bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating VITEK MS for the identification of clinically relevant Aspergillus species
Authors: M Américo Fernanda , P Machado Siqueira Lumena , B Del Negro Gilda Maria , M Favero Gimenes Viviane , S Trindade Mario Roberto , L Motta Adriana , Santos de Freitas Roseli , Rossi Flavia , L Colombo Arnaldo , Benard Gil , N de Almeida Júnior João 
Published: May 2019

AbstractAspergillus spp. identification has become more relevant in clinical practice since azole-resistant cryptic species have been related to invasive fungal infections. Conventional morphologic identification is not able to discriminate Aspergillus species, and DNA sequencing is not feasible for clinical laboratories. MALDI-TOF mass spectrometry is an emergent technology that has been explored to provide fast and accurate identification of microorganisms, including clinically relevant moulds. However, only a few studies have explored the platform VITEK MS for the identification of Aspergillus species. Hence, we provided additional data regarding the performance of the VITEK MS system for the identification of Aspergillus species, including azole-resistant ones. We also improved the RUO system by adding additional spectral profiles from well-identified Aspergillus strains belonging to different noncryptic and cryptic species. The IVD library correctly identified 91.6% of the organisms at genus and section level, and 84.7% at species level, including the azole-resistant Aspergillus lentulus and Aspergillus calidoustus. The organisms belonging to Aspergillus cryptic species had only 31.2% of correct species identification. The RUO library plus our in-house SuperSpectra correctly identified 100% of the organisms at genus and section level and 91.6% at species level. Among organisms belonging to Aspergillus cryptic species, 68.7% had correct species identification. Some closely related Aspergillus cryptic species showed similar spectral profiles and were difficult to be differentiated.
Stochastic modelling of star-formation histories I: the scatter of the star-forming main sequence
Authors: Caplar Neven , Tacchella Sandro 
Published: May 2019

ABSTRACT
We present a framework for modelling the star-formation histories of galaxies as a stochastic process. We define this stochastic process through a power spectrum density with a functional form of a broken power law. Star-formation histories are correlated on short time-scales, the strength of this correlation described by a power-law slope, α, and they decorrelate to resemble white noise over a time-scale that is proportional to the time-scale of the break in the power spectrum density, τbreak. We use this framework to explore the properties of the stochastic process that, we assume, gives rise to the log-normal scatter about the relationship between star-formation rate and stellar mass, the so-called galaxy star-forming main sequence. Specifically, we show how the measurements of the normalization and width (σMS) of the main sequence, measured in several passbands that probe different time-scales, give a constraint on the parameters of the underlying power spectrum density. We first derive these results analytically for a simplified case where we model observations by averaging over the recent star-formation history. We then run numerical simulations to find results for more realistic observational cases. As a proof of concept, we use observational estimates of the main sequence scatter at z ∼ 0 and M⋆ ≈ 1010 M⊙ measured in H α, UV+IR, and the u-band. The result is degenerate in the τbreak-α space, but if we assume α = 2, we measure $\tau _{\rm break}=170^{+169}_{-85}~\mathrm{Myr}$. This implies that star-formation histories of galaxies lose ‘memory’ of their previous activity on a time-scale of ∼200 Myr.
Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair
Authors: Chen Wei , McKenna Aaron , Schreiber Jacob , Haeussler Maximilian , Yin Yi , Agarwal Vikram , Noble William Stafford , Shendure Jay 
Published: May 2019

Abstract
Non-homologous end-joining (NHEJ) plays an important role in double-strand break (DSB) repair of DNA. Recent studies have shown that the error patterns of NHEJ are strongly biased by sequence context, but these studies were based on relatively few templates. To investigate this more thoroughly, we systematically profiled ∼1.16 million independent mutational events resulting from CRISPR/Cas9-mediated cleavage and NHEJ-mediated DSB repair of 6872 synthetic target sequences, introduced into a human cell line via lentiviral infection. We find that: (i) insertions are dominated by 1 bp events templated by sequence immediately upstream of the cleavage site, (ii) deletions are predominantly associated with microhomology and (iii) targets exhibit variable but reproducible diversity with respect to the number and relative frequency of the mutational outcomes to which they give rise. From these data, we trained a model that uses local sequence context to predict the distribution of mutational outcomes. Exploiting the bias of NHEJ outcomes towards microhomology mediated events, we demonstrate the programming of deletion patterns by introducing microhomology to specific locations in the vicinity of the DSB site. We anticipate that our results will inform investigations of DSB repair mechanisms as well as the design of CRISPR/Cas9 experiments for diverse applications including genome-wide screens, gene therapy, lineage tracing and molecular recording.
Effect of Mass Artesunate-Amodiaquine Distribution on Mortality of Patients With Ebola Virus Disease During West African Outbreak
Authors: Garbern Stephanie C , Yam Derrick , Aluisio Adam R , Cho Daniel K , Kennedy Stephen B , Massaquoi Moses , Sahr Foday , Perera Shiromi M , Levine Adam C , Liu Tao 
Published: May 2019

AbstractBackgroundExperiments in vitro have shown that the drug amodiaquine may inhibit Ebola virus activity. During the Ebola virus disease (EVD) epidemic in West Africa in 2014–2016, 2 mass drug administrations (MDAs) of artesunate-amodiaquine (ASAQ) were implemented to decrease the burden of malaria. The objective of this study was to assess the effect of the ASAQ MDAs on the mortality of patients with EVD.MethodsA retrospective cohort design was used to analyze mortality data for patients with EVD admitted to 5 Ebola treatment units in Liberia and Sierra Leone. Patients admitted to the ETUs during the time period of ASAQ’s therapeutic effect from areas where the MDA was implemented were matched to controls not exposed to ASAQ, using a range of covariates, including malaria co-infection status, and a logistic regression analysis was performed. The primary outcome was Ebola treatment unit mortality.ResultsA total of 424 patients with EVD had sufficient data for analysis. Overall, the mortality of EVD patients was 57.5%. A total of 22 EVD patients were exposed to ASAQ during the MDAs and were found to have decreased risk of death compared with those not exposed in a matched analysis, but this did not reach statistical significance (relative risk, 0.63; 95% confidence interval, 0.37–1.07; P = .086).ConclusionsThere was a non–statistically significantly decreased risk of mortality in EVD patients exposed to ASAQ during the 2 MDAs as compared with EVD patients not exposed to ASAQ. Further prospective trials are needed to determine the direct effect of ASAQ on EVD mortality.
Conclusion: Natural Resource Justice and Climate Change
Authors: Blomfield Megan 
Published: May 2019

Abstract
This chapter summarizes the argument of the work. It situates the conception of natural resource justice that has been defended between the (egalitarian) principle of equal division and the (statist) principle of resource sovereignty. As an interpretation of relational egalitarianism concerning natural resources, the view is shown to avoid three of the most common objections to global egalitarianism. This is because the view is compatible with collective self-determination, protects cultural diversity, and avoids the metric problem. The chapter concludes that the method of partial integrationism adopted in the work, considering questions of climate justice by reference to a conception of justice for natural resources alone, has been productive. A remaining task is to integrate this conception of natural resource justice with a more general theory of global justice, encompassing other important goods, institutions, practices, and relations.
Why should a non-profit organization be attractive for an investor?
Authors: Specht Keno 
Published: May 2019

Abstract
Should an investor invest in a non-profit organization? The question seems odd. Discussing that topic, the author shows how SOS Children’s Villages International started to measure the impact of their work and what they learned from it—for their programmes and for the society of the future—and why this question is—in the end—a sustainable base for an investment decision.
Soil moisture regime and palm height influence embolism resistance in oil palm
Authors: Waite Pierre-André , Schuldt Bernhard , Mathias Link Roman , Breidenbach Natalie , Triadiati Triadiati , Hennings Nina , Saad Asmadi , Leuschner Christoph 
Published: May 2019

AbstractWith the prospect of climate change and more frequent El Niño-related dry spells, the drought tolerance of oil palm (Elaeis guineensis Jacq.), one of the most important tropical crop species, is of major concern. We studied the influence of soil water availability and palm height on the plasticity of xylem anatomy of oil palm fronds and their embolism resistance at well-drained and seasonally flooded riparian sites in lowland Sumatra, Indonesia. We found overall mean P12 and P50 values, i.e., the xylem pressures at 12% or 50% loss of hydraulic conductance, of −1.05 and − 1.86 MPa, respectively, indicating a rather vulnerable frond xylem of oil palm. This matches diurnal courses of stomatal conductance, which in combination with the observed low xylem safety evidence a sensitive water loss regulation. While the xylem anatomical traits vessel diameter (Dh), vessel density and potential hydraulic conductivity (Kp) were not different between the sites, palms in the moister riparian plots had on average by 0.4 MPa higher P50 values than plants in the well-drained plots. This could largely be attributed to differences in palm height between systems. As a consequence, palms of equal height had 1.3 MPa less negative P50 values in the moister riparian plots than in the well-drained plots. While palm height was positively related to P50, Dh and Kp decreased with height. The high plasticity in embolism resistance may be an element of the drought response strategy of oil palm, which, as a monocot, has a relatively deterministic hydraulic architecture. We conclude that oil palm fronds develop a vulnerable water transport system, which may expose the palms to increasing drought stress in a warmer and drier climate. However, the risk of hydraulic failure may be reduced by considerable plasticity in the hydraulic system and the environmental control of embolism resistance, and a presumably large stem capacitance.
Expected and observed genotype complexity in prokaryotes: correlation between 16S-rRNA phylogeny and protein domain content
Authors: Koehorst Jasper J. , Saccenti Edoardo , dos Santos Vitor Martins , Suarez-Diez Maria , Schaap Peter J. 
Published: May 2019

ABSTRACTBackgroundThe omnipresent 16S ribosomal RNA gene (16S-rRNA) is commonly used to identify and classify bacteria though it does not take into account the distinctive functional characteristics of taxa. We explored functional domain landscapes of over 5700 complete bacterial genomes, representing a wide coverage of the bacterial tree of life, and investigated to what extent the observed protein domain diversity correlates with the expected evolutionary diversity, using 16S-rRNA as metric for evolutionary distance.ResultsAnalysis of protein domains showed that 83% of the bacterial genes code for at least one of the 9722 domain classes identified. By comparing clade specific and global persistence scores, candidate horizontal gene transfer and signifying domains could be identified. 16S-rRNA and functional domain content distances were used to evaluate and compare species divergence and overall a sigmoid curve is observed. Already at close 16S-rRNA evolutionary distances, high levels of functional diversity can be observed. At a larger 16S-rRNA distance, functional differences accumulate at a relatively lower pace.ConclusionsAnalysis of 16S-rRNA sequences in the same taxa suggests that, in many cases, additional means of classification are required to obtain reliable phylogenetic relationships. Whole genome protein domain class phylogenies correlate with, and complement 16S-rRNA sequence-based phylogenies. Moreover, domain-based phylogenies can be constructed over large evolutionary distances and provide an in-depth insight of the functional diversity within and among species and enables large scale functional comparisons. The increased granularity obtained paves way for new applications to better predict the relationships between genotype, physiology and ecology.
The client-binding domain of the cochaperone Sgt2 has a helical-hand structure that binds a short hydrophobic helix
Authors: Lin Ku-Feng , Fry Michelle Y. , Saladi Shyam M. , Clemons William M. 
Published: May 2019

AbstractThe targeting and insertion of tail-anchored (TA) integral membrane proteins (IMP) into the correct membrane is critical for cellular homeostasis. The fungal protein Sgt2, and its human homolog SGTA, binds hydrophobic clients and is the entry point for targeting of ER-bound TA IMPs. Here we reveal molecular details that underlie the mechanism of Sgt2 binding to TA IMP clients. We establish that the Sgt2 C-terminal region is flexible but conserved and sufficient for client binding. A molecular model for this domain reveals a helical hand forming a hydrophobic groove, consistent with a higher affinity for TA IMP clients with hydrophobic faces and a minimal length of 11 residues. This work places Sgt2 into a broader family of TPR-containing co-chaperone proteins.
Seasonal microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments
Authors: Alex Gobbi , Ifigeneia Kyrkou , Elisa Filippi , Lea Ellegaard-Jensen , Hestbjerg Hansen Lars 
Published: May 2019

AbstractWinemakers have long used copper as a fungicide on grapevine. However, the potential of copper to accumulate on soil and affect the biota poses a challenge to achieving sustainable agriculture. One recently developed option is the use of biocontrol agents to replace or complement traditional methods. In the present study, a field experiment was conducted in South Africa in which the leaves in two blocks of a vineyard were periodically treated with either copper sulphate or sprayed withLactobacillus plantarumMW-1 as a biocontrol agent. This study evaluated the impact of the two treatments on the bacterial and fungal communities as they changed during the growing season. To do this, NGS was combined with quantitative strain-specific and community qPCRs. The results revealed the progression of the microbial communities throughout the season and how the different treatments affected the microbiota. Bacteria appeared to be relatively stable at the different time points, with the only taxa that systematically changed between treatments beingLactobacillaceae, which included reads from the biocontrol agent. Cells ofLactobacillus plantarumMW-1 were only detected on treated leaves using strain-specific qPCR, with its amount spanning from 103to 105cells/leaves. Conversely the fungal community was largely shaped by a succession of different dominant taxa over the months. Between treatments, only a few fungal taxa appeared to change significantly and the number of ITS copies was also comparable. In this regards, the two treatments seemed to affect the microbial community similarly, revealing the potential of this biocontrol strain as a promising alternative among sustainable fungicide treatments, although further investigation is required.
Analysis of the expression of PIWI-interacting RNAs during cardiac differentiation of human pluripotent stem cells
Authors: La Greca Alejandro , Scarafía María Agustina , Cañás María Clara Hernández , Pérez Nelba , Castañeda Sheila , Colli Carolina , Möbbs Alan Miqueas , Velazque Natalia Lucía Santín , Neiman Gabriel , Garate Ximena , Aban Cyntia , Waisman Ariel , Moro Lucía , Sevlever Gustavo , Luzzani Carlos , Miriuka Santiago 
Published: May 2019

SummaryPIWI-interacting RNAs (piRNAs) are a class of non-coding RNAs initially thought to be restricted almost exclusively to germ line cells. In recent years, accumulating evidence has demonstrated that piRNAs are actually expressed in somatic cells like pluripotent, neural, cardiac and even cancer cells. However, controversy still remains around the existence and function of somatic piRNAs. Using small RNA-seq samples from H9 pluripotent stem cells differentiated to mesoderm progenitors and cardiomyocytes we identified the expression of 447 piRNAs, of which 241 were detected in pluripotency, 218 in mesoderm and 171 in cardiac cells. The majority of them originated from the sense strand of protein coding and lncRNAs genes in all stages of differentiation, though no evidences for secondary piRNAs (ping-pong loop) were found. Genes hosting piRNAs in cardiac samples were related to critical biological processes in the heart, like contraction and cardiac muscle development. Our results indicate that somatic piRNAs might have a role in fine-tuning the expression of genes involved in the differentiation of pluripotent cells to cardiomyocytes.
The first functional characterization of ancient interleukin-15-like (IL-15L) reveals shared and distinct functions of the IL-2, -15 and -15L family cytokines
Authors: Yamaguchi Takuya , Karger Axel , Keller Markus , Wangkahart Eakapol , Wang Tiehui , Secombes Christopher J. , Kimoto Azusa , Furihata Mitsuru , Hashimoto Keiichiro , Fischer Uwe , Dijkstra Johannes M. 
Published: May 2019

AbstractThe ancient cytokine interleukin 15-like (IL-15L) was lost in humans and mice but not throughout mammals. This is the first study to describe IL-15L functions, namely in the fish rainbow trout. Fish have only one α-chain receptor geneIL-15Rα, whereas in mammalian evolution this gene duplicated and evolved intoIL-15RαplusIL-2Rα. Trout IL-2, IL-15 and IL-15L all could bind IL-15Rα and were able to induce phosphorylation of transcription factor STAT5. Reminiscent of the mammalian situation, trout IL-15 was more dependent on “intrans” presentation by IL-15Rα than IL-2. However, whereas trout IL-15 could also function as a free cytokine as known for mammalian IL-15, trout IL-15L function showed a total dependency on intranspresentation by IL-15Rα. Trout lymphocytes from the mucosal tissues gill and intestine were sensitive to IL-15, but refractory to IL-2 and IL-15L, which is reminiscent of sensitivities to IL-15 in mammals. Distinguishing engagement of the IL-2Rα/IL-15Rα receptor chain may explain why IL-2 and IL-15 were selected in evolution as major growth factors for regulatory T cells and lymphocytes in mucosal tissues, respectively. Trout IL-15L efficiently induced expression ofIL-4andIL-13homologues in CD4-CD8-IgM-splenocytes, and we speculate that the responsive cells within that population were type 2 innate lymphoid cells (ILC2). In contrast, trout IL-15 efficiently induced expression ofinterferon γandperforinin CD4-CD8-IgM-splenocytes, and we speculate that in this case the responsive cells were natural killer (NK) cells. In fish, in apparent absence of IL-25, IL-33 and TSLP, primitive IL-15L may have an important role early in the type 2 immunity cytokine cascade. Among trout thymocytes, only CD4-CD8-thymocytes were sensitive to IL-15L, and different than in mammals the CD4+CD8+thymocytes were quite sensitive to IL-2. In addition, the present study provides (i) the first molecular evidence for inter-species cytokine with receptor chain interaction across fish-mammal borders, and (ii) suggestive evidence for a tendency of IL-2/15/15L cytokines to form homodimers as an ancient family trait. This is the first comprehensive study on IL-2/15/15L functions in fish and it provides important insights into the evolution of this cytokine family.
A universal method for gene expression engineering
Authors: Lale Rahmi , Tietze Lisa , Nesje Jenny , Onsager Ingerid , Engelhardt Kerstin , Wong Che Fai Alex , Akan Madina , Hummel Niklas , Kalinowski Jörn , Rückert Christian , Hohmann-Marriott Martin Frank 
Published: May 2019

AbstractThe precise expression of genes is one of the foundations of biotechnology. Here we present GeneEE, a straightforward method for generating artificial gene expression systems. We demonstrate that GeneEE segments, containing a 200 nucleotide DNA with random nucleotide composition, can facilitate constitutive and inducible gene expression. To highlight the universal character of our method, we demonstrate GeneEE-mediated gene and protein expression in six bacterial species and Baker’s yeast.
Can education be personalised using pupils’ genetic data?
Authors: Morris Tim T , Davies Neil M , Smith George Davey 
Published: May 2019

AbstractThe increasing predictive power of polygenic scores for education has led to their promotion by some as a potential tool for genetically informed policy. How well polygenic scores predict educational performance conditional on other phenotypic data is however not well understood. Using data from a UK cohort study, we investigated how well polygenic scores for education predicted pupils’ realised achievement over and above phenotypic data that are available to schools. Across our sample, prediction of educational outcomes from polygenic scores were inferior to those from parental socioeconomic factors. There was high overlap between the polygenic score and achievement distributions, leading to weak predictive accuracy at the individual level. Furthermore, conditional on prior achievement polygenic scores were not predictive of later achievement. Our results suggest that while polygenic scores can be informative for identifying group level differences, they currently have limited use for predicting individual educational performance or for personalised education.