bluuebunny/crossref_metadata_2025_split huggingface dataset:
Savanna in equatorial Borneo during the late Pleistocene
Authors: Wurster Christopher M. , Rifai Hamdi , Zhou Bin , Haig Jordahna , Bird Michael I. 
Published: April 2019

AbstractEquatorial Southeast Asia is a key region for global climate change. Here, the Indo-Pacific Warm Pool (IPWP) is a critical driver of atmospheric convection that plays a dominant role in global atmospheric circulation. However, fluctuating sea-levels during the Pleistocene produced the most drastic land-sea area changes on Earth, with the now-drowned continent of Sundaland being exposed as a contiguous landmass for most of the past 2 million years. How vegetation responded to changes in rainfall that resulted from changing shelf exposure and glacial boundary conditions in Sundaland remains poorly understood. Here we use the stable carbon isotope composition (δ13C) of bat guano and High Molecular Weight n-alkanes, from Saleh Cave in southern Borneo to demonstrate that open vegetation existed during much the past 40,000 yrs BP. This location is at the southern equatorial end of a hypothesized ‘savanna corridor’ and the results provide the strongest evidence yet for its existence. The corridor would have operated as a barrier to east-west dispersal of rainforest species, and a conduit for north-south dispersal of savanna species at times of lowered sea level, explaining many modern biogeographic patterns. The Saleh Cave record also exhibits a strong correspondence with insolation and sea surface temperatures of the IPWP, suggesting a strong sensitivity of vegetation to tropical climate change on glacial/interglacial timeframes.
Barley yield formation under abiotic stress depends on the interplay between flowering time genes and environmental cues
Authors: Wiegmann Mathias , Maurer Andreas , Pham Anh , March Timothy J. , Al-Abdallat Ayed , Thomas William T. B. , Bull Hazel J. , Shahid Mohammed , Eglinton Jason , Baum Michael , Flavell Andrew J. , Tester Mark , Pillen Klaus 
Published: April 2019

AbstractSince the dawn of agriculture, crop yield has always been impaired through abiotic stresses. In a field trial across five locations worldwide, we tested three abiotic stresses, nitrogen deficiency, drought and salinity, using HEB-YIELD, a selected subset of the wild barley nested association mapping population HEB-25. We show that barley flowering time genes Ppd-H1, Sdw1, Vrn-H1 and Vrn-H3 exert pleiotropic effects on plant development and grain yield. Under field conditions, these effects are strongly influenced by environmental cues like day length and temperature. For example, in Al-Karak, Jordan, the day length-sensitive wild barley allele of Ppd-H1 was associated with an increase of grain yield by up to 30% compared to the insensitive elite barley allele. The observed yield increase is accompanied by pleiotropic effects of Ppd-H1 resulting in shorter life cycle, extended grain filling period and increased grain size. Our study indicates that the adequate timing of plant development is crucial to maximize yield formation under harsh environmental conditions. We provide evidence that wild barley alleles, introgressed into elite barley cultivars, can be utilized to support grain yield formation. The presented knowledge may be transferred to related crop species like wheat and rice securing the rising global food demand for cereals.
Insight into the microbial world of Bemisia tabaci cryptic species complex and its relationships with its host
Authors: Wang Hua-Ling , Lei Teng , Xia Wen-Qiang , Cameron Stephen L. , Liu Yin-Quan , Zhang Zhen , Gowda Maruthi M. N. , De Barro Paul , Navas-Castillo Jesús , Omongo Christopher A. , Delatte Hélène , Lee Kyeong-Yeoll , Patel Mitulkumar V. , Krause-Sakate Renate , Ng James , Wu San-Ling , Fiallo-Olivé Elvira , Liu Shu-Sheng , Colvin John , Wang Xiao-Wei 
Published: April 2019

AbstractThe 37 currently recognized Bemisia tabaci cryptic species are economically important species and contain both primary and secondary endosymbionts, but their diversity has never been mapped systematically across the group. To achieve this, PacBio sequencing of full-length bacterial 16S rRNA gene amplicons was carried out on 21 globally collected species in the B. tabaci complex, and two samples from B. afer were used here as outgroups. The microbial diversity was first explored across the major lineages of the whole group and 15 new putative bacterial sequences were observed. Extensive comparison of our results with previous endosymbiont diversity surveys which used PCR or multiplex 454 pyrosequencing platforms showed that the bacterial diversity was underestimated. To validate these new putative bacteria, one of them (Halomonas) was first confirmed to be present in MED B. tabaci using Hiseq2500 and FISH technologies. These results confirmed PacBio is a reliable and informative venue to reveal the bacterial diversity of insects. In addition, many new secondary endosymbiotic strains of Rickettsia and Arsenophonus were found, increasing the known diversity in these groups. For the previously described primary endosymbionts, one Portiera Operational Taxonomic Units (OTU) was shared by all B. tabaci species. The congruence of the B. tabaci-host and Portiera phylogenetic trees provides strong support for the hypothesis that primary endosymbionts co-speciated with their hosts. Likewise, a comparison of bacterial alpha diversities, Principal Coordinate Analysis, indistinct endosymbiotic communities harbored by different species and the co-divergence analyses suggest a lack of association between overall microbial diversity with cryptic species, further indicate that the secondary endosymbiont-mediated speciation is unlikely to have occurred in the B. tabaci species group.
Efficient message passing for cascade size distributions
Authors: Burkholz Rebekka 
Published: April 2019

AbstractHow big is the risk that a few initial failures of networked nodes amplify to large cascades that endanger the functioning of the system? Common answers refer to the average final cascade size. Two analytic approaches allow its computation: (a) (heterogeneous) mean field approximation and (b) belief propagation. The former applies to (infinitely) large locally tree-like networks, while the latter is exact on finite trees. Yet, cascade sizes can have broad and multi-modal distributions that are not well represented by their average. Full distribution information is essential to identify likely events and to estimate the tail risk, i.e. the probability of extreme events. We therefore present an efficient message passing algorithm that calculates the cascade size distribution in finite networks. It is exact on finite trees and for a large class of cascade processes. An approximate version applies to any network structure and performs well on locally tree-like networks, as we show with several examples.
Cerebral mitochondrial electron transport chain dysfunction in multiple system atrophy and Parkinson’s disease
Authors: Foti Sandrine C. , Hargreaves Iain , Carrington Stephanie , Kiely Aoife P. , Houlden Henry , Holton Janice L. 
Published: April 2019

AbstractMultiple system atrophy (MSA) is a neurodegenerative disease characterised by glial cytoplasmic inclusions (GCIs), containing α-synuclein. Mutated COQ2, encoding an enzyme essential for co-enzyme Q10 (CoQ10) biosynthesis, has been associated with MSA. CoQ10 is an electron carrier in the mitochondrial electron transport chain (ETC) and antioxidant. It has been shown to be deficient in MSA brain tissue, thus implicating mitochondrial dysfunction in MSA. To investigate mitochondrial dysfunction in MSA further we examined ETC activity in MSA and control brain tissue, compared with Parkinson’s disease (PD) where mitochondrial dysfunction is known to be important. Using cerebellar and occipital white matter ETC complex I, II/III and IV activities were measured spectrophotometrically, selected individual components of the ETC were assessed by immunoblotting and cellular complex IV activity was analysed by enzyme histochemistry. We show decreased complex II/III activity with increased complex I and IV activity in MSA cerebellar white matter. This corresponds with the deficit in CoQ10 previously described in MSA and reflects the high regional pathological burden of GCIs. This study highlights mitochondrial dysfunction in MSA pathogenesis, suggests an influence on selective regional vulnerability to disease and points to shared disease mechanisms in α-synucleinopathies.
Manganese-induced cellular disturbance in the baker’s yeast, Saccharomyces cerevisiae with putative implications in neuronal dysfunction
Authors: Hernández Raúl Bonne , Moteshareie Houman , Burnside Daniel , McKay Bruce , Golshani Ashkan 
Published: April 2019

AbstractManganese (Mn) is an essential element, but in humans, chronic and/or acute exposure to this metal can lead to neurotoxicity and neurodegenerative disorders including Parkinsonism and Parkinson’s Disease by unclear mechanisms. To better understand the effects that exposure to Mn2+ exert on eukaryotic cell biology, we exposed a non-essential deletion library of the yeast Saccharomyces cerevisiae to a sub-inhibitory concentration of Mn2+ followed by targeted functional analyses of the positive hits. This screen produced a set of 43 sensitive deletion mutants that were enriched for genes associated with protein biosynthesis. Our follow-up investigations demonstrated that Mn reduced total rRNA levels in a dose-dependent manner and decreased expression of a β-galactosidase reporter gene. This was subsequently supported by analysis of ribosome profiles that suggested Mn-induced toxicity was associated with a reduction in formation of active ribosomes on the mRNAs. Altogether, these findings contribute to the current understanding of the mechanism of Mn-triggered cytotoxicity. Lastly, using the Comparative Toxicogenomic Database, we revealed that Mn shared certain similarities in toxicological mechanisms with neurodegenerative disorders including amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s and Huntington’s diseases.
Low-Dose Tacrolimus Prevents Dysregulated Peri-Conceptional Ovarian and Systemic Immune Cellular Homeostasis in Subjects with PCOS
Authors: Albaghdadi Ahmad J. H. , Feeley Carolyn Ann , Kan Frederick W. K. 
Published: April 2019

AbstractPolycystic ovary syndrome (PCOS) is characterized by failure of ovulation and is associated with obesity and chronic inflammation. Recent evidence suggests that anomalous activation of ovarian macrophages and numerical and functional deficits in the Th17 (CD4+IL17A+) and the CD4+CD25+CD127lowTregs plays crucial role in PCOS. We have shown that the pre-pregnancy use of tacrolimus prevents adverse reproductive outcomes in a mouse model of PCOS. Here we used the HFD-NONcNZO mice to test a hypothesized beneficial use of tacrolimus relative to metformin in favorably influencing the ovarian and systemic immune milieux conducive to gestational success in subjects with PCOS. Compared to normative controls, our data revealed an aberrant peri-conceptional suppression of the CD4+CD25+CD127lowTregs together with an overexpression of the Th17 T cells and lack of coordinated activation of ovarian macrophages in untreated HFD-dNONcNZO mice. Significant variances in treatment outcomes favoured the use of tacrolimus over metformin in treated mice. Consistent with the human fertility studies, this investigation reveals a beneficial systemic use of tacrolimus (0.1 mg/kg) in promoting early pregnancy in individuals with PCOS and suggests the need for further research into the selective inhibition of IL17A as a plausibly alternative immunotherapeutic approach in the clinical management of infertile individuals with PCOS.
Ocular biometry and refractive outcomes using two swept-source optical coherence tomography-based biometers with segmental or equivalent refractive indices
Authors: Omoto Miki Kamikawatoko , Torii Hidemasa , Masui Sachiko , Ayaki Masahiko , Tsubota Kazuo , Negishi Kazuno 
Published: April 2019

AbstractThis study compared the axial length (AL), central corneal thickness (CCT), anterior chamber depth (ACD), lens thickness (LT), mean anterior corneal radius of curvature (Rm), and postoperative refractive outcomes obtained from two different swept-source optical coherence biometers, the ARGOS (Movu, Aichi, Japan), which uses the segmental refractive index for each segment, and the IOLMaster 700 (Carl Zeiss Meditec, Jena, Germany), which uses an equivalent refractive index for the entire eye. One hundred and six eyes of 106 patients with cataracts were included. The refractive outcomes using the Barrett Universal II, Haigis, Hoffer Q, and SRK/T formulas were evaluated. The mean AL, CCT, ACD, and Rm differed significantly (P < 0.001) with the IOLMaster 700 (25.22 mm, 559 µm, 3.23 mm, and 7.69 mm) compared with the ARGOS (25.14 mm, 533 µm, 3.33 mm, and 7.66 mm). The mean LTs did not differ significantly. The percentages of eyes within ±0.50 and ±1.00 diopter of the predicted refraction did not differ significantly (P > 0.05). The accuracy of the intraocular lens power calculations was clinically acceptable with both biometers, although the ocular biometry using these two biometers exhibited certain differences.
Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan
Authors: Sato Yukuto , Mizuyama Masaru , Sato Megumi , Minamoto Toshifumi , Kimura Ryosuke , Toma Claudia 
Published: April 2019

AbstractLeptospires, which cause the zoonotic disease leptospirosis, persist in soil and aqueous environments. Several factors, including rainfall, the presence of reservoir animals, and various abiotic and biotic components interact to influence leptospiral survival, persistence, and pathogenicity in the environment. However, how these factors modulate the risk of infection is poorly understood. Here we developed an approach using environmental DNA (eDNA) metabarcoding for detecting the microbiome, vertebrates, and pathogenic Leptospira in aquatic samples. Specifically, we combined 4 sets of primers to generate PCR products for high-throughput sequencing of multiple amplicons through next-generation sequencing. Using our method to analyze the eDNA of leptospirosis-endemic areas in northern Okinawa, Japan, we found that the microbiota in each river shifted over time. Operating taxonomic units corresponding to pathogenic L. alstonii, L. kmetyi, and L. interrogans were detected in association with 12 nonpathogenic bacterial species. In addition, the frequencies of 11 of these species correlated with the amount of rainfall. Furthermore, 10 vertebrate species, including Sus scrofa, Pteropus dasymallus, and Cynops ensicauda, showed high correlation with leptospiral eDNA detection. Our eDNA metabarcoding method is a powerful tool for understanding the environmental phase of Leptospira and predicting human infection risk.
A systematic approach re-analyzing the effects of temperature disturbance on the microbial community of mesophilic anaerobic digestion
Authors: Shaw Grace Tzun-Wen , Weng Chieh-Yin , Chen Cheng-Yu , Weng Francis Cheng-Hsuan , Wang Daryi 
Published: April 2019

AbstractMicrobial communities are key drivers of ecosystem processes, but their behavior in disturbed environments is difficult to measure. How microbial community composition and function respond disturbances is a common challenge in biomedical, environmental, agricultural, and bioenergy research. A novel way to solve this problem is to use a systems-level perspective and describe microbial communities as networks. Based on a mesophilic anaerobic digestion system of swine manure as a tool, we propose a simple framework to investigate changes in microbial communities via compositions, metabolic pathways, genomic properties and interspecies relationships in response to a long-term temperature disturbance. After temperature disturbance, microbial communities tend towards a competitive interaction network with higher GC content and larger genome size. Based on microbial interaction networks, communities responded to the disturbance by showing a transition from acetotrophic (Methanotrichaceae and Methanosarcinaceae) to methylotrophic methanogens (Methanomassiliicoccaceae and Methanobacteriaceae) and a fluctuation in rare biosphere taxa. To conclude, this study may be important for exploring the dynamic relationships between disturbance and microbial communities as a whole, as well as for providing researchers with a better understanding of how changes in microbial communities relate to ecological processes.
Discovery of selective activators of PRC2 mutant EED-I363M
Authors: Suh Junghyun L. , Barnash Kimberly D. , Abramyan Tigran M. , Li Fengling , The Juliana , Engelberg Isabelle A. , Vedadi Masoud , Brown Peter J. , Kireev Dmitri B. , Arrowsmith Cheryl H. , James Lindsey I. , Frye Stephen V. 
Published: April 2019

AbstractMany common disease-causing mutations result in loss-of-function (LOF) of the proteins in which they occur. LOF mutations have proven recalcitrant to pharmacologic intervention, presenting a challenge for the development of targeted therapeutics. Polycomb repressive complex 2 (PRC2), which contains core subunits (EZH2, EED, and SUZ12), regulates gene activity by trimethylation of histone 3 lysine 27. The dysregulation of PRC2 catalytic activity by mutations has been implicated in cancer and other diseases. Among the mutations that cause PRC2 malfunction, an I363M LOF mutation of EED has been identified in myeloid disorders, where it prevents allosteric activation of EZH2 catalysis. We describe structure-based design and computational simulations of ligands created to ameliorate this LOF. Notably, these compounds selectively stimulate the catalytic activity of PRC2-EED-I363M over wildtype-PRC2. Overall, this work demonstrates the feasibility of developing targeted therapeutics for PRC2-EED-I363M that act as allosteric agonists, potentially correcting this LOF mutant phenotype.
Radiative transfer modelling reveals why canopy reflectance follows function
Authors: Kattenborn Teja , Schmidtlein Sebastian 
Published: April 2019

AbstractOptical remote sensing is potentially highly informative to track Earth’s plant functional diversity. Yet, causal explanations of how and why plant functioning is expressed in canopy reflectance remain limited. Variation in canopy reflectance can be described by radiative transfer models (here PROSAIL) that incorporate plant traits affecting light transmission in canopies. To establish causal links between canopy reflectance and plant functioning, we investigate how two plant functional schemes, i.e. the Leaf Economic Spectrum (LES) and CSR plant strategies, are related to traits with relevance to reflectance. These traits indeed related to both functional schemes, whereas only traits describing leaf properties correlated with the LES. In contrast, traits related to canopy structure showed no correlation to the LES, but to CSR strategies, as the latter integrates both plant economics and size traits, rather than solely leaf economics. Multiple optically relevant traits featured comparable or higher correspondence to the CSR space than those traits originally used to allocate CSR scores. This evidences that plant functions and strategies are directly expressed in reflectance and entails that canopy ‘reflectance follows function’. This opens up new possibilities to understand differences in plant functioning and to harness optical remote sensing data for monitoring Earth´s functional diversity.
Predicting Growth and Carcass Traits in Swine Using Microbiome Data and Machine Learning Algorithms
Authors: Maltecca Christian , Lu Duc , Schillebeeckx Constantino , McNulty Nathan P. , Schwab Clint , Shull Caleb , Tiezzi Francesco 
Published: April 2019

AbstractIn this paper, we evaluated the power of microbiome measures taken at three time points over the growth test period (weaning, 15 and 22 weeks) to foretell growth and carcass traits in 1039 individuals of a line of crossbred pigs. We measured prediction accuracy as the correlation between actual and predicted phenotypes in a five-fold cross-validation setting. Phenotypic traits measured included live weight measures and carcass composition obtained during the trial as well as at slaughter. We employed a null model excluding microbiome information as a baseline to assess the increase in prediction accuracy stemming from the inclusion of operational taxonomic units (OTU) as predictors. We further contrasted performance of models from the Bayesian alphabet (Bayesian Lasso) as well machine learning approaches (Random Forest and Gradient Boosting) and semi-parametric kernel models (Reproducing Kernel Hilbert space). In most cases, prediction accuracy increased significantly with the inclusion of microbiome data. Accuracy was more substantial with the inclusion of microbiome information taken at weeks 15 and 22, with values ranging from approximately 0.30 for loin traits to more than 0.50 for back fat. Conversely, microbiome composition at weaning resulted in most cases in marginal gains of prediction accuracy, suggesting that later measures might be more useful to include in predictive models. Model choice affected predictions marginally with no clear winner for any model/trait/time point. We, therefore, suggest average prediction across models as a robust strategy in fitting microbiome information. In conclusion, microbiome composition can effectively be used as a predictor of growth and composition traits, particularly for fatness traits. The inclusion of OTU predictors could potentially be used to promote fast growth of individuals while limiting fat accumulation. Early microbiome measures might not be good predictors of growth and OTU information might be best collected at later life stages. Future research should focus on the inclusion of both microbiome as well as host genome information in predictions, as well as the interaction between the two. Furthermore, the influence of the microbiome on feed efficiency as well as carcass and meat quality should be investigated.
Impact of Percoll purification on isolation of primary human hepatocytes
Authors: Horner R. , Gassner J. G. M. V. , Kluge M. , Tang P. , Lippert S. , Hillebrandt K. H. , Moosburner S. , Reutzel-Selke A. , Pratschke J. , Sauer I. M. , Raschzok N. 
Published: April 2019

AbstractResearch and therapeutic applications create a high demand for primary human hepatocytes. The limiting factor for their utilization is the availability of metabolically active hepatocytes in large quantities. Centrifugation through Percoll, which is commonly performed during hepatocyte isolation, has so far not been systematically evaluated in the scientific literature. 27 hepatocyte isolations were performed using a two-step perfusion technique on tissue obtained from partial liver resections. Cells were seeded with or without having undergone the centrifugation step through 25% Percoll. Cell yield, function, purity, viability and rate of bacterial contamination were assessed over a period of 6 days. Viable yield without Percoll purification was 42.4 × 106 (SEM ± 4.6 × 106) cells/g tissue. An average of 59% of cells were recovered after Percoll treatment. There were neither significant differences in the functional performance of cells, nor regarding presence of non-parenchymal liver cells. In five cases with initial viability of <80%, viability was significantly increased by Percoll purification (71.6 to 87.7%, p = 0.03). Considering our data and the massive cell loss due to Percoll purification, we suggest that this step can be omitted if the initial viability is high, whereas low viabilities can be improved by Percoll centrifugation.