bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ocular Motor Manifestations of Multiple Sclerosis
Authors: Nerrant Elodie , Tilikete Caroline 
Published: April 2017

Background:
Multiple sclerosis (MS) is a demyelinating disease of the central nervous system leading to disability, especially in young patients. Acute or chronic lesions of MS within the brainstem and the cerebellum frequently result in ocular motor disorders.

Evidence Acquisition:
This review encompasses the spectrum of ocular motor disorders in patients with MS emphasizing prevalence, examination findings, diagnostic features, functional consequences, classification of MS course, and management of these disturbances of ocular motility.

Results:
Ocular motor manifestations of MS can occur acutely in relapse or chronically, the latter as a consequence of previous relapses or as a chronic course of the disease. The most frequent and specific acute ocular motor manifestation is uni- or bilateral internuclear ophthalmoplegia (INO). The most frequent chronic manifestations include INO and cerebellar ocular motor disorders such as gaze-evoked nystagmus, saccadic hypermetria, and lack of vestibulo-ocular reflex inhibition. The most disabling syndrome is pendular nystagmus.

Conclusions:
The high prevalence of ocular motor manifestations emphasizes the importance of neuro-ophthalmological examination among patients with MS. Because chronic manifestations may cause minimal or no symptoms, a systematic investigation of the most common manifestations should be performed in daily practice. Appropriate treatment may improve visual outcome in some of these ocular motor disorders.
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

ABSTRACTBackgroundAdiponectin, 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.ObjectivesOur 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.MethodsWe 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.ResultsIn 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.ConclusionOur 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

AbstractThe 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

AbstractMotility 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.SignificanceMotility 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

AbstractMany 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

SummaryThe 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

ABSTRACTWith 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

AbstractRecently, 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.
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

ABSTRACTDespite 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.
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

AbstractClimate 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

AbstractPrimary 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.
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

ABSTRACT
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT
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

ABSTRACT

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

ABSTRACT

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.