bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolic profiling of adiponectin levels in adults: Mendelian randomization analysis
Authors: Maria Carolina Borges , Aluísio JD Barros , Diana L Santos Ferreira , Juan Pablo Casas , Bernardo Lessa Horta , Mika Kivimaki , Meena Kumari , Menon Usha , Tom R Gaunt , Yoav Ben-Shlomo , Deise F Freitas , Isabel O Oliveira , Aleksandra Gentry-Maharaj , Evangelia Fourkala , Debbie A Lawlor , Aroon D Hingorani
Published: April 2017

Background

Adiponectin, a circulating adipocyte-derived protein has insulin-sensitizing, anti-inflammatory, anti-atherogenic, and cardiomyocyte-protective properties in animal models. However, the systemic effects of adiponectin in humans are unknown.

Objectives

Our aims were to define the metabolic profile associated with higher blood adiponectin concentration and investigate whether variation in adiponectin concentration affects the systemic metabolic profile.

Methods

We applied multivariable regression in up to 5,906 adults and Mendelian randomization (using cis-acting genetic variants in the vicinity of the adiponectin gene as instrumental variables) for analysing the causal effect of adiponectin in the metabolic profile of up to 38,058 adults. Participants were largely European from six longitudinal studies and one genome-wide association consortium.

Results

In the multivariable regression analyses, higher circulating adiponectin was associated with higher HDL lipids and lower VLDL lipids, glucose levels, branched-chain amino acids, and inflammatory markers. However, these findings were not supported by Mendelian randomization analyses for most metabolites. Findings were consistent between sexes and after excluding high risk groups (defined by age and occurrence of previous cardiovascular event) and one study with admixed population.

Conclusion

Our findings indicate that blood adiponectin concentration is more likely to be an epiphenomenon in the context of metabolic disease than a key determinant.
Nanopore detection of bacterial DNA base modifications
Authors: McIntyre Alexa B.R. , Alexander Noah , Burton Aaron S. , Castro-Wallace Sarah , Chiu Charles Y. , John Kristen K. , Stahl Sarah E. , Li Sheng , Mason Christopher E.
Published: April 2017

The common bacterial base modification N6-methyladenine (m6A) is involved in many pathways related to an organism’s ability to survive and interact with its environment. Recent research has shown that nanopore sequencing can detect m5C with per-read accuracy of upwards of 80% but m6A with significantly lower accuracy. Here we use a binary classifier to improve m6A classification by marking adenines as methylated or unmethylated based on differences between measured and expected current values as each adenine travels through the nanopore. We also illustrate the importance of read quality for base modification detection and compare to PacBio methylation calls. With recent demonstrations of nanopore sequencing in Antarctica and onboard the International Space Station, the ability to reliably characterize m6A presents an opportunity to further examine the role of methylation in bacterial adaptation to extreme or very remote environments.
Binding of a Newly Identified Essential Light Chain to ExpressedPlasmodium falciparumClass XIV Myosin Enhances Actin Motility
Authors: Bookwalter Carol S. , Tay Chwen L. , McCrorie Rama , Previs Michael J. , Krementsova Elena B. , Fagnant Patricia M. , Baum Jake , Trybus Kathleen M.
Published: April 2017

Motility of the apicomplexan parasitePlasmodium falciparum, the causative agent of malaria, is enabled by the glideosome, a multi-protein complex containing the class XIV myosin motor, PfMyoA. Parasite motility is necessary for invasion into host cells and for virulence. Here we show that milligram quantities of functional PfMyoA can be expressed using the baculovirus/Sf9 cell expression system, provided that a UCS (UNC-45/CRO1/She4p) family myosin co-chaperone fromPlasmodium spp. is co-expressed with the heavy chain. The homologous chaperone from the apicomplexanToxoplasma gondiidoes not functionally substitute. We expressed a functional full-length PfMyoA with boundmyosintailinteractingprotein (MTIP), the only known light chain of PfMyoA. We then identified an additional “essential” light chain (PfELC) that co-purified with PfMyoA isolated from parasite lysates. PfMyoA expressed with both light chains moved actin at ~3.8 μm/sec, more than twice that of PfMyoA-MTIP (~1.7 μm/sec), consistent with the light chain binding domain acting as a lever arm to amplify nucleotide-dependent motions in the motor domain. Surprisingly, PfMyoA moved skeletal actin or expressedP. falciparumactin at the same speed. Duty ratio estimates suggest that PfMyoA may be able to move actin at maximal speed with as few as 6 motors. Under unloaded conditions, neither phosphorylation of Ser19 of the heavy chain, phosphorylation of several Ser residues in the N-terminal extension of MTIP, or calcium affected the speed of actin motion. These studies provide the essential framework for targeting the glideosome as a potential drug target to inhibit invasion by the malaria parasite.

Significance

Motility of the apicomplexan parasitePlasmodium falciparum, the causative agent of malaria, relies on a divergent actomyosin system powered by the class XIV myosin, PfMyoA. We show that functional PfMyoA can be expressed inSf9cells if aPlasmodium spp. myosin chaperone is co-expressed. We identified an “essential” light chain (PfELC) that binds to PfMyoA in parasites.In vitroexpression of PfMyoA heavy chain with PfELC and the known light chain MTIP produced the fastest speeds of actin movement (~3.8 μm/sec). Duty ratio estimates suggest that ~6 PfMyoA motors can move actin at maximal speed, a feature that may facilitate interaction with short, dynamicPlasmodiumactin filaments. Our findings enable drug screening for myosin-based inhibitors ofPlasmodiumcellular invasion.
Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Singlecell Transcriptomes
Authors: Zhou Joseph X. , Taramelli Roberto , Pedrini Edoardo , Knijnenburg Theo , Huang Sui
Published: April 2017

Many behaviors of cancer, such as progression, metastasis and drug resistance etc., cannot be fully understood by genetic mutations or intracellular signaling alone. Instead, they are emergent properties of cell community that forms a tumor. Studies of tumor heterogeneity reveal that many cancer behaviors critically depend on the intercellular communication mediated by secreted signaling ligands and their cognate receptors that take place between cancer cells and stromal cells. Owing to systematic cancer omics efforts, we studied such cell-cell interactions using data from cancer transcriptome database. We curated a list of more than 2,500 ligand-receptor pairs and developed a method to identify their enrichment in tumors from TCGA pancancer data and to build a cell interaction network from single-cell data for the case of melanoma. Using the specificity of the ligand-receptor interaction and their expressions measured in individual cells, we built a map of a cell-cell communication network which indicate what signal is exchanged between which cell types. Such networks establish a new formal phenotypes which are embodied by the cell communication structure - it may offer new opportunities to identify the molecular signatures which may influence cancer cell behaviors by changing cell population dynamics.
Mapping Human Hematopoietic Hierarchy at Single Cell Resolution by Microwell-seq
Authors: Lai Shujing , Xu Yang , Huang Wentao , Jiang Mengmeng , Chen Haide , Ye Fang , Wang Renying , Qiu Yunfei , Jiang Xinyi , Huang Daosheng , Mao Jie , Li Yanwei , Lu Yingru , Xie Jin , Fang Qun , Li Tiefeng , Huang He , Han Xiaoping , Guo Guoji
Published: April 2017

The classical hematopoietic hierarchy, which is mainly built with fluorescence-activated cell sorting (FACS) technology, proves to be inaccurate in recent studies. Single cell RNA-seq (scRNA-seq) analysis provides a solution to overcome the limit of FACS-based cell type definition system for the dissection of complex cellular hierarchy. However, large-scale scRNA-seq is constrained by the throughput and cost of traditional methods. Here, we developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using extremely simple devices. Using Microwell-seq, we constructed a single-cell resolution transcriptome atlas of human hematopoietic differentiation hierarchy by profiling more than 50,000 single cells throughout adult human hematopoietic system. We found that adult human hematopoietic stem and progenitor cell (HSPC) compartment is dominated by progenitors primed with lineage specific regulators. Our analysis revealed differentiation pathways for each cell types, through which HSPCs directly progress to lineage biased progenitors before differentiation. We propose a revised adult human hematopoietic hierarchy independent of oligopotent progenitors. Our study also demonstrates the broad applicability of Microwell-seq technology.
Defining the functional significance of intergenic transcribed regions
Authors: Lloyd John P. , Tsai Zing Tsung-Yeh , Sowers Rosalie P. , Panchy Nicholas L. , Shiu Shin-Han
Published: April 2017

With advances in transcript profiling, the presence of transcriptional activities in intergenic regions has been well established. However, whether intergenic expression reflects transcriptional noise or activity of novel genes remains unclear. We identified intergenic transcribed regions (ITRs) in 15 diverse flowering plant species and found that the amount of intergenic expression correlates with genome size, a pattern that could be expected if intergenic expression is largely nonfunctional. To further assess the functionality of ITRs, we first built machine learning classifiers usingArabidopsis thalianaas a model that accurately distinguish functional sequences (phenotype genes) and likely nonfunctional ones (pseudogenes and unexpressed intergenic regions) by integrating 93 biochemical, evolutionary, and sequence-structure features. Next, by applying the models genome-wide, we found that 4,427 ITRs (38%) and 796 annotated ncRNAs (44%) had features significantly similar to benchmark protein-coding or RNA genes and thus were likely parts of functional genes. Approximately 60% of ITRs and ncRNAs were more similar to nonfunctional sequences and were likely transcriptional noise. The predictive framework established here provides not only a comprehensive look at how functional, genic sequences are distinct from likely nonfunctional ones, but also a new way to differentiate novel genes from genomic regions with noisy transcriptional activities.
Enhancing Multiplex Genome Editing by Natural Transformation (MuGENT) via inactivation of ssDNA exonucleases
Authors: Dalia Triana N. , Yoon Soo Hun , Galli Elisa , Barre Francois-Xavier , Waters Christopher M. , Dalia Ankur B.
Published: April 2017

Recently, we described a method for multiplex genome editing by natural transformation (MuGENT). Mutant constructs for MuGENT require large arms of homology (>2000 bp) surrounding each genome edit, which necessitates laboriousin vitroDNA splicing. InVibriocholerae, we uncover that this requirement is due to cytoplasmic ssDNA exonucleases, which inhibit natural transformation. In ssDNA exonuclease mutants, one arm of homology can be reduced to as little as 40 bp while still promoting integration of genome edits at rates of ~50% without selectionin cis. Consequently, editing constructs are generated in a single PCR reaction where one homology arm is oligonucleotide encoded. To further enhance editing efficiencies, we also developed a strain for transient inactivation of the mismatch repair system. As a proof-of-concept, we used these advances to rapidly mutate 10 high-affinity binding sites for the nucleoid occlusion protein SlmA and generated a duodecuple mutant of 12 diguanylate cyclases inV. cholerae. Whole genome sequencing revealed little to no off-target mutations in these strains. Finally, we show that ssDNA exonucleases inhibit natural transformation inAcinetobacter baylyi. Thus, rational removal of ssDNA exonucleases may be broadly applicable for enhancing the efficacy and ease of MuGENT in diverse naturally transformable species.
Co-evolution of dispersal with social behaviour favours social polymorphism
Authors: Mullon Charles , Keller Laurent , Lehmann Laurent
Published: April 2017

Dispersal determines gene flow among groups in a population and so plays a major role in many ecological and evolutionary processes, from biological invasions to species extinctions. Because patterns of gene flow shape kin structure, dispersal is also important to the evolution of social behaviours that influence reproduction and survival within groups. Conversely, dispersal patterns depend on kin structure and social behaviour. Dispersal and social behaviour therefore co-evolve but the nature and consequences of this interplay are not well understood. Here, we model this co-evolution and show that it readily leads to the emergence and maintenance of two broadly-defined social morphs: a sessile, benevolent morph expressed by individuals who tend to increase the fecundity of others within their group relative to their own; and a dispersive, self-serving morph expressed by individuals who tend to increase their own fecundity relative to others’ within their group. This social polymorphism arises as a consequence of a positive linkage between the loci responsible for dispersal and social behaviour, leading to benevolent individuals preferentially interacting with relatives and self-serving individuals with non-relatives. We find that this positive linkage is favoured under a large spectrum of conditions, which suggests that an association between dispersal proclivity and other social traits should be common in nature. In line with this prediction, dispersing individuals across a wide range of organisms have been reported to differ in their social tendencies from non-dispersing individuals.
Intracellular metabolic circuits shape inter-species microbial interactions
Authors: Zomorrodi Ali R. , Segrè Daniel
Published: April 2017

Metabolite exchanges in microbial communities give rise to ecological interaction networks that influence ecosystem diversity and stability1-6. These exchanges depend on complex intracellular pathways thus raising the question of whether ecological interactions are inferable from genomes. We address these questions by integrating genome-scale models of metabolism7, to compute the fitness of interacting microbes, with evolutionary game theory, which uses these fitness values to infer evolutionarily stable interactions in multi-species microbial “games”. After validating our approach using data on sucrose hydrolysis byS. cerevisiae, we performed over 80,000in silicoexperiments to evaluate the rise of unidirectional and cross-feeding metabolic dependencies in populations ofEscherichia colisecreting 189 amino acid pairs. We found that, despite the diversity of exchanged amino acids, most pairs conform to general patterns of inter-species interactions. However, several amino acid pairs deviate from these patterns due to pleiotropy and epistasis in metabolic pathways. To better understand the emergence of cross-feeding, we performedin silicoinvasion experiments and found possible evolutionary paths that could lead to such association. Overall, our study provides mechanistic insights into the rise of evolutionarily stable interdependencies, with important implications for biomedicine and microbiome engineering8-10.
De novotranscriptome sequencing and comparative analysis of midgut tissues of four non-model insects pertaining to Hemiptera, Coleoptera, Diptera and Lepidoptera
Authors: Gazara Rajesh K. , Cardoso Christiane , Bellieny-Rabelo Daniel , Ferreira Clélia , Terra Walter R. , Venancio Thiago M.
Published: April 2017

Despite the great morphological diversity of insects, there is a regularity in their digestive functions, which is apparently related to their physiology. In the present work we report thede novomidgut transcriptomes of four non-model insects from four distinct orders:Spodoptera frugiperda(Lepidoptera),Musca domestica(Diptera),Tenebrio molitor(Coleoptera) andDysdercus peruvianus(Hemiptera). We employed a computational strategy to merge assemblies obtained with two different algorithms, which substantially increased the quality of the final transcriptomes. Unigenes were annotated and analyzed using the eggNOG database, which allowed us to assign some level of functional and evolutionary information to 79.7% to 93.1% of the transcriptomes. We found interesting transcriptional patterns, such as: i) the intense use of lysozymes in digestive functions ofM. domesticalarvae, which are streamlined and adapted to feed on bacteria; ii) the up-regulation of orthologous UDP-glycosyl transferase and cytochrome P450 genes in the whole midguts different species, supporting the presence of an ancient defense frontline to counter xenobiotics; iii) evidence supporting roles for juvenile hormone binding proteins in the midgut physiology, probably as a way to activate genes that help fight anti-nutritional substances (e.g. protease inhibitors). The results presented here shed light on the digestive and structural properties of the digestive systems of these distantly related species. Furthermore, the produced datasets will also be useful for scientists studying these insects.
Variability in prior expectations explains biases in confidence reports
Authors: Tano Pablo , Meyniel Florent , Sigman Mariano , Salles Alejo
Published: April 2017

Confidence in a decision is defined statistically as the probability of that decision being correct. Humans, however, display systematic confidence biases, as has been exposed in various experiments. Here, we show that these biases vanish when taking into account participants' prior expectations, which we measure independently of the confidence report. We use a wagering experiment to show that modeling subjects' choices allows for classifying individuals according to their prior biases, which fully explain from first principles the differences in their later confidence reports. Our parameter-free confidence model predicts two counterintuitive patterns for individuals with different prior beliefs: pessimists should report higher confidence than optimists, and, for the same task difficulty, the confidence of pessimists should increase with the generosity of the task. These findings show how systematic confidence biases can be simply understood as differences in prior expectations.
Governing knowledge sharing behaviour in post-Soviet Kazakhstan
Authors: Kozhakhmet Sanat , Nazri Mohammad
Published: April 2017

Purpose

The purpose of this study is to expand the understanding of knowledge governance approaches by examining governance mechanisms that can be used to enhance affective commitment. Then, this paper aims to investigate the mediating effects of affective commitment on the relationship between knowledge governance mechanisms (KGMs) and knowledge sharing.

Design/methodology/approach

Self-administered questionnaires were used to gather data from 391 employees working in a wide range of organizations operating in Kazakhstan. Regression analysis and structure equation models (SPSS and AMOS) were used to assess the research model.

Findings

The empirical results indicated that formal and informal KGMs have a significant impact on knowledge sharing. Moreover, the results revealed that affective commitment mediates the relationship between KGMs and knowledge sharing.

Practical implications

The proposed KGM is a response to practical necessity to promote the affective commitment by combinations of organizational antecedents.

Originality/value

It is the first attempt in post-Soviet Kazakhstan to systematically analyze the effect of knowledge governance on affective commitment. In addition, this paper offers a conceptual framework where affective commitment plays the mediating role in successful knowledge sharing.
Optimal Environmental Taxation with Capital Mobility*
Authors: Schwerhoff Gregor , Franks Max
Published: April 2017

Climate policy exemptions for energy‐intensive sectors are often justified with distributional concerns. One concern is that households employed in energy‐intensive sectors might be affected disproportionally because of (international) capital mobility. By assuming that workers cannot move freely between sectors, we can reproduce this concern: uniform climate policy causes more inequality between the sectors when capital is mobile than when it is not. However, we find that affected households can be relieved more effectively with sector‐specific labour taxes than with sector‐specific climate policy. The reason for this finding is that households benefit more directly from sector‐specific labour tax cuts than from climate policy exemptions. Keeping climate policy uniform across sectors has the added benefit of creating incentives for long‐term decarbonisation. In addition, we find that the differential effect of capital mobility depends on the government's degree of inequality aversion – redistribution is more expensive when capital is mobile.
Pathogenicity of two COQ7 mutations and responses to 2,4‐dihydroxybenzoate bypass treatment
Authors: Wang Ying , Smith Christopher , Parboosingh Jillian S. , Khan Aneal , Innes Micheil , Hekimi Siegfried
Published: April 2017

Primary ubiquinone (co‐enzyme Q) deficiency results in a wide range of clinical features due to mitochondrial dysfunction. Here, we analyse and characterize two mutations in the ubiquinone biosynthetic gene COQ7. One mutation from the only previously identified patient (V141E), and one (L111P) from a 6‐year‐old girl who presents with spasticity and bilateral sensorineural hearing loss. We used patient fibroblast cell lines and a heterologous expression system to show that both mutations lead to loss of protein stability and decreased levels of ubiquinone that correlate with the severity of mitochondrial dysfunction. The severity of L111P is enhanced by the particular COQ7 polymorphism (T103M) that the patient carries, but not by a mitochondrial DNA mutation (A1555G) that is also present in the patient and that has been linked to aminoglycoside‐dependent hearing loss. We analysed treatment with the unnatural biosynthesis precursor 2,4‐dihydroxybenzoate (DHB), which can restore ubiquinone synthesis in cells completely lacking the enzymatic activity of COQ7. We find that the treatment is not beneficial for every COQ7 mutation and its outcome depends on the extent of enzyme activity loss.
Use of Bank and Nonbank Financial Services: Financial Decision Making by Immigrants and Native Born
Authors: Northwood Joyce M. , Rhine Sherrie L.W.
Published: April 2017

This study examines the joint decisions made by immigrant and native‐born families about whether or not to have a bank account and to use nonbank financial services (NBFS). Immigrant families, especially those from Mexico or other Latin American countries, have a higher probability of usingNBFSthan native‐born families, regardless of their banking status. Residing in concentrated ethnic enclaves or being aUScitizen, however, lowers the probability of using these services. Similarly, native‐born Black and Hispanic families are more likely to use these services than native‐born White families. Our findings support continued efforts to encourage mainstream participation among immigrant and minority native‐born families. Having access to mainstream financial services can help these families establish financial stability and economic mobility. To our knowledge, this is the first comprehensive study of immigrant families' joint decision making about usingNBFSand bank account ownership.
Modeling and observations of an elevated, moving infrasonic source: Eigenray methods
Authors: Blom Philip , Waxler Roger
Published: April 2017

The acoustic ray tracing relations are extended by the inclusion of auxiliary parameters describing variations in the spatial ray coordinates and eikonal vector due to changes in the initial conditions. Computation of these parameters allows one to define the geometric spreading factor along individual ray paths and assists in identification of caustic surfaces so that phase shifts can be easily identified. A method is developed leveraging the auxiliary parameters to identify propagation paths connecting specific source-receiver geometries, termed eigenrays. The newly introduced method is found to be highly efficient in cases where propagation is non-planar due to horizontal variations in the propagation medium or the presence of cross winds. The eigenray method is utilized in analysis of infrasonic signals produced by a multi-stage sounding rocket launch with promising results for applications of tracking aeroacoustic sources in the atmosphere and specifically to analysis of motor performance during dynamic tests.
Stimulus coherence influences sound-field localization and fusion/segregation of leading and lagging sounds
Authors: Grosse Julian , van de Par Steven , Trahiotis Constantine
Published: April 2017

The ability to localize sound sources in reverberant environments is dependent upon first-arriving information, an outcome commonly termed “the precedence effect.” For example, in laboratory experiments, the combination of a leading (direct) sound followed by a lagging (reflected) sound is localized in the direction of the leading sound. This study was designed to measure the degree to which stimulus compactness/diffuseness (i.e., coherence as represented by interaural cross correlation) of leading and lagging sounds influences performance. The compactness/diffuseness of leading or lagging sounds was varied by either presenting a sound from a single loudspeaker or by presenting mutually uncorrelated versions of similar sounds from nine adjacent loudspeakers. In separate experiments, the listener's task was to point to the perceived location of leading and lagging 10-ms long low-pass filtered white noises or 2-s long tokens of speech. The leading and lagging stimuli were presented either from speakers located directly in front of the listeners or from speakers located ±45° to the right or left. The results indicate that leading compact (coherent) sounds influence perceived location more so than do leading diffuse (incoherent) sounds. This was true independent of whether the sounds were Gaussian noises or tokens of speech.
Types and rates of forest disturbance in Brazilian Legal Amazon, 2000–2013
Authors: Tyukavina Alexandra , Hansen Matthew C. , Potapov Peter V. , Stehman Stephen V. , Smith-Rodriguez Kevin , Okpa Chima , Aguilar Ricardo
Published: April 2017

Primary forest clearing as a share of gross disturbance in Brazilian Legal Amazon changed from 67% in 2001 to 47% in 2013.
Climate legacies drive global soil carbon stocks in terrestrial ecosystems
Authors: Delgado-Baquerizo Manuel , Eldridge David J. , Maestre Fernando T. , Karunaratne Senani B. , Trivedi Pankaj , Reich Peter B. , Singh Brajesh K.
Published: April 2017

Our findings indicate the importance of paleoclimatic information to improve quantitative predictions of global soil C stocks.
CRISPR-Cpf1 correction of muscular dystrophy mutations in human cardiomyocytes and mice
Authors: Zhang Yu , Long Chengzu , Li Hui , McAnally John R. , Baskin Kedryn K. , Shelton John M. , Bassel-Duby Rhonda , Olson Eric N.
Published: April 2017

CRISPR-Cpf1–mediated correction of Duchenne muscular dystrophy mutations in human cells and a mouse model.
Direct 4D printing via active composite materials
Authors: Ding Zhen , Yuan Chao , Peng Xirui , Wang Tiejun , Qi H. Jerry , Dunn Martin L.
Published: April 2017

A 4D printing method is developed where the shape of a 3D-printed part can change rapidly into a new permanent one by heating.
Ephrin B1–mediated repulsion and signaling control germinal center T cell territoriality and function
Authors: Lu Peiwen , Shih Changming , Qi Hai
Published: April 2017

Guiding immune cells to the center

Germinal centers (GCs) are the site of antibody affinity maturation. The GC response fundamentally depends on contact-dependent signal exchange between antigen-specific T and B lymphocytes. Lu
et al.
uncovered a repulsive guidance system that inhibits GC recruitment and retention of T follicular helper (T
FH
) cells while simultaneously promoting their helper activities locally (see the Perspective by Moschovakis and Forster). This system comprises the GC-specific transmembrane ephrin B1 (EFNB1) molecule and two EFNB1 receptors—EPHB4 and EPHB6—expressed by activated T cells, including T
FH
cells. In the absence of EFNB1 on GC B cells or when EPHB6 was suppressed on T cells, inappropriately large numbers of T cells were recruited to and retained in the GC as a result of relaxed repulsion of T
FH
cells.

Science
, this issue p.
eaai9264
; see also p.
703
Nucleic acid detection with CRISPR-Cas13a/C2c2
Authors: Gootenberg Jonathan S. , Abudayyeh Omar O. , Lee Jeong Wook , Essletzbichler Patrick , Dy Aaron J. , Joung Julia , Verdine Vanessa , Donghia Nina , Daringer Nichole M. , Freije Catherine A. , Myhrvold Cameron , Bhattacharyya Roby P. , Livny Jonathan , Regev Aviv , Koonin Eugene V. , Hung Deborah T. , Sabeti Pardis C. , Collins James J. , Zhang Feng
Published: April 2017

Sensitive and specific CRISPR diagnostics

Methods are needed that can easily detect nucleic acids that signal the presence of pathogens, even at very low levels. Gootenberg
et al.
combined the allele-specific sensing ability of CRISPR-Cas13a with recombinase polymerase amplification methods to detect specific RNA and DNA sequences. The method successfully detected attomolar levels of Zika virus, as well as the presence of pathogenic bacteria. It could also be used to perform human genotyping from cell-free DNA.

Science
, this issue p.
438
Complete Genome Sequence of a Novel Porcine Circovirus Type 3 Strain, PCV3/CN/Hubei-618/2016, Isolated from China
Authors: Fan Shengxian , Ku Xugang , Chen Fangzhou , Wang Ying , Yu Xuexiang , He Qigai
Published: April 2017

In October 2016, porcine circovirus type 3 (PCV3) was identified as a pathogen agent for pigs in the United States. Here, we report the genome sequence of a Chinese PCV3 strain, PCV3/CN/Hubei-618/2016. This will help us better understand the epidemiology and genetic characteristics of PCV3.
Draft Genome Sequence of
Chryseobacterium
sp. JV274 Isolated from Maize Rhizosphere
Authors: Vacheron Jordan , Dubost Audrey , Chapulliot David , Prigent-Combaret Claire , Muller Daniel
Published: April 2017

We report the draft genome sequence of
Chryseobacterium
sp. JV274. This strain was isolated from the rhizosphere of maize during a greenhouse experiment. JV274 harbors genes involved in flexirubin production (
darA
and
darB
genes), bacterial competition (type VI secretion system), and gliding (bacterial motility; type IX secretion system).
Genome Sequence of
Cobetia
sp. Strain MM1IDA2H-1, a Hydrocarbon-Degrading and Biosurfactant-Producing Marine Bacterium
Authors: Ibacache-Quiroga Claudia , Canales Christian , Charifeh Mariam , Dinamarca M. Alejandro
Published: April 2017

Cobetia
sp. strain MM1IDA2H-1 is a marine bacterium isolated from seawater samples that uses the heterocyclic aromatic hydrocarbon dibenzothiophene as the sole carbon source and produces a biosurfactant that inhibits bacterial quorum sensing. The
Cobetia
sp. MM1IDA2H-1 genome was sequenced, processed, assembled, and annotated for basic and applied studies.
Draft Genome Sequence of Permafrost Bacterium
Nesterenkonia
sp. Strain PF2B19, Revealing a Cold Adaptation Strategy and Diverse Biotechnological Potential
Authors: Singh Purnima , Kapse Neelam , Roy Utpal , Singh Shiv Mohan , Dhakephalkar P. K.
Published: April 2017

Nesterenkonia
sp. strain PF2B19, a psychrophilic bacterium, was isolated from 44,800-year-old permafrost. The draft genome sequence of this strain revealed the presence of genes involved in the production of cold active enzymes, carotenoid biosynthesis, fatty acid biosynthesis, and resistance to heavy metals. These results show the immense potential of the strain.
Complete Genome Sequences of Chikungunya Viruses Isolated from Plasma Specimens Collected from Haitians in 2014
Authors: White Sarah K. , Morris J. Glenn , Elbadry Maha A. , Beau De Rochars Valery Madsen , Okech Bernard A. , Lednicky John A.
Published: April 2017

Ten chikungunya virus isolates from human plasma collected in Haiti from May to August 2014, in the midst of a chikungunya fever outbreak, were fully sequenced. The resulting genomic sequences are nearly identical, and phylogenetic analyses indicate they belong to the Asian lineage of the virus.
Draft Genome Sequences of Two Clinical Methicillin-Resistant Staphylococcus aureus Strains Isolated from Healthy Children in Brazil
Authors: de Carvalho Suzi P. , de Almeida Jéssica B. , de Freitas Leandro M. , Guimaraes Ana Marcia S. , do Nascimento Naíla C. , dos Santos Andrea P. , Messick Joanne B. , Timenetsky Jorge , Marques Lucas M.
Published: April 2017

We report here the draft genome sequences of two community-associated methicillin-resistant
Staphylococcus aureus
(CA-MRSA) strains, C18 and C80, isolated from healthy children from day care centers. To our knowledge, these are the first draft genome sequences of CA-MRSA ST398/CC398/Scc
mec
V and CA-MRSA ST5/CC5/Scc
mec
IVa isolated from healthy children in Brazil.
Draft Genome Sequence of a Kale (
Brassica oleracea
L.) Root Endophyte,
Pseudomonas
sp. Strain C9
Authors: Laugraud Aurelie , Young Sandra , Gerard Emily , O’Callaghan Maureen , Wakelin Steven
Published: April 2017

Pseudomonas
sp. strain C9 is a plant growth–promoting bacterium isolated from the root tissue of
Brassica oleracea
L. grown in soil from Marlborough, New Zealand. Its draft genome of 6,350,161 bp contains genes associated with plant growth promotion and biological control.
Draft Whole-Genome Sequence of “
Candidatus
Liberibacter asiaticus” Strain TX2351 Isolated from Asian Citrus Psyllids in Texas, USA
Authors: Kunta Madhurababu , Zheng Zheng , Wu Fengnian , da Graca John V. , Park Jong-Won , Deng Xiaoling , Chen Jianchi
Published: April 2017

We report here the draft genome sequence of “
Candidatus
Liberibacter asiaticus” strain TX2351, collected from Asian citrus psyllids in south Texas, USA. The TX2351 genome has a size of 1,252,043 bp, a G+C content of 36.5%, 1,184 predicted open reading frames, and 52 RNA genes.
Permanent Draft Genome Sequence of the French Bean Symbiont
Rhizobium
sp. Strain RSm-3 Isolated from the Eastern Himalayan Region of India
Authors: Rai Ritu , Swanson Erik , Sarkar Indrani , Lama Dorjay , Abebe-Aleke Feseha , Simpson Stephen , Morris Krystalynne , Thomas W. Kelley , Kar Pallab , Gtari Maher , Sen Arnab , Tisa Louis S.
Published: April 2017

The genus
Rhizobium
contains many species able to form nitrogen-fixing nodules on plants of the legume family. Here, we report the 6.9-Mbp draft genome sequence of
Rhizobium
sp. strain RSm-3, with a G+C content of 61.4% and 6,511 candidate protein-coding genes.
Treatment of Latent Tuberculosis Infection
Authors: Haley Connie A.
Published: April 2017

There are approximately 56 million people who harbor
Mycobacterium tuberculosis
that may progress to active tuberculosis (TB) at some point in their lives. Modeling studies suggest that if only 8% of these individuals with latent TB infection (LTBI) were treated annually, overall global incidence would be 14-fold lower by 2050 compared to incidence in 2013, even in the absence of additional TB control measures. This highlights the importance of identifying and treating latently infected individuals, and that this intervention must be scaled up to achieve the goals of the Global End TB Strategy. The efficacy of LTBI treatment is well established, and the most commonly used regimen is 9 months of daily self-administered isoniazid. However, its use has been hindered by limited provider awareness of the benefits, concern about potential side effects such as hepatotoxicity, and low rates of treatment completion. There is increasing evidence that shorter rifamycin-based regimens are as effective, better tolerated, and more likely to be completed compared to isoniazid. Such regimens include four months of daily self-administered rifampin monotherapy, three months of once weekly directly observed isoniazid-rifapentine, and three months of daily self-administered isoniazid-rifampin. The success of LTBI treatment to prevent additional TB disease relies upon choosing an appropriate regimen individualized to the patient, monitoring for potential adverse clinical events, and utilizing strategies to promote adherence. Safer, more cost-effective, and more easily completed regimens are needed and should be combined with interventions to better identify, engage, and retain high-risk individuals across the cascade from diagnosis through treatment completion of LTBI.
Determinants of institutional delivery among young married women in Nepal: Evidence from the Nepal Demographic and Health Survey, 2011
Authors: Shahabuddin ASM , De Brouwere Vincent , Adhikari Ramesh , Delamou Alexandre , Bardaj Azucena , Delvaux Therese
Published: April 2017

Objectives

To identify the determinants of institutional delivery among young married women in Nepal.

Design

Nepal Demographic and Health Survey (NDHS) data sets 2011 were analysed. Bivariate and multivariate logistic regression analyses were performed using a subset of 1662 ever-married young women (aged 15–24 years).

Outcome measure

Place of delivery.

Results

The rate of institutional delivery among young married women was 46%, which is higher than the national average (35%) among all women of reproductive age. Young women who had more than four antenatal care (ANC) visits were three times more likely to deliver in a health institution compared with women who had no antenatal care visit (OR: 3.05; 95% CI: 2.40 to 3.87). The probability of delivering in an institution was 69% higher among young urban women than among young women who lived in rural areas. Young women who had secondary or above secondary level education were 1.63 times more likely to choose institutional delivery than young women who had no formal education (OR: 1.626; 95% CI: 1.171 to 2.258). Lower use of a health institution for delivery was also observed among poor young women. Results showed that wealthy young women were 2.12 times more likely to deliver their child in an institution compared with poor young women (OR: 2.107; 95% CI: 1.53 to 2.898). Other factors such as the age of the young woman, religion, ethnicity, and ecological zone were also associated with institutional delivery.

Conclusions

Maternal health programs should be designed to encourage young women to receive adequate ANC (at least four visits). Moreover, health programs should target poor, less educated, rural, young women who live in mountain regions, are of Janajati ethnicity and have at least one child as such women are less likely to choose institutional delivery in Nepal.
Damage control laparotomy trial: design, rationale and implementation of a randomized controlled trial
Authors: Harvin John A , Podbielski Jeanette , Vincent Laura E , Fox Erin E , Moore Laura J , Cotton Bryan A , Wade Charles E , Holcomb John B
Published: April 2017

Background

Damage control laparotomy (DCL) is an abbreviated operation intended to prevent the development of hypothermia, acidosis, and coagulopathy in seriously injured patients. The indications for DCL have since been broadened with no high-quality data to guide treatment. For patients with an indication for DCL, we aim to determine the effect of definitive laparotomy on patient morbidity.

Method

This is a pragmatic, parallel-group, randomized controlled pilot trial. Emergent laparotomy is defined as admission directly to the operating room from the emergency department within 90 min of arrival. DCL indications excluded from the study include packing of the liver or retroperitoneum, abdominal compartment syndrome prophylaxis, to expedite interventional radiology for hemorrhage control, and the need for ongoing transfusions and/or continuous vasopressor support. When a surgeon determines a DCL is indicated, the patient will be screened for inclusion and exclusion criteria. Patients with any indication for DCL that is not excluded are eligible for randomization. Patients will be randomized intraoperatively to DCL (control) or definitive fascial closure of the laparotomy (intervention). The primary outcome will be major abdominal complication or death within 30 days. Major abdominal complication is a composite outcome including fascial dehiscence, organ/space surgical site infection, enteric suture line failure, and unplanned reopening of the abdomen. Outcomes will be compared using both frequentist and Bayesian statistics.

Discussion

In patients with an indication for DCL, this trial will determine the effect of definitive laparotomy on major abdominal complications and death and will inform clinicians on the risks and benefits of this procedure. Regardless of the study outcome, the results will improve the quality of care provided to injured patients.

Trial registration number

NCT02706041.
Mesozoic and older rift basins on the SE Greenland Shelf offshore Ammassalik
Authors: Gerlings Joanna , Hopper John R. , Fyhn Michael B. W. , Frandsen Nicolas
Published: April 2017

Seismic reflection data and shallow cores from the SE Greenland margin show that rift basins formed by the mid- to Late Cretaceous in the offshore area near Ammassalik. Here termed the Ammassalik Basin, this contribution documents the area using reprocessed older shallow seismic reflection data together with a more recent, commercial deep seismic reflection profile. The data show that the basin is at least 4 km deep and may be regionally quite extensive. Interpretation of gravity anomaly data indicate that the basin potentially covers an area of nearly 100 000 km
2
. The sediments in the basins are at least of Cretaceous age, as indicated by a sample from just below the basalt cover that was dated as Albian. Dipping sediment layers in the basins indicate that older sediments are present. Comparison of the data to the conjugate Hatton margin where older basins are exposed beneath the volcanic cover shows similar stratigraphy of similar ages. Reconstructions of the position of the basin during the Permian–Triassic and Jurassic suggest that older sedimentary strata could also be possible. In contrast to the conjugate Hatton margin, possible older strata subcrop out below the seafloor along the shallow margin, providing a future opportunity to sample some of the oldest sediments to determine the onset of rifting between SE Greenland and the Hatton margin.
Geological studies in the Baalsrudfjellet nunatak between the Schirmacher Oasis and the Wohlthat Mountains to establish the continuation of the East African Orogen (EAO) in central Dronning Maud Land, East Antarctica
Authors: Roy S. K. , Pant N. C. , Kundu A. , Dharwadkar A. , Kumar P. K. , Joshi Sonalika , Raghuram  , Sadiq Mohd. , Pandey Mayuri
Published: April 2017

The 600–660 Ma East African Orogen (EAO) granulites of the Mozambique Belt were correlated and extended into a coast marginal area of East Antarctica through the NNW–SSW-trending granulite-bearing Schirmacher Oasis. Tracing similarities in lithological association, granulite-facies metamorphism and geochronological data, the 640 Ma EAO was extended by another 110 km south of Schirmacher into the Humboldt Mountains in central Dronning Maud Land (cDML). Based on younger anorogenic magmatism east and west of the Humboldt Mountains, a 10–20 km-wide linear corridor of the EAO from the Schirmacher to the Humboldt Mountains was proposed.

There are eight nunataks between Schirmacher and the Humboldt Mountains projected above the ice sheet. These nunataks are strategically placed because they represent the small (4–10 km
2
), isolated rock exposures in approximately 5000 km
2
of ice-covered area. Baalsrudfjellet is one of these nunataks that is located at the easternmost margin of the proposed EAO corridor and represents a significant outcrop to validate the presence of the EAO between Schirmacher and the Humboldt Mountains. This study brings out a two-stage metamorphic evolution (
c.
660–680 Ma and
c.
580 Ma) with melt generation associated with the younger event. Geochronological constraints by monazite chemical dating from metapelites confirm and validate the continuation of the EAO in-between the Schirmacher Oasis and the Humboldt Mountains.

Supplementary material:
Monazite analyses, computed ages and age errors of three grains from the high- and low-melt metapelite are available at
https://doi.org/10.6084/m9.figshare.c.3738362
The Eastern Ghats Belt, India, in the context of supercontinent assembly
Authors: Dasgupta Somnath , Bose Sankar , Bhowmik Santanu Kumar , Sengupta Pulak
Published: April 2017

The Eastern Ghats Belt (India) bears testimony to the assembly and dispersal of both the Columbia and Rodinia supercontinents, and possibly the formation of East Gondwana. The belt itself is a collage of different lithotectonic and isotopic domains, and therefore the petrological evolution of each domain is to be considered separately prior to the formation of the belt. In this paper, we present an updated review on the petrological and tectonic evolution of the different domains along with geochronological constraints. We develop tectonic models to show how different lithotectonic domains fit into supercontinent cycles in the Proterozoic period.
System-Level Design Optimization for Security-Critical Cyber-Physical-Social Systems
Authors: Zeng Jing , Yang Laurence T. , Lin Man , Shao Zili , Zhu Dakai
Published: April 2017

Cyber-physical-social systems (CPSS), an emerging computing paradigm, have attracted intensive attentions from the research community and industry. We are facing various challenges in designing secure, reliable, and user-satisfied CPSS. In this article, we consider these design issues as a whole and propose a system-level design optimization framework for CPSS design where energy consumption, security-level, and user satisfaction requirements can be fulfilled while satisfying constraints for system reliability. Specifically, we model the constraints (energy efficiency, security, and reliability) as the penalty functions to be incorporated into the corresponding objective functions for the optimization problem. A smart office application is presented to demonstrate the feasibility and effectiveness of our proposed design optimization approach.
Extracting Maya Glyphs from Degraded Ancient Documents via Image Segmentation
Authors: Hu Rui , Odobez Jean-Marc , Gatica-Perez Daniel
Published: April 2017

We present a system for automatically extracting hieroglyph strokes from images of degraded ancient Maya codices. Our system adopts a region-based image segmentation framework. Multi-resolution super-pixels are first extracted to represent each image. A Support Vector Machine (SVM) classifier is used to label each super-pixel region with a probability to belong to foreground glyph strokes. Pixelwise probability maps from multiple super-pixel resolution scales are then aggregated to cope with various stroke widths and background noise. A fully connected Conditional Random Field model is then applied to improve the labeling consistency. Segmentation results show that our system preserves delicate local details of the historic Maya glyphs with various stroke widths and also reduces background noise. As an application, we conduct retrieval experiments using the extracted binary images. Experimental results show that our automatically extracted glyph strokes achieve comparable retrieval results to those obtained using glyphs manually segmented by epigraphers in our team.