bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated genomic view of SARS-CoV-2 in India
Authors: Kumar Pramod , Pandey Rajesh , Sharma Pooja , Dhar Mahesh S , Vivekanand A , Uppili Bharathram , Vashisht Himanshu , Wadhwa Saruchi , Tyagi Nishu , Fatihi Saman , Sharma Uma , Singh Priyanka , Lall Hemlata , Datta Meena , Gupta Poonam , Saini Nidhi , Tewari Aarti , Nandi Bibhash , Kumar Dhirendra , Bag Satyabrata , Deepanshi  , Rathore Surabhi , Jatana Nidhi , Jaiswal Varun , Gogia Hema , Madan Preeti , Singh Simrita , Singh Prateek , Dash Debasis , Bala Manju , Kabra Sandhya , Singh Sujeet , Mukerji Mitali , Thukral Lipi , Faruq Mohammed , Agrawal Anurag , Rakshit Partha 
Published: June 2020

SUMMARYIndia first detected SARS-CoV-2, causal agent of COVID-19 in late January-2020, imported from Wuhan, China. March-2020 onwards; importation of cases from rest of the countries followed by seeding of local transmission triggered further outbreaks in India. We used ARTIC protocol based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT from Oxford Nanopore Technology to understand introduction and local transmission. The analyses revealed multiple introductions of SARS-CoV-2 from Europe and Asia following local transmission. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, here, proposed as A4-clade based on its divergence within A-cluster. The viral haplotypes may link their persistence to geo-climatic conditions and host response. Despite the effectiveness of non-therapeutic interventions in India, multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.
Induction of Muscle Regenerative Multipotent Stem Cells from Human Adipocytes by PDGF-AB and 5-Azacytidine
Authors: Yeola Avani , Subramanian Shruthi , Oliver Rema A. , Lucas Christine A. , Thoms Julie A. I. , Yan Feng , Olivier Jake , Chacon Diego , Tursky Melinda L. , Hung Tzongtyng , Power Carl , Hardy Philip , Ma David D. , McCarroll Joshua , Kavallaris Maria , Hesson Luke B. , Beck Dominik , Curtis David J. , Wong Jason W.H. , Hardeman Edna C. , Walsh William R. , Mobbs Ralph , Chandrakanthan Vashe , Pimanda John E. 
Published: June 2020

ABSTRACTTerminally differentiated murine osteocytes and adipocytes can be reprogrammed using platelet-derived growth factor–AB and 5-Azacytidine into multipotent stem cells with stromal cell characteristics. To generate a product that is amenable for therapeutic application, we have modified and optimised culture conditions to reprogram human adipocytes into induced multipotent stem cells (iMS) and expand them in vitro. The basal transcriptomes of adipocyte-derived iMS cells and matched adipose-tissue-derived mesenchymal stem cells were remarkably similar. However, there were distinct changes in histone modifications and CpG methylation at cis-regulatory regions consistent with an epigenetic landscape that was primed for tissue development and differentiation. In a non-specific tissue injury xenograft model, iMS cells contributed directly to new muscle, bone, cartilage and blood vessels with no evidence of teratogenic potential. In a cardiotoxin muscle injury model, iMS cells contributed specifically to satellite cells and myofibres without ectopic tissue formation. Taken together, human adipocyte derived iMS cells regenerate tissues in a context dependent manner without ectopic or neoplastic growth.
Providing recombinant gonadotropin-based therapies that induce complete oogenesis and produce viable larvae from an immature teleost, flathead grey mullet (Mugil cephalus)
Authors: Ramos-Júdez Sandra , Chauvigné François , González-López Wendy Ángela , Rosenfeld Hanna , Cerdà Joan , Giménez Ignacio , Duncan Neil 
Published: June 2020

AbstractUnder intensive captive conditions, wild-caught flathead grey mullet (Mugil cephalus) females remained arrested at early gonad development and no sperm could be obtained from males. With the aim to induce and complete oogenesis, induce the release of sperm and obtain fertilized eggs, adult female and male grey mullet were treated with M. cephalus single-chain recombinant gonadotropins (rGths), follicle-stimulating (rFsh) and luteinizing (rLh) hormones. In Experiment 1, fish were treated with a weekly dose of rFsh (15 μg kg−1), which in females significantly (P < 0.001) increased plasma concentration of 17β-estradiol and induced vitellogenic oocyte growth up to a maximum mean diameter of 425 ± 19 μm after 9 weeks of treatment. In Experiment 2, fish were treated with weekly injections of both rFsh and rLh at different doses (from 2.5 to 12 μg kg−1). Oocyte diameter reached 609 ± 5 μm, from which final oocyte maturation and ovulation was induced with 30 μg kg−1 of rLh and 40 mg kg−1 of progesterone. Good quality sperm (> 75% motile spermatozoa) was obtained from males in both experiments, and in Exp. 2 the addition of rLh induced the production of higher quantities of sperm that were used to fertilise the eggs. Although fertilisation was low (0.4 %), these fertilized eggs with embryo development produced viable larvae (71% hatching rate). This is the first report in a teleost species, to obtain larvae from eggs that were from immature females induced through to maturation with rGths. In comparison, control females remained arrested as immature fish and control males did not produce sperm. The study demonstrated that both rGths are effective to induce the entire process of oogenesis in sexually immature female grey mullet and to obtain flowing sperm from males, adding more data to confirm the roles of the Gths in teleost gametogenesis. This advance provides the bases of a therapy for the use in the aquaculture of teleost of commercial interest or the conservation of endangered species.
Explaining #TheShoe based on the optimal color hypothesis: The role of chromaticity vs. luminance distribution in ambiguous image
Authors: Morimoto Takuma , Fukuda Kazuho , Uchikawa Keiji 
Published: June 2020

AbstractThe image of #theShoe is a derivative image of #theDress which induced vastly different color experiences across individuals. The majority of people perceive that the shoe has grey leather with turquoise laces, but others report pink leather with white laces. We hypothesized #theShoe presents the problem of color constancy, where different people estimated different illuminants falling onto the shoe. The present study specifically aimed to understand what cues in the shoe image caused the ambiguity based on the optimal color hypothesis: our visual system knows the gamut of surface colors under various illuminants and applies the knowledge for illuminant estimation. The analysis showed that estimated illuminant chromaticity largely changes depending on the assumed intensity of the illuminant. When the illuminant intensity was assumed to be low, a high color temperature was estimated. In contrast, assuming high illuminant intensity led to the estimation of low color temperature. A simulation based on a von Kries correction showed that the subtraction of estimated illuminants from the original image shifts the appearance of the shoe towards the reported states (i.e. gray-turquoise or pink-white). These results suggest that the optimal color hypothesis provides a theoretical interpretation to the #theShoe phenomenon. Moreover, this luminance-dependent color-shift was observed in #theDress phenomenon, supporting the notion that the same trigger induced #theShoe.
DNMT3b Dysfunction Promotes DNA cleavages at Centromeric R-loops to Increase Centromere Instability
Authors: Shih Hsueh-Tzu , Chen Wei-Yi , Wang Hsin-Yen , Huang Hsien-Da , Chou Chih-Hung , Chang Zee-Fen 
Published: June 2020

ABSTRACTThis study investigates how DNA methyltransferase 3b (DNMT3b) dysfunction causes genome instability. We showed that in DNMT3b deficient cells, R-loops contribute to prominent γH2AX signal, which was mapped to repetitive satellite sequences including centromere regions. By ChIP and DRIP analyses, our data revealed that centromeric R-loops in DNMT3b deficient cells are removed by XPG/XPF, thus generating DNA breaks in centromeres to increase mitotic aberration. In immunodeficiency-centromeric instability-facial anomalies (ICF) patient cells carrying the loss-of-function mutation atDNMT3b, knockdown of XPG/XPF in ICF cells also reduces DNA breaks in centromere while bringing up centromeric R-loop to the level similar to that in wild-type cells. These results suggest that DNMT3b has a critical function in preventing XPG/XPF-mediated cleavages at centromeric R-loop sites. Finally, we showed the involvement of non-homologous end-joining repair at centromeric sites in ICF cells. Thus, DNA cleavages at centromeric R-loops with error-prone repair undermine centromere stability in ICF cells.
Systematic analysis of mutational spectra associated with DNA repair deficiency inC. elegans
Authors: Meier B , Volkova NV , Hong Y , Bertolini S , González-Huici V , Petrova T , Boulton S , Campbell PJ , Gerstung M , Gartner A 
Published: June 2020

AbstractGenome integrity is particularly important in germ cells to faithfully preserve genetic information across generations. As yet little is known about the contribution of various DNA repair pathways to prevent mutagenesis. Using theC. elegansmodel we analyse mutational spectra that arise in wild-type and 61 DNA repair and DNA damage response mutants cultivated over multiple generations. Overall, 44% of lines show >2-fold increased mutagenesis with a broad spectrum of mutational outcomes including changes in single or multiple types of base substitutions induced by defects in base excision or nucleotide excision repair, or elevated levels of 50-400 bp deletions in translesion polymerase mutantsrev-3(pol ζ) andpolh-1(pol η). Mutational signatures associated with defective homologous recombination fall into two classes: 1) mutants lackingbrc-1/BRCA1orrad-51/RAD51 paralogs show elevated base substitutions, indels and structural variants, while 2) deficiency for MUS-81/MUS81 and SLX-1/SLX1 nucleases, and HIM-6/BLM, HELQ-1/HELQ and RTEL-1/RTEL1 helicases primarily cause structural variants. Genome-wide investigation of mutagenesis patterns identified elevated rates of tandem duplications often associated with inverted repeats inhelq-1mutants, and a unique pattern of ‘translocation’ events involving homeologous sequences inrip-1paralog mutants.atm-1/ATM DNA damage checkpoint mutants harboured complex structural variants enriched in subtelomeric regions, and chromosome end-to-end fusions. Finally, while inactivation of thep53-like genecep-1did not affect mutagenesis, combinedbrc-1 cep-1deficiency displayed increased, locally clustered mutagenesis. In summary, we provide a global view of how DNA repair pathways prevent germ cell mutagenesis.
Mg2+Sensing by an RNA Fragment: Role of Mg2+Coordinated Water Molecules
Authors: Halder Antarip , Kumar Sunil , Valsson Omar , Reddy Govardhan 
Published: June 2020

AbstractRNA molecules selectively bind to specific metal ions to populate their functional active states making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied the role of different metal ions (Mg2+, Ca2+and K+) in the folding of a small RNA hairpin motif (5′-ucCAAAga-3′) using unbiased all-atom molecular dynamics simulations. The advantage in studying this small system is that it requires specific binding of a single metal ion to fold to its native state. We find that even for this small RNA, the folding free energy surface (FES) is multidimensional as different metal ions present in the solution can simultaneously facilitate folding. The FES shows that specific binding of a metal ion is indispensable for its folding. We further show that in addition to the negatively charged phosphate groups, spatial organization of electronegative nucleobase atoms drive the site specific binding of the metal ion. Even though the binding site cannot discriminate between different metal ions, RNA folds efficiently only in Mg2+solution. We show that the rigid network of Mg2+coordinated water molecules facilitate the formation of important interactions in the transition state. The other metal ions such as K+and Ca2+cannot facilitate the formation of such interactions. These results allow us to hypothesize possible metal sensing mechanisms in large metallo-riboswitches and they also provide useful insights for the design of appropriate collective variables for studying large RNA molecules using enhanced sampling methods.
Assessing the re-introduction ofAedes aegyptiin Europe. Will the Yellow Fever Mosquito colonize the Old World?
Authors: Da Re Daniele , Montecino-Latorre Diego , Vanwambeke Sophie O. , Marcantonio Matteo 
Published: June 2020

AbstractAedes aegyptiare feared invasive mosquitoes as they transmit pathogens which cause debilitating diseases in humans. Although mainland Europe has not yet witnessed re-establishment and diffusion ofAe. aegyptipopulations, several urban areas along coastlines represent suitable habitats for the species. In addition, European coastal areas are characterized by a high exotic species propagule pressure, due to the dense international ship traffic.Here, we applied a process-based population dynamical model to simulate both the life cycle and dispersal ofAe. aegyptiat the local scale after its introduction through ship traffic. We selected five European ports along a gradient of latitude by considering both environmental conditions and the economical importance of ports: Algeciras and Barcelona in Spain; Venice and Genoa in Italy and Rotterdam in the Netherlands. The model was informed using parameters relevant forAe. aegyptibiology, fine-scale temperature time-series, urban structures and road networks.According to model results, the introduction of small quantities ofAe. aegyptieggs, from 10 to 1000, has the potential to cause species establishment, high local densities and slow initial dispersal in the two southernmost study areas, Algeciras and Barcelona, whereas Genoa may be considered only close to suitability. Barcelona had the highest simulated mosquito densities (584 females/ha), whereas Algeciras densities were never more than 32 females/ha, but remained higher during winter. The spatial spread of the species varied between a few hundred meters to 2 km/year and was affected by the structure of the road network, topography and urban sprawl along the coast in the surrounding of the port of introduction. The study areas of Genoa, Venice and Rotterdam were found not suitable for establishment of this mosquito species, however climate change could create conditions forAe. aegyptiinvasion in these regions in the next decades.It is commonly accepted that targeted monitoring and early control actions are the most effective methods to hinder the establishment of invasive species in new areas. Our findings and model framework may support surveillance initiatives for those European coastal urban areas which have a known high propagule pressure and a high modelled probability ofAe. aegyptiestablishment.HighlightsEuropean coasts present favourable conditions forAedes aegyptiestablishmentWe assess the species introduction and establishment using a process-based modelWe selected five ports: Algeciras, Barcelona, Venice, Genoa and RotterdamAlgeciras and Barcelona were the most suitable areas for the species establishmentClimate change could make more suitable the northernmost study areas
Climate gradients, and patterns of biodiversity and biotic homogenization in urban residential yards
Authors: Bergey Elizabeth A. , Whipkey Benjamin E. 
Published: June 2020

AbstractResidential yards constitute a substantive biodiverse greenspace within urban areas. This biodiversity results from a combination of native and non-native species and can contribute to biotic homogenization. Geographical climatic patterns affect the distribution of native species and may differently affect non-native species. In this study, we examined biodiversity and biotic homogenization patterns of yard-dwelling land snails across 12 towns in Oklahoma and Kansas (USA). The 3 × 4 array of towns incorporated a N-S winter temperature gradient (mean low January temperature range = −8.4 to 0.1 °C) and an E-W annual rainfall gradient (annual rainfall range = 113.8 to 61.3 cm/yr). Ten yards per town were surveyed. We hypothesized that mild winter temperatures and greater annual rainfall would be associated with greater snail abundance and richness, and that the presence of non-native species would contribute to biotic homogenization. Non-native snails were present and often abundant in all towns. Snail communities varied with both rainfall and cold temperature. Contrary to our prediction, snail abundance was inversely related to annual rainfall – likely because drier conditions resulted in greater yard watering that both augmented rainfall and maintained moist conditions. Sørensen similarity between towns for the entire land snail community and for only non-native species both showed distance-decay patterns, with snail composition becoming less similar with increasing distance - patterns resulting from species turnover. The biotic homogenization index also showed a distance-decay pattern, such that closer towns were more likely to have biotic homogenization whereas more distant towns tended to have biotic differentiation. These results support the concept that biotic homogenization is more likely regionally and that climatic changes over distance result in species turnover and can reduce spatially broad biotic homogenization.
PROPER UTILIZATION OF IODIZED SALT AND ASSOCIATED FACTORS AMONG RURAL COMMUNITY OF HETOSA DISTRICT, OROMIA REGIONAL STATE, SOUTH EAST ETHIOPIA
Authors: Bulli Abu Tura , Aredo MeleseTadese , Fekadu Hailu , Regesu Ashenafi Habtamu 
Published: June 2020

AbstractIntroductionIodine is considered to be one of the most essential micronutrients for the normal physical and mental development of human beings. However, little is known about households’ use of iodized salt and associated factors.ObjectivesThis study was to assess the proper utilization of iodized salt at the household level and associated factors in Hetosa District, Southeast Ethiopia, 2019.MethodsA Community-based cross-sectional study was conducted from August 20 up to September 15/2019 in rural Hetosa District, Arsi Zone, and east-south Ethiopia. A total of 603 households were selected using a systematic random sampling technique. Data were collected employing structured and pre-tested questionnaires by face -to -face interview technique. The use of iodized salt at the household level was tested with the iodine rapid test kit. The data were checked, coded and entered into Epi Info Version 7 and export to SPSS version 21 for analysis.ResultA total of 596 participants were included in this study. The availability of adequately iodized salt was 61.1%. The proportion of proper utilization of iodized salt at the household level was 38.4%.Formal Educational (AOR=1.688, 95%CI (1.002, 2.846)),Practice of iodized salt use (AOR= 3.352, 95%CI (2.160, 5.202)), Knowledge on use of iodized salt (AOR=2.320, 95%CI (1.437, 3.745)) and level of iodine content in salt (AOR= 1.668, 95%CI (1.071, 2.597)) were statistically significant to utilization of iodized salt.ConclusionProper utilization of iodized salt remains very low, which was 38.4% in the district and does not meet the national goal. Educational status, level of iodized salt, good knowledge and good practice were significantly associated factors with proper utilization of adequately iodized salt in this study.
Woeseiales transcriptional response in Arctic fjord surface sediment
Authors: Buongiorno Joy , Sipes Katie , Wasmund Kenneth , Loy Alexander , Lloyd Karen G. 
Published: June 2020

AbstractDistinct lineages of Gammaproteobacteria clade Woeseiales are globally-distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.
Pleiotropic effects of heterozygosity for theSERPINA1Z allele in the UK Biobank
Authors: Fawcett Katherine A , Song Kijoung , Qian Guoqing , Farmaki Aliki-Eleni , Packer Richard , John Catherine , Shrine Nick , Granell Raquel , Ring Sue , Timpson Nicholas J , Yerges-Armstrong Laura M , Eastell Richard , Wain Louise V , Scott Robert A , Tobin Martin D , Hall Ian P 
Published: June 2020

AbstractHomozygosity for theSERPINA1Z allele causes alpha-1 antitrypsin deficiency, a rare condition that can cause lung and liver disease. However, the effects of Z allele heterozygosity on non-respiratory phenotypes, and on lung function in the general population, remain unclear. We conducted the largest population-based study to date to determine Z allele effects on >2,400 phenotypes using the UK Biobank study (N>303,353). We detected strong associations between heterozygosity and non-respiratory phenotypes including increased height, increased risk of gall bladder disease, reduced risk of heart disease and lower blood pressure, reduced risk of osteoarthritis and reduced bone mineral density, increased risk of headache and enlarged prostate, as well as with blood biomarkers of liver function. Heterozygosity was associated with higher lung function in non-smokers, but smoking appears to abolish this protective effect. Individuals heterozygous for the Z allele may therefore have altered risk of smoking-induced lung disease and other, non-respiratory conditions.