bluuebunny/crossref_metadata_2025_split huggingface dataset:
Municipality-Level Characteristics Associated with Very Low to Good Quality of Water Fluoridation in São Paulo State, Brazil, in 2015
Authors: Belotti L. , Zilbovicius C. , Soares C.C.d.S. , Narvai P.C. , Frazão P. 
Published: November 2020

Introduction: Community water fluoridation (CWF) is a measure of recognized importance due to its effectiveness in preventing tooth decay at the population level. However, for the maximum benefit to be achieved, the high-quality standard of CWF must be maintained over time. Objective: To analyze the municipality-level characteristics associated with quality of water fluoridation in São Paulo state, Brazil. Methods: An ecological study was performed using official data sources on fluoride concentration surveillance in 2015. The outcome was municipalities that have not met the quality standard, identified as those with less than 80% of water samples within the optimal level for caries prevention. The independent variables were municipality-level indicators related to demographics, economics, and sanitation characteristics. Crude and adjusted prevalence ratios were estimated using Poisson regression with robust variance. Results: In total, 43.4% municipalities exhibited the outcome. Adjusted by Gini index, the prevalence ratio was 32% higher in municipalities with lower annual gross domestic product per capita. Adjusted by social responsibility index and earlier variables, the prevalence was higher in the municipalities with higher per capita expenditure on sanitation and health surveillance, where the urban population rate was lower, and with a human development index ≤0.761. Adjusted by earlier variables, the prevalence ratio was twice and 3.5 times higher for municipalities, respectively, with per capita income less than or equal to US$574 and where the type of sanitation utility was municipal and private; 50% higher in those with less than 100,000 habitants; and 20% higher in those with a chlorine concentration nonconformity rate above 0.82%. Conclusions: To ensure high quality of CWF, additional management measures should be implemented in municipalities with less than 100,000 habitants, a higher chlorine concentration nonconformity rate, a lower per capita income, and where the type of sanitation utility was municipal or private. Knowledge Transfer Statement: The study showed that the quality of fluoridation was associated with municipality-level characteristics. The findings can be used by policy makers to identify and support municipalities that will need to improve fluoridation quality if they are to reach oral health goals.
Manganoarrojadite-(KNa), KNa5MnFe13Al(PO4)11(PO3OH)(OH)2, a new arrojadite-group mineral from the Palermo No. 1 mine, New Hampshire, USA
Authors: Lykova Inna , Rowe Ralph , Poirier Glenn , Helwig Kate , Friis Henrik 
Published: November 2020

AbstractA new arrojadite-group mineral manganoarrojadite-(KNa), ideally KNa5MnFe13Al(PO4)11(PO3OH)(OH)2, was found in a phosphate-bearing granite pegmatite at the Palermo No. 1 mine, New Hampshire, USA. It forms anhedral grains up to 1 × 1.5 cm in size combined in aggregates with vivianite, goyazite, quartz and calcite. The mineral is olive green with a pale green streak and vitreous to greasy lustre. The cleavage is good in one direction. The Mohs hardness is 4½. Dcalc is 3.53 g/cm3. Manganoarrojadite-(KNa) is optically biaxial (–), α = 1.658(2), β = 1.666(2), γ = 1.670(2), 2Vmeas. = 67(1)° and 2Vcalc. = 70° (589 nm). The infrared spectrum is reported. The composition (wt.%) is Na2O 6.97, K2O 1.78, CaO 0.31, MgO 2.17, MnO 12.30, FeO 31.17, Al2O3 2.43, P2O5 40.48, F 0.30, H2O 1.32, O = F2 –0.13, total 99.10. The empirical formula calculated on the basis of 12 P and (O+OH+F) = 50 apfu is Na4.73K0.80Ca0.12Mg1.13Mn2+3.65Fe2+9.13Al1.00P12.00O46.59OH3.08F0.33. The ideal structural formula is A1KA2NaB1NaB2NaNa1,2Na2Na3□ CMnMFe13Al(PO4)11(PO3OH)W(OH)2. The mineral is monoclinic, Cc, a = 16.5345(3), b = 10.0406(2), c = 24.6261(5) Å, β = 105.891(2)°, V = 3932.09(14) Å3 and Z = 4. The strongest reflections of the powder X-ray diffraction pattern [d,Å(I)(hkl)] are: 5.902(24)(202), 5.025(24)(020), 3.208(47)(206,$\;\bar{1}$32), 3.048(100)($\bar{5}$14,$\bar{4}$24), 2.758(24)($\bar{6}$02) and 2.704(70)(226). The crystal structure, refined from single-crystal X-ray diffraction data (R1 = 0.025), is of the arrojadite structure type. Manganoarrojadite-(KNa) is the first arrojadite-group mineral with Mn dominant on the site usually occupied by Ca and without Ca as the dominant cation at any cation site.
A 50-kb deletion disrupting the RSPO2 gene is associated with tetradysmelia in Holstein Friesian cattle
Authors: Becker Doreen , Weikard Rosemarie , Schulze Christoph , Wohlsein Peter , Kühn Christa 
Published: November 2020

AbstractBackgroundTetradysmelia is a rare genetic disorder that is characterized by an extremely severe reduction of all limb parts distal of the scapula and pelvic girdle. We studied a Holstein Friesian backcross family with 24 offspring, among which six calves displayed autosomal recessive tetradysmelia. In order to identify the genetic basis of the disorder, we genotyped three affected calves, five dams and nine unaffected siblings using a Bovine Illumina 50 k BeadChip and sequenced the whole genome of the sire.ResultsPathological examination of four tetradysmelia cases revealed a uniform and severe dysmelia of all limbs. Applying a homozygosity mapping approach, we identified a homozygous region of 10.54 Mb on chromosome 14 (Bos taurusBTA14). Only calves that were diagnosed with tetradysmelia shared a distinct homozygous haplotype for this region. We sequenced the whole genome of the cases’ sire and searched for heterozygous single nucleotide polymorphisms (SNPs) and small variants on BTA14 that were uniquely present in the sire and absent from 3102 control whole-genome sequences of the 1000 Bull Genomes Project, but none were identified in the 10.54-Mb candidate region on BTA14. Therefore, we subsequently performed a more comprehensive analysis by also considering structural variants and detected a 50-kb deletion in the targeted chromosomal region that was in the heterozygous state in the cases’ sire. Using PCR, we confirmed that this detected deletion segregated perfectly within the family with tetradysmelia. The deletion spanned three exons of the bovineR-spondin 2(RSPO2) gene, which encode three domains of the respective protein. R-spondin 2 is a secreted ligand of leucine-rich repeats containing G protein-coupled receptors that enhance Wnt signalling and is involved in a broad range of developmental processes during embryogenesis.ConclusionsWe identified a 50-kb deletion on BTA14 that disrupts the coding sequence of theRSPO2gene and is associated with bovine tetradysmelia. To our knowledge, this is the first reported candidate causal mutation for tetradysmelia in a large animal model. Since signalling pathways involved in limb development are conserved across species, the observed inherited defect may serve as a model to further elucidate fundamental pathways of limb development.
Novel domain expansion methods to improve the computational efficiency of the Chemical Master Equation solution for large biological networks
Authors: Kosarwal Rahul , Kulasiri Don , Samarasinghe Sandhya 
Published: November 2020

Abstract
Background
Numerical solutions of the chemical master equation (CME) are important for understanding the stochasticity of biochemical systems. However, solving CMEs is a formidable task. This task is complicated due to the nonlinear nature of the reactions and the size of the networks which result in different realizations. Most importantly, the exponential growth of the size of the state-space, with respect to the number of different species in the system makes this a challenging assignment. When the biochemical system has a large number of variables, the CME solution becomes intractable. We introduce the intelligent state projection (ISP) method to use in the stochastic analysis of these systems. For any biochemical reaction network, it is important to capture more than one moment: this allows one to describe the system’s dynamic behaviour. ISP is based on a state-space search and the data structure standards of artificial intelligence (AI). It can be used to explore and update the states of a biochemical system. To support the expansion in ISP, we also develop a Bayesian likelihood node projection (BLNP) function to predict the likelihood of the states.

Results
To demonstrate the acceptability and effectiveness of our method, we apply the ISP method to several biological models discussed in prior literature. The results of our computational experiments reveal that the ISP method is effective both in terms of the speed and accuracy of the expansion, and the accuracy of the solution. This method also provides a better understanding of the state-space of the system in terms of blueprint patterns.

Conclusions
The ISP is the de-novo method which addresses both accuracy and performance problems for CME solutions. It systematically expands the projection space based on predefined inputs. This ensures accuracy in the approximation and an exact analytical solution for the time of interest. The ISP was more effective both in predicting the behavior of the state-space of the system and in performance management, which is a vital step towards modeling large biochemical systems.
Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms
Authors: Rao Junhua , Peng Lihua , Liang Xinming , Jiang Hui , Geng Chunyu , Zhao Xia , Liu Xin , Fan Guangyi , Chen Fang , Mu Feng 
Published: November 2020

Abstract

Background
DNBSEQ™ platforms are new massively parallel sequencing (MPS) platforms that use DNA nanoball technology. Use of data generated from DNBSEQ™ platforms to detect single nucleotide variants (SNVs) and small insertions and deletions (indels) has proven to be quite effective, while the feasibility of copy number variants (CNVs) detection is unclear.

Results
Here, we first benchmarked different CNV detection tools based on Illumina whole-genome sequencing (WGS) data of NA12878 and then assessed these tools in CNV detection based on DNBSEQ™ sequencing data from the same sample. When the same tool was used, the CNVs detected based on DNBSEQ™ and Illumina data were similar in quantity, length and distribution, while great differences existed within results from different tools and even based on data from a single platform. We further estimated the CNV detection power based on available CNV benchmarks of NA12878 and found similar precision and sensitivity between the DNBSEQ™ and Illumina platforms. We also found higher precision of CNVs shorter than 1 kbp based on DNBSEQ™ platforms than those based on Illumina platforms by using Pindel, DELLY and LUMPY. We carefully compared these two available benchmarks and found a large proportion of specific CNVs between them. Thus, we constructed a more complete CNV benchmark of NA12878 containing 3512 CNV regions.

Conclusions
We assessed and benchmarked CNV detections based on WGS with DNBSEQ™ platforms and provide guidelines for future studies.
Dictyocoela microsporidia diversity and co-diversification with their host, a gammarid species complex (Crustacea, Amphipoda) with an old history of divergence and high endemic diversity
Authors: Quiles Adrien , Wattier Rémi A. , Bacela-Spychalska Karolina , Grabowski Michal , Rigaud Thierry 
Published: November 2020

Abstract

Background
Although the processes of co-evolution between parasites and their hosts are well known, evidence of co-speciation remains scarce. Microsporidian intracellular parasites, due to intimate relationships with their hosts and mixed mode of transmission (horizontal but also vertical, from mother to offspring), may represent an interesting biological model for investigating co-speciation. Amphipod crustaceans, especially gammarids, are regular hosts of microsporidian parasites, in particular the Dictyocoela spp., which have so far been found limited to these amphipods and are known to use a vertical mode of transmission. The amphipod genus Gammarus has a diversification history spanning the last 50–60 Mya and an extensive cryptic diversity in most of the nominal species. Here, we investigated the degree of co-diversification between Dictyocoela and Gammarus balcanicus, an amphipod with high degrees of ancient cryptic diversification and lineage endemism, by examining the genetic diversity of these parasites over the entire geographic range of the host. We hypothesised that the strong host diversification and vertical transmission of Dictyocoela would promote co-diversification.

Results
Using the parasite SSU rDNA as a molecular marker, analyzing 2225 host specimens from 88 sites covering whole host range, we found 31 haplogroups of Dictyocoela, 30 of which were novel, belonging to four Dictyocoela species already known to infect other Gammarus spp. The relationships between Dictyocoela and gammarids is therefore ancient, with the speciation in parasites preceding those of the hosts. Each novel haplogroup was nevertheless specific to G. balcanicus, leaving the possibility for subsequent co-diversification process during host diversification. A Procrustean Approach to Co-phylogeny (PACo) analysis revealed that diversification of Dictyocoela was not random with respect to that of the host. We found high degrees of congruence between the diversification of G. balcanicus and that of Dictyocoela roeselum and D. muelleri. However, we also found some incongruences between host and Dictyocoela phylogenies, e.g. in D. duebenum, probably due to host shifts between different G. balcanicus cryptic lineages.

Conclusion
The evolutionary history of Dictyocoela and Gammarus balcanicus represents an example of an overall host-parasite co-diversification, including cases of host shifts.
Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment
Authors: Guo Da-Long , Wang Zhen-Guang , Pei Mao-Song , Guo Li-Li , Yu Yi-He 
Published: November 2020

Abstract

Background
In a previous study, the early ripening of Kyoho grape following H2O2 treatment was explored at the physiological level, but the mechanism by which H2O2 promotes ripening at the molecular level is unclear. To reveal the molecular mechanism, RNA-sequencing analysis was conducted on the different developmental stages of Kyoho berry treated with H2O2.

Results
In the comparison of treatment and control groups, 406 genes were up-regulated and 683 were down-regulated. Time course sequencing (TCseq) analysis showed that the expression patterns of most of the genes were similar between the treatment and control, except for some genes related to chlorophyll binding and photosynthesis. Differential expression analysis and the weighted gene co-expression network were used to screen significantly differentially expressed genes and hub genes associated with oxidative stress (heat shock protein, HSP), cell wall deacetylation (GDSL esterase/lipase, GDSL), cell wall degradation (xyloglucan endotransglucosylase/ hydrolase, XTH), and photosynthesis (chlorophyll a-b binding protein, CAB1). Gene expression was verified with RT-qPCR, and the results were largely consistent with those of RNA sequencing.

Conclusions
The RNA-sequencing analysis indicated that H2O2 treatment promoted the early ripening of Kyoho berry by affecting the expression levels of HSP, GDSL, XTH, and CAB1 and- photosynthesis- pathways.
A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants
Authors: Dhorne-Pollet Sophie , Barrey Eric , Pollet Nicolas 
Published: November 2020

Abstract

Background
Mitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to sequence whole mitochondrial genomes using nanopore long-read sequencing. Our method relies on the selective elimination of nuclear DNA using an exonuclease treatment and on the amplification of circular mitochondrial DNA using a multiple displacement amplification step.

Results
We optimized each preparative step to obtain a 100 million-fold enrichment of horse mitochondrial DNA relative to nuclear DNA. We sequenced these amplified mitochondrial DNA using nanopore sequencing technology and obtained mitochondrial DNA reads that represented up to half of the sequencing output. The sequence reads were 2.3 kb of mean length and provided an even coverage of the mitochondrial genome. Long-reads spanning half or more of the whole mtDNA provided a coverage that varied between 118X and 488X. We evaluated SNPs identified using these long-reads by Sanger sequencing as ground truth and found a precision of 100.0%; a recall of 93.1% and a F1-score of 0.964 using the Twilight horse mtDNA reference. The choice of the mtDNA reference impacted variant calling efficiency with F1-scores varying between 0.947 and 0.964.

Conclusions
Our method to amplify mtDNA and to sequence it using the nanopore technology is usable for mitochondrial DNA variant analysis. With minor modifications, this approach could easily be applied to other large circular DNA molecules.
Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns
Authors: Lu Yuan , Boswell Mikki , Boswell William , Salinas Raquel Ybanez , Savage Markita , Reyes Jose , Walter Sean , Marks Rebecca , Gonzalez Trevor , Medrano Geraldo , Warren Wesley C. , Schartl Manfred , Walter Ronald B. 
Published: November 2020

AbstractBackgroundStudying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shifts in basal gene expression patterns are important factors to be considered when studying genetic functions. However, adequate efforts have not been applied to studying basal gene expression variation on a global scale to establish transcriptional activity baselines for each organ. Furthermore, the investigation of cyclic expression pattern comparisons between genome duplication created paralogs, and potential functional divergence between them has been neglected. To address these questions, we utilized a teleost fish species,Xiphophorus maculatus,and profiled gene expression within 9 organs at 3-h intervals throughout a 24-h diurnal period.ResultsOur results showed 1.3–21.9% of genes in different organs exhibited cyclic expression patterns, with eye showing the highest fraction of cycling genes while gonads yielded the lowest. A majority of the duplicated gene pairs exhibited divergences in their basal level expression patterns wherein only one paralog exhibited an oscillating expression pattern, or both paralogs exhibit oscillating expression patterns, but each gene duplicate showed a different peak expression time, and/or in different organs.ConclusionsThese observations suggest cyclic genes experienced significant sub-, neo-, or non-functionalization following the teleost genome duplication event. In addition, we developed a customized, web-accessible, gene expression browser to facilitate data mining and data visualization for the scientific community.
Changes in transcriptomic and metabolomic profiles of morphotypes of Ophiocordyceps sinensis within the hemocoel of its host larvae, Thitarodes xiaojinensis
Authors: Li Miaomiao , Meng Qian , Zhang Huan , Shu Ruihao , Zhao Yanni , Wu Peipei , Li Xuan , Zhou Guiling , Qin Qilian , Zhang Jihong 
Published: November 2020

AbstractBackgroundOphiocordyceps sinensis(Berk.) is a well-known entomopathogenic and medicinal fungus. It parasitizes and mummifies the underground ghost moth larvae to produce a fruiting body named Chinese cordyceps. Specific for the fungus,O. sinensisexperiences a biotrophic vegetative growth period spanning over 5 months. During this vegetative growth, it appears successively in the host hemocoel in three/four morphotypes, namely, the yeast-like blastospores (subdivided into proliferative (BP) and stationary phase (BS)), prehyphae (PreHy) and the hyphae (Hy). This peculiar morphogenesis has been elucidated through morphological and ultrastructural observations, but its molecular basis remains cryptic. In this study, transcriptome and metabolome profiling of BP, BS, PreHy and Hy stages were performed to characterize the key genes, metabolites, and signaling pathways that regulated the vegetative development ofO. sinensisinThitarodes xiaojinensislarva.ResultsThe molecular events and metabolic pathways that regulated different intracellular processes at various stages were examined. Cluster analyses of differentially expressed genes across the four stages revealed the stage specifically enriched pathways. Analysis of metabolome profiles showed that carbon metabolism and several amino acids biosynthesis were significantly perturbed during the tested development stages ofO. sinensisin the host hemocoel. Genes homologous toSaccharomyces cerevisiaeMAPK cascade were significantly up-regulated during the transition from blastospore to hypha. The up-regulation of Sho1, a regulator protein, suggested nutrient starvation act a role in activation of MAPK pathway and filamentous growth. In addition, up-regulation of several fatty acid synthesis genes and their corresponding products accumulation in the samples of BS might explain more lipid droplets were observed in BS than in BP. Coupled with the up-regulation of fatty acid degradation during PreHy and Hy stages, it is presumed that lipid accumulation and mobilization play important roles in filamentous development.ConclusionsThis is the first report comprehensively describing developmental transcriptomics and metabolomics ofO. sinensisin vivo.Our findings provide new perspectives into the key pathways and hub genes involved in morphological changes of fungus developed in the hemocoel of its host, and are expected to guide future studies on morphogenesis and morphotype changes of entomopathogenic fungi in vivo.