of HIV-1 minority variants
Authors: Sidhu Gurjit , Schuster Layla , Liu Lin , Tamashiro Ryan , Li Eric , Langaee Taimour , Wagner Richard , Wang Gary P. 
Published: May 2020

AbstractHIV drug resistance is a major threat to achieving long-term viral suppression in HIV-positive individuals. Drug resistant HIV variants, including minority variants, can compromise response to antiretroviral therapy. Many studies have investigated the clinical relevance of drug resistant minority variants, but the level at which minority variants become clinically relevant remains unclear. A combination of Primer-ID and deep sequencing is a promising approach that may quantify minority variants more accurately compared to standard deep sequencing. However, most studies that used the Primer-ID method have analyzed clinical samples directly. Thus, its sensitivity and quantitative accuracy have not been adequately validated using known controls. Here, we constructed defined proportions of artificial RNA and virus quasispecies and measured their relative proportions using the Primer-ID based, quantitative single-variant sequencing (qSVS) assay. Our results showed that minority variants present at 1% of quasispecies were detected reproducibly with minimal variations between technical replicates. In addition, the measured frequencies were comparable to the expected frequencies. These data validate the accuracy and reproducibility of the qSVS assay in quantifying authentic HIV minority variants, and support the use of this approach to examine the impacts of minority HIV variants on virologic response and clinical outcome.
Immunorthodontics: in vivo gene expression of orthodontic tooth movement
Authors: Klein Yehuda , Fleissig Omer , Polak David , Barenholz Yechezkel , Mandelboim Ofer , Chaushu Stella 
Published: May 2020

AbstractOrthodontic tooth movement (OTM) is a “sterile” inflammatory process. The present study aimed to reveal the underlying biological mechanisms, by studying the force associated-gene expression changes, in a time-dependent manner. Ni-Ti springs were set to move the upper 1st-molar in C57BL/6 mice. OTM was measured by μCT. Total-RNA was extracted from tissue blocks at 1,3,7 and 14-days post force application, and from two control groups: naïve and inactivated spring. Gene-expression profiles were generated by next-generation-RNA-sequencing. Gene Set Enrichment Analysis, K-means algorithm and Ingenuity pathway analysis were used for data interpretation. Genes of interest were validated with qRT-PCR. A total of 3075 differentially expressed genes (DEGs) were identified, with the greatest number at day 3. Two distinct clusters patterns were recognized: those in which DEGs peaked in the first days and declined thereafter (tissue degradation, phagocytosis, leukocyte extravasation, innate and adaptive immune system responses), and those in which DEGs were initially down-regulated and increased at day 14 (cell proliferation and migration, cytoskeletal rearrangement, tissue homeostasis, angiogenesis). The uncovering of novel innate and adaptive immune processes in OTM led us to propose a new term “Immunorthodontics”. This genomic data can serve as a platform for OTM modulation future approaches.
Risk of cancer in patients with glaucoma: A nationwide population-based cohort study
Authors: Jung Younhea , Han Kyungdo , Na Kyung-sun , Kim Gee-hyun , Ha Minji , Paik Ji-Sun , Moon Jung Il 
Published: May 2020

AbstractTo compare the risk of cancer development between patients with glaucoma and those without, we conducted a nationwide population-based cohort study using the Korean National Health Insurance Database. Individuals with diagnosis of glaucoma between 2007 and 2016 were identified, and controls were 1:1 matched based on age and sex. We calculated the incidence rates(IR) and hazard ratios(HR) before and after adjusting for age, gender, diabetes, smoking history, and body mass index. A total of 107,536 individuals with glaucoma and the same number of individuals without glaucoma were included. The IR of overall cancer were 12.23 and 11.62 per 1,000 individuals in the glaucoma and control groups, respectively. The HR of overall cancer was significantly higher in the glaucoma group before(HR: 1.053) and after adjusting for confounding factors(adjusted HR: 1.049) compared to that in the control group. The risk of overall cancer and specific cancers varied depending on gender and age groups, and the association was stronger in women and those under 65 years of age. Our study revealed that individuals with glaucoma showed higher risk of overall cancer and higher risk of specific cancers than those without glaucoma.
Denser Markers and Advanced Statistical Method Identified More Genetic Loci Associated with Husk Traits in Maize
Authors: Cui Zhenhai , Dong Haixiao , Zhang Ao , Ruan Yanye , Jiang Siqi , He Yan , Zhang Zhiwu 
Published: May 2020

AbstractThe husk—the leaf-like outer covering of maize ear—has multiple functions, including protecting the ear from diseases infection and dehydration. In previous studies, we genotyped an association panel of 508 inbred lines genotyped with a total of ~550,000 SNPs (Illumina 50 K SNP Chip and RNA-seq). Genome-Wide Association Studies (GWAS) were conducted on four husk traits: husk length (HL), husk layer number (HN), husk thickness (HT), and husk width (HW). Minimal associations were identified and none of them passed the P-value threshold after a Bonferroni multiple-test correction using a single locus test in framework of mixed linear model. In this study, we doubled the number of SNPs (~1,250,000 in total) by adding GBS and 600 K SNP Chip. GWAS, performed with the recently developed multiple loci model (BLINK), revealed six genetic loci associated with HN and HT above the Bonferroni multiple-test threshold. Five candidate genes were identified based on the linkage disequilibrium with these loci, including GRMZM2G381691 and GRMZM2G012416. These two genes were up-regulation and down-regulation in all husk related tissues, respectively. GRMZM2G381691 associated with HT encoded a CCT domain protein, which expressed higher in tropical than temperate maize. GRMZM2G012416 associated with HN encoded an Armadillo (ARM) repeat protein, which regulated GA signal pathway. These associated SNPs and candidate genes paved a path to understand the genetic architecture of husk in maize.
Maternal administration of probiotics promotes brain development and protects offspring’s brain from postnatal inflammatory insults in C57/BL6J mice
Authors: Lu Jing , Lu Lei , Yu Yueyue , Baranowski Jillian , Claud Erika C. 
Published: May 2020

AbstractNeonatal morbidities are associated with long term neurological deficits in life and have also been associated with dysbiosis. We tested whether optimizing the neonate’s microbiome through maternal probiotic supplementation can improve offspring’s neurodevelopmental outcomes. Maternal LB supplementation, carried out by givingLactobacillus acidophilusandBifidobacterium infantis(LB) to pregnant C57/BL6J mice daily from E16 to weaning, significantly suppressed postnatal peripheral proinflammatory insult-induced systemic inflammation and normalized compromised blood-brain barrier permeability and tight junction protein expression in the offspring at pre-weaned age. Maternal LB exposure also regulated markers associated with leukocyte transendothelial migration, extracellular matrix injury and neuroinflammation. The suppressed neuroinflammation by maternal LB supplementation was associated with reduced astrocyte/microglia activation and downregulation of the transcriptional regulators CEBPD and IκBα. Furthermore, maternal LB supplementation promoted neuronal and oligodendrocyte progenitor cell development. Our study demonstrates the efficacy of maternal LB supplementation in modulating systemic and central nervous system inflammation as well as promoting neural/oligodendrocyte progenitor development in the offspring. This evidence suggests that maternal probiotic supplementation may be a safe and effective strategy to improve neurological outcomes in the offspring.