Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
|---|
| malonic acid diazo esters for c,h - insertion crosslinking (chic) reactions: a versatile and powerful tool forthe generation of tailor made surfaces. | we report on a simple and versatile way for the modification of a broad spectrum of surfaces with thin polymer films through the thermally or photo-chemically induced generation of surface-attached polymer networks. the system is based on copoly-mers containingdiazomalonate groups which can be activated by heat or light. to this end, the co-polymers are deposited from solution onto organic or inorganic substrates. upon activation the diaz-omalonate decomposes and forms a carbene, which inducesc- ... | 2017 | 28846177 |
| a47 origin and possible genetic recombination of the middle east respiratory syndrome coronavirus from the first imported case in china: phylogenetics and coalescence analysis. | 2017 | 28845291 | |
| a25 phylogenetic analysis of the nucleocapsid and rna-dependent rna polymerase fragments of the first imported case of middle east respiratory syndrome coronavirus (mers-cov) infection in the philippines from saudi arabia, february 2015. | 2017 | 28845258 | |
| a46 mers-cov in arabian camels in africa and central asia. | 2017 | 28845242 | |
| mers coronavirus nsp1 participates in an efficient propagation through a specific interaction with viral rna. | mers-cov is the only lethal human cov still endemic in the arabian peninsula and neither vaccine nor therapeutics against mers-cov infection is available. the nsp1 of cov is thought to be a major virulence factor because it suppresses protein synthesis through the degradation of host mrna. in contrast, viral rna circumvents the nsp1-mediated translational shutoff for an efficient propagation. in this study, we identified amino acid residue in mers-cov nsp1 that differ from those of sars-cov nsp1 ... | 2017 | 28843094 |
| ensvmb: metagenomics fragments classification using ensemble svm and blast. | metagenomics brings in new discoveries and insights into the uncultured microbial world. one fundamental task in metagenomics analysis is to determine the taxonomy of raw sequence fragments. modern sequencing technologies produce relatively short fragments and greatly increase the number of fragments, and thus make the taxonomic classification considerably more difficult than before. therefore, fast and accurate techniques are called to classify large-scale fragments. we propose ensvm (ensemble ... | 2017 | 28842700 |
| performance evaluation of the powerchek mers (upe & orf1a) real-time pcr kit for the detection of middle east respiratory syndrome coronavirus rna. | molecular detection of middle east respiratory syndrome coronavirus (mers-cov) using real-time reverse transcription (rrt)-pcr assays is the method of choice for diagnosis of mers. we evaluated the performance of the powerchek mers (upe & orf1a) real-time pcr kit (powerchek mers assay; kogene biotech, korea) a one-step rrt-pcr assay for the qualitative detection of mers-cov. | 2017 | 28840986 |
| imported case of middle east respiratory syndrome coronavirus (mers-cov) infection from oman to thailand, june 2015. | thailand reported the first middle east respiratory syndrome (mers) case on 18 june 2015 (day 4) in an omani patient with heart condition who was diagnosed with pneumonia on hospital admission on 15 june 2015 (day 1). two false negative rt-pcr on upper respiratory tract samples on days 2 and 3 led to a 48-hour diagnosis delay and a decision to transfer the patient out of the negative pressure unit (npu). subsequent examination of sputum later on day 3 confirmed mers coronavirus (mers-cov) infect ... | 2017 | 28840828 |
| use of high b value diffusion-weighted magnetic resonance imaging in acute encephalopathy/encephalitis during childhood. | to determine the use of high b value diffusion-weighted imaging (dwi) in the diagnosis and assessment of acute febrile encephalopathy/encephalitis in childhood. | 2017 | 28838686 |
| mers-cov accessory orfs play key role for infection and pathogenesis. | while dispensable for viral replication, coronavirus (cov) accessory open reading frame (orf) proteins often play critical roles during infection and pathogenesis. utilizing a previously generated mutant, we demonstrate that the absence of all four middle east respiratory syndrome cov (mers-cov) accessory orfs (deletion of orf3, -4a, -4b, and -5 [dorf3-5]) has major implications for viral replication and pathogenesis. importantly, attenuation of the dorf3-5 mutant is primarily driven by dysregul ... | 2017 | 28830941 |
| middle east respiratory syndrome coronavirus: five years later. | in the past five years, there have been 1,936 laboratory-confirmed cases of middle east respiratory syndrome coronavirus (mers-cov) in 27 countries, with a mortality rate of 35.6%. most cases have arisen in the middle east, particularly the kingdom of saudi arabia, however there was a large hospital-associated outbreak in the republic of korea in 2015. exposure to dromedary camels has been recognized by the world health organization (who) as a risk factor in primary cases, but the exact mechanis ... | 2017 | 28826284 |
| serologic responses of 42 mers-coronavirus-infected patients according to the disease severity. | we evaluated serologic response of 42 middle east respiratory syndrome coronavirus (mers-cov)-infected patients according to 4 severity groups: asymptomatic infection (group 0), symptomatic infection without pneumonia (group 1), pneumonia without respiratory failure (group 2), and pneumonia progressing to respiratory failure (group 3). none of the group 0 patients showed seroconversion, while the seroconversion rate gradually increased with increasing disease severity (0.0%, 60.0%, 93.8%, and 10 ... | 2017 | 28821364 |
| conveyance contact investigation for imported middle east respiratory syndrome cases, united states, may 2014. | in 2014, the centers for disease control and prevention conducted conveyance contact investigations for 2 middle east respiratory syndrome cases imported into the united states, comprising all passengers and crew on 4 international and domestic flights and 1 bus. of 655 contacts, 78% were interviewed; 33% had serologic testing. no secondary cases were identified. | 2017 | 28820379 |
| a random forest classifier for detecting rare variants in ngs data from viral populations. | we propose a random forest classifier for detecting rare variants from sequencing errors in next generation sequencing (ngs) data from viral populations. the method utilizes counts of varying length of k-mers from the reads of a viral population to train a random forest classifier, called multires, that classifies k-mers as erroneous or rare variants. our algorithm is rooted in concepts from signal processing and uses a frame-based representation of k-mers. frames are sets of non-orthogonal basi ... | 2017 | 28819548 |
| enhanced inflammation in new zealand white rabbits when mers-cov reinfection occurs in the absence of neutralizing antibody. | the middle east respiratory syndrome coronavirus (mers-cov) is a zoonotic betacoronavirus that was first detected in humans in 2012 as a cause of severe acute respiratory disease. as of july 28, 2017, there have been 2,040 confirmed cases with 712 reported deaths. while many infections have been fatal, there have also been a large number of mild or asymptomatic cases discovered through monitoring and contact tracing. new zealand white rabbits are a possible model for asymptomatic infection with ... | 2017 | 28817732 |
| large-scale machine learning of media outlets for understanding public reactions to nation-wide viral infection outbreaks. | from may to july 2015, there was a nation-wide outbreak of middle east respiratory syndrome (mers) in korea. mers is caused by mers-cov, an enveloped, positive-sense, single-stranded rna virus belonging to the family coronaviridae. despite expert opinions that the danger of mers might be exaggerated, there was an overreaction by the public according to the korean mass media, which led to a noticeable reduction in social and economic activities during the outbreak. to explain this phenomenon, we ... | 2017 | 28813689 |
| immunogenicity and structures of a rationally designed prefusion mers-cov spike antigen. | middle east respiratory syndrome coronavirus (mers-cov) is a lineage c betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. as in other coronaviruses, the spike (s) glycoprotein of mers-cov mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. here we use structure-based design to develop a generalizable strategy for retaining coronavirus s proteins in th ... | 2017 | 28807998 |
| evaluation and clinical validation of two field-deployable reverse transcription-insulated isothermal pcr assays for the detection of the middle east respiratory syndrome coronavirus. | middle east respiratory syndrome (mers) is an emerging zoonotic viral respiratory disease that was first identified in saudi arabia in 2012. in 2015, the largest mers outbreak outside of the middle east region occurred in the republic of korea. the rapid nosocomial transmission of mers-coronavirus (mers-cov) in korean healthcare settings highlighted the importance and urgent need for a rapid and reliable on-site diagnostic assay to implement effective control and preventive measures. here, we de ... | 2017 | 28807812 |
| new episode of middle east respiratory syndrome coronavirus outbreak in saudi arabia: an emerging public health threat. | 2017 | 28802180 | |
| an efficient strategy using k-mers to analyse 16s rrna sequences. | the use of k-mers has been a successful strategy for improving metagenomics studies, including taxonomic classifications, or de novo assemblies, and can be used to obtain sequences of interest from the available databases. the aim of this manuscript was to propose a simple but efficient strategy to generate k-mers and to use them to obtain and analyse in silico 16s rrna sequence fragments. a total of 513,309 bacterial sequences contained in the silva database were considered for the study, and h ... | 2017 | 28795166 |
| the history and epidemiology of middle east respiratory syndrome corona virus. | corona viruses cause common cold, and infections caused by corona viruses are generally self-resolving. during the last 4 years, corona viruses have become the most important viruses worldwide because of the occurrence of several recent deaths caused by corona viruses in saudi arabia. spread of the infection occurred worldwide; however, most cases of mortality have occurred in the middle east. owing to the predominance of outbreaks in the middle eastern countries, the virus was renamed a middle ... | 2017 | 28794876 |
| recovery from the middle east respiratory syndrome is associated with antibody and t-cell responses. | the middle east respiratory syndrome coronavirus (mers-cov) causes a highly lethal pneumonia. mers was recently identified as a candidate for vaccine development, but most efforts focus on antibody responses, which are often transient after cov infections. cov-specific t cells are generally long-lived, but the virus-specific t cell response has not been addressed in mers patients. we obtained peripheral blood mononuclear cells and/or sera from 21 mers survivors. we detected mers-cov-specific cd4 ... | 2017 | 28778905 |
| suggestions on improvement of infectious disease law and regulations. | the study's perspective is through examining an enactment for the new amendment for legislation, to make proposals for a more rational and concrete basis in the interpretation and application of the korean legal regime in global infectious disease emergency situations. | 2017 | 28774161 |
| short (16-mer) locked nucleic acid splice-switching oligonucleotides restore dystrophin production in duchenne muscular dystrophy myotubes. | splice-switching antisense oligonucleotides (ssos) offer great potential for rna-targeting therapies, and two sso drugs have been recently approved for treating duchenne muscular dystrophy (dmd) and spinal muscular atrophy (sma). despite promising results, new developments are still needed for more efficient chemistries and delivery systems. locked nucleic acid (lna) is a chemically modified nucleic acid that presents several attractive properties, such as high melting temperature when bound to ... | 2017 | 28742140 |
| genetic characteristics of coronaviruses from korean bats in 2016. | bats have increasingly been recognized as the natural reservoir of severe acute respiratory syndrome (sars), coronavirus, and other coronaviruses found in mammals. however, little research has been conducted on bat coronaviruses in south korea. in this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in south korea. rt-pcr and sequencing were performed for specific coronavirus genes to identify the bat c ... | 2017 | 28725945 |
| predictors of mortality in middle east respiratory syndrome (mers). | we evaluated the clinical characteristics, cytokine/chemokine concentrations, viral shedding and antibody kinetics in 30 patients with middle east respiratory syndrome (mers), including 6 non-survivors admitted to 3 mers-designated hospitals. old age, low albumin, altered mentality and high pneumonia severity index score at admission were risk factors for mortality. in addition, severe signs of inflammation at initial presentation (at hospital days 1-4), such as high inducible protein-10 (p=0.00 ... | 2017 | 28724637 |
| the effects of sampling on the efficiency and accuracy of k-mer indexes: theoretical and empirical comparisons using the human genome. | one of the most common ways to search a sequence database for sequences that are similar to a query sequence is to use a k-mer index such as blast. a big problem with k-mer indexes is the space required to store the lists of all occurrences of all k-mers in the database. one method for reducing the space needed, and also query time, is sampling where only some k-mer occurrences are stored. most previous work uses hard sampling, in which enough k-mer occurrences are retained so that all similar s ... | 2017 | 28686614 |
| "it feels like i'm the dirtiest person in the world.": exploring the experiences of healthcare providers who survived mers-cov in saudi arabia. | in summer 2015, a saudi 1000-bed tertiary care hospital experienced a serious outbreak among patients of middle eastern respiratory syndrome (mers); during which, some healthcare providers contracted the virus, but none died. the outbreak provoked not only fear and stress; but also professional, emotional, ethical, and social conflicts and tension among healthcare providers and patients alike. therefore, this study aims to explore what healthcare providers, who survived coronavirus infection, ha ... | 2017 | 28676285 |
| host factors in coronavirus replication. | coronaviruses are pathogens with a serious impact on human and animal health. they mostly cause enteric or respiratory disease, which can be severe and life threatening, e.g., in the case of the zoonotic coronaviruses causing severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers) in humans. despite the economic and societal impact of such coronavirus infections, and the likelihood of future outbreaks of additional pathogenic coronaviruses, our options to prevent or ... | 2017 | 28643204 |
| targeting coronaviral replication and cellular jak2 mediated dominant nf-κb activation for comprehensive and ultimate inhibition of coronaviral activity. | tylophorine-based compounds exert broad spectral, potent inhibition of coronaviruses. nf-κb activation is a common pro-inflammatory response of host cells to viral infection. the aims of this study were to (i) find an effective combination treatment for coronaviral infections through targeting of the virus per se and cellular nf-κb activity; and (ii) to study the underling mechanisms. we found that tylophorine-based compounds target the tgev viral rna and effectively inhibit tgev replication. nf ... | 2017 | 28642467 |
| kmerpyramid: an interactive visualization tool for nucleobase and k -mer frequencies. | bioinformatics methods often incorporate the frequency distribution of nulecobases or k -mers in dna or rna sequences, for example as part of metagenomic or phylogenetic analysis. because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. we present the r-package 'kmerpyramid' that allows to display each sequence, based on its nucleobase or k -mer distribution projected to the space of principal components, as a point with ... | 2017 | 28633391 |
| size matters: chemical synthesis of a homogenous arabinogalactan 92-mer. | 31+30+31: ye and colleagues have synthesized a branched 92-mer of arabinogalactan-a major component of the cell wall of m. tuberculosis-by linking a linear oligogalactan 30-mer with two d-arabinofuranose 31-mers. their approach capitalizes on sequential, one-pot glycosylation reactions that result in a rapid increase in molecular complexity and efficient synthesis of a branched oligosaccharide. | 2017 | 28628733 |
| diffusion-driven self-assembly of rodlike particles: monte carlo simulation on a square lattice. | the diffusion-driven self-assembly of rodlike particles was studied by means of monte carlo simulation. the rods were represented as linear k-mers (i.e., particles occupying k adjacent sites). in the initial state, they were deposited onto a two-dimensional square lattice of size l×l up to the jamming concentration using a random sequential adsorption algorithm. the size of the lattice, l, was varied from 128 to 2048, and periodic boundary conditions were applied along both x and y axes, while t ... | 2017 | 28618463 |
| zoos and public health: a partnership on the one health frontier. | today, accredited zoos are not just places for entertainment, they are actively involved in research for conservation and health. during recent decades in which the challenges for biodiversity conservation and public health have escalated, zoos have made significant changes to address these difficulties. zoos increasingly have four key areas of focus: education, recreation, conservation, and research. these key areas are important in addressing an interrelated global conservation (i.e. habitat a ... | 2017 | 28616495 |
| h-bond self-assembly: folding versus duplex formation. | linear oligomers equipped with complementary h-bond donor (d) and acceptor (a) sites can interact via intermolecular h-bonds to form duplexes or fold via intramolecular h-bonds. these competing equilibria have been quantified using nmr titration and dilution experiments for seven systems featuring different recognition sites and backbones. for all seven architectures, duplex formation is observed for homo-sequence 2-mers (aa·dd) where there are no competing folding equilibria. the corresponding ... | 2017 | 28470070 |
| a cohort-study of patients suspected for mers-cov in a referral hospital in saudi arabia. | 2017 | 28606432 | |
| the camkii holoenzyme structure in activation-competent conformations. | the ca(2+)/calmodulin-dependent protein kinase ii (camkii) assembles into large 12-meric holoenzymes, which is thought to enable regulatory processes required for synaptic plasticity underlying learning, memory and cognition. here we used single particle electron microscopy (em) to determine a pseudoatomic model of the camkiiα holoenzyme in an extended and activation-competent conformation. the holoenzyme is organized by a rigid central hub complex, while positioning of the kinase domains is hig ... | 2017 | 28589927 |
| comparative genomic analysis mers cov isolated from humans and camels with special reference to virus encoded helicase. | middle east respiratory syndrome coronavirus (mers cov) is a new emerging viral disease characterized by high fatality rate. understanding mers cov genetic aspects and codon usage pattern is important to understand mers cov survival, adaptation, evolution, resistance to innate immunity, and help in finding the unique aspects of the virus for future drug discovery experiments. in this work, we provide comprehensive analysis of 238 mers cov full genomes comprised of human (hmers) and camel (cmers) ... | 2017 | 28769010 |
| effective therapy with infliximab for clinically mild encephalitis/encephalopathy with a reversible splenial lesion in an infant with kawasaki disease. | kawasaki disease (kd) is a systemic vasculitis in infants. in kd, encephalopathy is rarely (0.1%) associated, however, clinically mild encephalitis/encephalopathy with a reversible splenial lesion (mers) has previously been reported in some pediatric patients. here, we report on a 2-year-old girl who had kd complicated with mers. the patient experienced generalized clonic convulsion and prolonged consciousness disturbance with fever for 2 days. her head mri showed a high signal intensity lesion ... | 2017 | 28747606 |
| cosine: non-seeding method for mapping long noisy sequences. | third generation sequencing (tgs) are highly promising technologies but the long and noisy reads from tgs are difficult to align using existing algorithms. here, we present cosine, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors. cosine computes the context similarity of two stretches of nucleobases given the similarity over distributions of their short k-mers (k = 3-4) along the sequences. the results on simulated and real data show ... | 2017 | 28586438 |
| mild encephalopathy/encephalitis with a reversible splenial lesion (mers): a report of five neonatal cases. | mild encephalopathy/encephalitis with a reversible splenial (mers) lesion is a clinic-radiological entity. the clinical features of mers in neonates are still not systemically reported. this paper presents five cases of mers, and the up-to-date reviews of previously reported cases were collected and analyzed in the literature. here we describe five cases clinically diagnosed with mers. all of them were neonates and the average age was about 4 days. they were admitted for the common neurological ... | 2017 | 28585150 |
| gauging the performance of some density functionals including dispersion and nonlocal corrections for relative energies of water 20-mers. | currently, development of density functional theory approximations and their benchmarking for accurately modeling different types of molecular interactions become a very active field of research. in this report, performance of the dispersion (d3) and nonlocal (nl) corrected density functionals has been compared with generalized energy-based fragmentation approach at the complete basis set limit for predicting the relative energies of 10 low-energy isomers of water nanoclusters (h2o)20 as an illu ... | 2017 | 28570983 |
| middle east respiratory syndrome corona virus alert verification in mirpur, azad kashmir. | middle east respiratory-corona virus (mers-cov), sars like virus, identified in september 2012 in middle-east. february 2013, an elderly man, who visited pakistan and ksa, was confirmed as mrs-cov in uk. a team visited mirpur to assess current and past sari trends in major indoor facilities, to explore possible contact of the patient with known or suspected sari case during his stay in pakistan and enlist close contacts. | 2017 | 28712204 |
| phase ordering dynamics of reconstituting particles. | we consider the large-time dynamics of one-dimensional processes involving adsorption and desorption of extended hard-core particles (dimers, trimers, ..., k-mers), while interacting through their constituent monomers. desorption can occur whether or not these latter adsorbed together, which leads to reconstitution of k-mers and the appearance of sectors of motion with nonlocal conservation laws for k≥3. dynamic exponents of the sector including the empty chain are evaluated by finite-size scali ... | 2017 | 28709284 |
| estimating and modelling the transmissibility of middle east respiratory syndrome coronavirus during the 2015 outbreak in the republic of korea. | emerging respiratory infections represent a significant public health threat. because of their novelty, there are limited measures available to control their early spread. learning from past outbreaks is important for future preparation. the middle eastern respiratory syndrome coronavirus (mers-cov ) 2015 outbreak in the republic of korea (rok) provides one such opportunity. | 2017 | 28703921 |
| 6s rna in rhodobacter sphaeroides: 6s rna and prna transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype. | the function of 6s rna, a global regulator of transcription, was studied in the photosynthetic α-proteobacterium rhodobacter sphaeroides. the cellular levels of r. sphaeroides 6s rna peak toward the transition to stationary phase and strongly decrease during extended stationary phase. the synthesis of so-called product rna transcripts (mainly 12-16-mers) on 6s rna as template by rna polymerase was found to be highest in late exponential phase. product rna ≥ 13-mers are expected to trigger the di ... | 2017 | 28692405 |
| fastgt: an alignment-free method for calling common snvs directly from raw sequencing reads. | we have developed a computational method that counts the frequencies of unique k-mers in fastq-formatted genome data and uses this information to infer the genotypes of known variants. fastgt can detect the variants in a 30x genome in less than 1 hour using ordinary low-cost server hardware. the overall concordance with the genotypes of two illumina "platinum" genomes is 99.96%, and the concordance with the genotypes of the illumina humanomniexpress is 99.82%. our method provides k-mer database ... | 2017 | 28566690 |
| mers-cov papain-like protease (pl(pro)): expression, purification, and spectroscopic/thermodynamic characterization. | within a decade, mers-cov emerged with nearly four times higher case fatality rate than an earlier outbreak of sars-cov and spread out in 27 countries in short span of time. as an emerging virus, combating it requires an in-depth understanding of its molecular machinery. therefore, conformational characterization studies of coronavirus proteins are necessary to advance our knowledge of the matter for the development of antiviral therapies. in this study, mers-cov papain-like protease (pl(pro)) w ... | 2017 | 28560640 |
| an improved filtering algorithm for big read datasets and its application to single-cell assembly. | for single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample dna get covered by the reads produced. this leads to huge datasets with lots of redundant data. a filtering of this data prior to assembly is advisable. brown et al. (2012) presented the algorithm diginorm for this purpose, which filters reads based on the abundance of their k-mers. | 2017 | 28673253 |
| alignment-free inference of hierarchical and reticulate phylogenomic relationships. | we are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. moreover, genomes of microbes, viruses and plasmids evolve not only by tree-l ... | 2017 | 28673025 |
| optimisation of peptides that actively cross the tympanic membrane by random amino acid extension: a phage display study. | local treatment of middle ear (me) disease currently requires surgical penetration of the tympanic membrane (tm). we previously discovered 12-mer peptides that are actively transported across the intact tm, a process that could be used for non-invasive drug delivery into the me. to optimise transport and provide further understanding of the peptides transport mechanism, we extended two of the candidate peptides by six additional amino acids at random, and screened the resulting 18-mers libraries ... | 2017 | 28658990 |
| a novel neutralizing monoclonal antibody targeting the n-terminal domain of the mers-cov spike protein. | this corrects the article doi: 10.1038/emi.2017.18. | 2017 | 28655936 |
| rnacompete-s: combined rna sequence/structure preferences for rna binding proteins derived from a single-step in vitro selection. | rna-binding proteins recognize rna sequences and structures, but there is currently no systematic and accurate method to derive large (>12base) motifs de novo that reflect a combination of intrinsic preference to both sequence and structure. to address this absence, we introduce rnacompete-s, which couples a single-step competitive binding reaction with an excess of random rna 40-mers to a custom computational pipeline for interrogation of the bound rna sequences and derivation of ssms (sequence ... | 2017 | 28651966 |
| a comparison study for dna motif modeling on protein binding microarray. | transcription factor binding sites (tfbss) are relatively short (5-15 bp) and degenerate. identifying them is a computationally challenging task. in particular, protein binding microarray (pbm) is a high-throughput platform that can measure the dna binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical pbm experiment can measure binding signal intensities of a protein to all possible dna k-mers (k = 8∼10). since proteins can often bind to dna with differe ... | 2017 | 27045826 |
| accurate self-correction of errors in long reads using de bruijn graphs. | new long read sequencing technologies, like pacbio smrt and oxford nanopore, can produce sequencing reads up to 50 000 bp long but with an error rate of at least 15%. reducing the error rate is necessary for subsequent utilization of the reads in, e.g. de novo genome assembly. the error correction problem has been tackled either by aligning the long reads against each other or by a hybrid approach that uses the more accurate short reads produced by second generation sequencing technologies to co ... | 2017 | 27273673 |
| spike gene deletion quasispecies in serum of patient with acute mers-cov infection. | the spike glycoprotein of the middle east respiratory coronavirus (mers-cov) facilitates receptor binding and cell entry. during investigation of a multi-facility outbreak of mers-cov in taif, saudi arabia, we identified a mixed population of wild-type and variant sequences with a large 530 nucleotide deletion in the spike gene from the serum of one patient. the out of frame deletion predicted loss of most of the s2 subunit of the spike protein leaving the s1 subunit with an intact receptor bind ... | 2017 | 27486688 |
| stringmlst: a fast k-mer based tool for multilocus sequence typing. | rapid and accurate identification of the sequence type (st) of bacterial pathogens is critical for epidemiological surveillance and outbreak control. cheaper and faster next-generation sequencing (ngs) technologies have taken preference over the traditional method of amplicon sequencing for multilocus sequence typing (mlst). but data generated by ngs platforms necessitate quality control, genome assembly and sequence similarity searching before an isolate's st can be determined. these are comput ... | 2017 | 27605103 |
| the search for therapeutic options for middle east respiratory syndrome (mers). | 2017 | 27050470 | |
| mers-cov diagnosis: an update. | diagnosis of mers-cov still a major concern in most of daignostic laboratories. to date the real-time polymerase chain reaction (rt-pcr) is the mainstay for diagnosis of mers-cov. rt-pcr has limitations, including a long turnaround time and lack of common measurements and correlations with viral load (vl). it is recommended to screen for mers-cov using rt-pcr of the upstream of envelope gene (upe) followed by confirmation of the presence of one of the following genes; open reading frame 1a, 1b g ... | 2017 | 27106390 |
| iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly. | next-generation sequencers such as illumina can now produce reads up to 300 bp with high throughput, which is attractive for genome assembly. a first step in genome assembly is to computationally correct sequencing errors. however, correcting all errors in these longer reads is challenging. here, we show that reads with remaining errors after correction often overlap repeats, where short erroneous k-mers occur in other copies of the repeat. we developed an iterative error correction pipeline tha ... | 2017 | 26868358 |
| mers cov: a trigger for healthcare transformation. | 2017 | 26719167 | |
| mild encephalitis/encephalopathy with reversible splenial lesion (mers) in adults-a case report and literature review. | mild encephalitis/encephalopathy with reversible splenial lesion (mers) is a rare clinico-radiological entity characterized by the magnetic resonance imaging (mri) finding of a reversible lesion in the corpus callosum, sometimes involved the symmetrical white matters. many cases of child-onset mers with various causes have been reported. however, adult-onset mers is relatively rare. the clinical characteristics and pathophysiologiccal mechanisms of adult-onset mers are not well understood. we re ... | 2017 | 28545419 |
| correction: serological evidence of mers-cov antibodies in dromedary camels (camelus dromedaries) in laikipia county, kenya. | [this corrects the article doi: 10.1371/journal.pone.0140125.]. | 2017 | 28542448 |
| hospital outbreaks of middle east respiratory syndrome, daejeon, south korea, 2015. | from may through july 2015, a total of 26 cases of middle east respiratory syndrome were reported from 2 hospitals in daejeon, south korea, including 1 index case and 25 new cases. we examined the epidemiologic features of these cases and found an estimated median incubation period of 6.1 days (8.8 days in hospital a and 4.6 days in hospital b). the overall attack rate was 3.7% (4.7% in hospital a and 3.0% in hospital b), and the attack rates among inpatients and caregivers in the same ward were ... | 2017 | 28516865 |
| chimerscope: a novel alignment-free algorithm for fusion transcript prediction using paired-end rna-seq data. | the rna-seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. the 'fusion' or 'chimeric' transcripts have improved the diagnosis and prognosis of several tumors, and have led to the development of novel therapeutic regimen. the fusion transcript detection is currently accomplished by several software packages, primarily relying on sequence alignment ... | 2017 | 28472320 |
| kmc 3: counting and manipulating k -mer statistics. | counting all k -mers in a given dataset is a standard procedure in many bioinformatics applications. we introduce kmc3, a significant improvement of the former kmc2 algorithm together with kmc tools for manipulating k -mer databases. usefulness of the tools is shown on a few real problems. | 2017 | 28472236 |
| pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology. | human coronaviruses (hcovs) can be divided into low pathogenic and highly pathogenic coronaviruses. the low pathogenic covs infect the upper respiratory tract and cause mild, cold-like respiratory illness. in contrast, highly pathogenic hcovs such as severe acute respiratory syndrome cov (sars-cov) and middle east respiratory syndrome cov (mers-cov) predominantly infect lower airways and cause fatal pneumonia. severe pneumonia caused by pathogenic hcovs is often associated with rapid virus repli ... | 2017 | 28466096 |
| ntcard: a streaming algorithm for cardinality estimation in genomics data. | many bioinformatics algorithms are designed for the analysis of sequences of some uniform length, conventionally referred to as k -mers. these include de bruijn graph assembly methods and sequence alignment tools. an efficient algorithm to enumerate the number of unique k -mers, or even better, to build a histogram of k -mer frequencies would be desirable for these tools and their downstream analysis pipelines. among other applications, estimated frequencies can be used to predict genome sizes, ... | 2017 | 28453674 |
| estimation of maintenance energy requirements in german shepherd and labrador retriever dogs in bangalore, india. | maintenance energy requirements (mers) were calculated for 17 german shepherd and 20 labrador retriever adult dogs using an in-home prospective dietary trial. the dogs were fed the same dry pet food and body weight, food intake, body condition score and physical activity were monitored for 10 weeks. labrador retrievers were significantly heavier and had higher body condition scores than german shepherd dogs, but there was no difference between males and females within each group. body weights re ... | 2017 | 28447394 |
| size-variable zone in v3 region of 16s rrna. | the size distribution of complete 16s-rrna sequences from the silva-database and nucleotide shifts that might interfere with the secondary structure of the molecules were evaluated. overall, 513,309 sequences recorded in silva were used to estimate the size of hypervariable regions of the gene. redundant sequences were treated as a single sequence to achieve a better representation of the molecular diversity. nucleotides found in each position in 95% of the sequences were considered the consensu ... | 2017 | 28440695 |
| solution behaviour of poly(n-isopropylacrylamide) stereoisomers in water: a molecular dynamics simulation study. | the water affinity of poly(n-isopropylacrylamide), pnipam, is tuned by tacticity, since the hydrophobicity rises with the increase of the degree of isotacticity. on the basis of this experimental evidence, atomistic molecular dynamics simulations of pairs of pnipam stereoisomers in 1.6% w/w polymer aqueous solution, a condition intermediate between the dilute and semidilute regimes, were carried out to comparatively investigate the solution behaviour and hydration of atactic and isotactic-rich p ... | 2017 | 28436518 |
| structure of the s1 subunit c-terminal domain from bat-derived coronavirus hku5 spike protein. | accumulating evidence indicates that mers-cov originated from bat coronaviruses (batcovs). previously, we demonstrated that both mers-cov and batcov hku4 use cd26 as a receptor, but how the batcovs evolved to bind cd26 is an intriguing question. here, we solved the crystal structure of the s1 subunit c-terminal domain of hku5 (hku5-ctd), another batcov that is phylogenetically related to mers-cov but cannot bind to cd26. we observed that the conserved core subdomain and those of other betacorona ... | 2017 | 28432925 |
| the dnak chaperone uses different mechanisms to promote and inhibit replication of vibrio cholerae chromosome 2. | replication of vibrio cholerae chromosome 2 (chr2) depends on molecular chaperone dnak to facilitate binding of the initiator (rctb) to the replication origin. the binding occurs at two kinds of site, 12-mers and 39-mers, which promote and inhibit replication, respectively. here we show that dnak employs different mechanisms to enhance the two kinds of binding. we found that mutations in rctb that reduce dnak binding also reduce 12-mer binding and initiation. the initiation defect is suppressed ... | 2017 | 28420739 |
| zseq: an approach for preprocessing next-generation sequencing data. | next-generation sequencing technology generates a huge number of reads (short sequences), which contain a vast amount of genomic data. the sequencing process, however, comes with artifacts. preprocessing of sequences is mandatory for further downstream analysis. we present zseq, a linear method that identifies the most informative genomic sequences and reduces the number of biased sequences, sequence duplications, and ambiguous nucleotides. zseq finds the complexity of the sequences by counting ... | 2017 | 28414515 |
| accurate relative energies and binding energies of large ice-liquid water clusters and periodic structures. | relative energies and binding energies are crucial quantities that determine various molecular properties of ice and water. we developed a new effective method to compute those energies of bulk ice-liquid water systems. in this work, ten ice-liquid 144-mers and ten periodic ice-liquid (h2o)64 systems are taken from the molecular dynamics simulations in the melting process of ice-ih crystals. they are investigated at the levels of density functional theory (dft), explicitly correlated second-orde ... | 2017 | 28414444 |
| basic scholarship in biosafety is critically needed to reduce risk of laboratory accidents. | our firm conducted a risk/benefit assessment of "gain-of-function" research, as part of the deliberative process following a u.s. moratorium on the research (u.s. department of health and human services, u.s. government gain-of-function deliberative process and research funding pause on selected gain-of-function research involving influenza, mers, and sars viruses, 2014). due to significant missing but theoretically acquirable data, our biosafety assessment faced limitations, and we were forced ... | 2017 | 28405626 |
| tarean: a computational tool for identification and characterization of satellite dna from unassembled short reads. | satellite dna is one of the major classes of repetitive dna, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. this type of genomic organization makes satellite dna difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. here, we present tandem repeat analyzer (tarean), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from un ... | 2017 | 28402514 |
| in situ structural studies of tripeptidyl peptidase ii (tppii) reveal spatial association with proteasomes. | tripeptidyl peptidase ii (tppii) is a eukaryotic protease acting downstream of the 26s proteasome; it removes tripeptides from the degradation products released by the proteasome. structural studies in vitro have revealed the basic architecture of tppii, a two-stranded linear polymer that assembles to form a spindle-shaped complex of ∼6 mda. dependent on protein concentration, tppii has a distinct tendency for polymorphism. therefore, its structure in vivo has remained unclear. to resolve this i ... | 2017 | 28396430 |
| cryo-em structures of mers-cov and sars-cov spike glycoproteins reveal the dynamic receptor binding domains. | the envelope spike (s) proteins of mers-cov and sars-cov determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. here, we present high-resolution structures of the trimeric mers-cov and sars-cov s proteins in its pre-fusion conformation by single particle cryo-electron microscopy. the overall structures resemble that from other coronaviruses including hku1, mhv and nl63 reported recently, with the except ... | 2017 | 28393837 |
| middle east respiratory syndrome risk perception among students at a university in south korea, 2015. | the 2015 middle east respiratory syndrome (mers) outbreak in south korea was a serious threat to public health, and was exacerbated by the inappropriate responses of major institutions and the public. this study examined the sources of confusion during the mers outbreak and identified the factors that can affect people's behavior. | 2017 | 28385465 |
| untargeted metabolite analysis-based uhplc-q-tof-ms reveals significant enrichment of p-hydroxybenzyl dimers of citric acids in fresh beige-scape gastrodia elata (wutianma). | in order to comprehensively elucidate the chemical biosynthesis process of the beige-scape gastrodia elata blume (wutianma) as a traditional herbal medicines, the untargeted analysis-based uhplc-pda-esi-q-tof-ms reveals the metabolites ranging from the skeletons to novel dimers of citric acids in fresh and dried immature/mature stem tubers. interestingly, two novel types of dimers for citric acids with the anhydride groups at sn-1 and/or sn-5 were discovered in fresh samples. moreover, the class ... | 2017 | 28380386 |
| gerbil: a fast and memory-efficient k-mer counter with gpu-support. | a basic task in bioinformatics is the counting of k-mers in genome sequences. existing k-mer counting tools are most often optimized for small k < 32 and suffer from excessive memory resource consumption or degrading performance for large k. however, given the technology trend towards long reads of next-generation sequencers, support for large k becomes increasingly important. | 2017 | 28373894 |
| positional bias in variant calls against draft reference assemblies. | whole genome resequencing projects may implement variant calling using draft reference genomes assembled de novo from short-read libraries. despite lower quality of such assemblies, they allowed researchers to extend a wide range of population genetic and genome-wide association analyses to non-model species. as the variant calling pipelines are complex and involve many software packages, it is important to understand inherent biases and limitations at each step of the analysis. | 2017 | 28351369 |
| string kernels for protein sequence comparisons: improved fold recognition. | the amino acid sequence of a protein is the blueprint from which its structure and ultimately function can be derived. therefore, sequence comparison methods remain essential for the determination of similarity between proteins. traditional approaches for comparing two protein sequences begin with strings of letters (amino acids) that represent the sequences, before generating textual alignments between these strings and providing scores for each alignment. when the similitude between the two pr ... | 2017 | 28245816 |
| middle east respiratory syndrome corona virus spike glycoprotein suppresses macrophage responses via dpp4-mediated induction of irak-m and pparγ. | middle east respiratory syndrome corona virus (mers-cov) is transmitted via the respiratory tract and causes severe acute respiratory distress syndrome by infecting lung epithelial cells and macrophages. macrophages can readily recognize the virus and eliminate it. mers-cov infects cells via its spike (s) glycoprotein that binds on dipeptidyl-peptidase 4 (dpp4) receptor present on macrophages. whether this spike/dpp4 association affects macrophage responses remains unknown. herein we demonstrate ... | 2017 | 28118607 |
| overview of the csiro australian animal health laboratory. | emerging infectious diseases arising from livestock and wildlife pose serious threats to global human health, as shown by a series of continuous outbreaks involving highly pathogenic influenza, sars, ebola and mers. the risk of pandemics and bioterrorism threats is ever present and growing, but our ability to combat them is limited by the lack of available vaccines, therapeutics and rapid diagnostics. the use of high bio-containment facilities, such as the csiro australian animal health laborato ... | 2017 | 27118215 |
| efficient conversion of n(6)-threonylcarbamoyladenosine (t(6)a) into a trna native hydantoin cyclic form (ct(6)a) performed at nucleoside and oligoribonucleotide levels. | a t(6)a nucleoside was efficiently and stereospecifically transformed into a hydantoin cyclic form of n(6)-l-threonylcarbamoyladenosine (ct(6)a) by the use of polymer bounded carbodiimide (edc-p) and hobt. the procedure was successfully applied for a post-synthetic conversion of t(6)a-containing rna 17-mers (of the sequences of anticodon stem and loop (asl) fragments of s. pombe trna(i) and e. coli trna(lys)) into the products bearing the ct(6)a unit. | 2017 | 28657616 |
| strainseeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees. | fast, accurate and high-throughput identification of bacterial isolates is in great demand. the present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. | 2017 | 28533988 |
| tuning in and catching on? examining the relationship between pandemic communication and awareness and knowledge of mers in the usa. | large-scale influenza outbreaks over the last decade, such as sars and h1n1, have brought to global attention the importance of emergency risk communication and prompted the international community to develop communication responses. since pandemic outbreaks are relatively infrequent, there is a dearth of evidence addressing the following questions: (i) have the resources invested in strategic and routine communication for past pandemic outbreaks yielded public health preparedness benefits? (ii) ... | 2017 | 27084759 |
| a molecular breadboard: removal and replacement of subunits in an hepatitis b virus capsid. | hepatitis b virus (hbv) core protein is a model system for studying assembly and disassembly of icosahedral structures. controlling disassembly will allow re-engineering the 120 subunit hbv capsid, making it a molecular breadboard. we examined removal of subunits from partially crosslinked capsids to form stable incomplete particles. to characterize incomplete capsids, we used two single molecule techniques, resistive-pulse sensing and charge detection mass spectrometry. we expected to find a bi ... | 2017 | 28795465 |
| sequence homology between hla-bound cytomegalovirus and human peptides: a potential trigger for alloreactivity. | human cytomegalovirus (hcmv) reactivation may often coincide with the development of graft-versus-host-disease (gvhd) in stem cell transplantation (sct). seventy seven sct donor-recipient pairs (drp) (hla matched unrelated donor (mud), n = 50; matched related donor (mrd), n = 27) underwent whole exome sequencing to identify single nucleotide polymorphisms (snps) generating alloreactive peptide libraries for each drp (9-mer peptide-hla complexes); human cmv cross (cross-reactive open source seque ... | 2017 | 28800601 |
| encephalitis with reversible splenial and deep cerebral white matter lesions associated with epstein-barr virus infection in adults. | approximately 200 cases of mild encephalitis with reversible splenial (mers) and deep cerebral white matter lesions have been reported since mers was first defined in 2004. mers occurs more frequently in children; in adults, only ~60 cases have been reported. until now, only four cases of mers in adults have been associated with epstein-barr virus (ebv). | 2017 | 28831257 |
| serological profiling of the ebv immune response in chronic fatigue syndrome using a peptide microarray. | epstein-barr-virus (ebv) plays an important role as trigger or cofactor for various autoimmune diseases. in a subset of patients with chronic fatigue syndrome (cfs) disease starts with infectious mononucleosis as late primary ebv-infection, whereby altered levels of ebv-specific antibodies can be observed in another subset of patients. | 2017 | 28604802 |
| spontaneous intracranial hemorrhage in a patient with middle east respiratory syndrome corona virus. | the middle east respiratory syndrome corona virus (mers-cov) is a novel positive sense singlestranded ribonucleic acid virus of the genus beta corona virus. this virus was first isolated from a patient who died from severe respiratory illness in june 2012 in jeddah, kingdom of saudi arabia. we describe an unusual case of a 42 year old healthcare worker who was admitted to our intensive care unit (icu)king abdul-aziz medical city, with mers-cov and severe acute respiratory distress syndrome and d ... | 2017 | 28133694 |
| proanthocyanidins purified from fruit pericarp of clausena lansium (lour.) skeels as efficient tyrosinase inhibitors: structure evaluation, inhibitory activity and molecular mechanism. | fruit pericarp of clausena lansium (lour.) skeels, a food waste, was selected as a raw material for proanthocyanidins. the proanthocyanidins' structures were integrally analyzed using three methods: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tof ms), high performance liquid chromatography electrospray ionization mass spectrometry (hplc-esi-ms) and (13)c nuclear magnetic resonance (nmr). the results elucidated that these compounds were composed of prodelph ... | 2017 | 28128839 |
| atheroprotective vaccination with mhc-ii-restricted apob peptides induces peritoneal il-10-producing cd4 t cells. | although immunization with major histocompatibility complex (mhc) class ii-restricted apolipoprotein b (apob) peptides has been shown to be atheroprotective, the mechanism is unclear. here, we investigated cd4(+) t cell populations in immunized atherosclerotic mice. peptides (16-mers) from mouse apob, the core protein of low-density lipoprotein (ldl), were screened for binding to i-a(b) by computer prediction and confirmed by radiolabeled peptide competition. three new peptides, p101 (fgkqgffpds ... | 2017 | 28087520 |
| the first case of recurrent ultra late onset group b streptococcal sepsis in a 3-year-old child. | group b streptococcus (gbs) is a commonly recognized cause of sepsis and meningitis in neonatal and young infants. invasive gbs infection is classified into early onset gbs disease (eod, day 0-6), late onset gbs disease (lod, day 7-89) and ultra late onset gbs disease (ulod, after 3 months of age). ulod is uncommon and recurrence is especially rare. we present the first recurrent case of ulod gbs sepsis in 3-year-old girl with a past medical history of hydrops fetalis and thoracic congenital lym ... | 2017 | 27920985 |
| simultaneous detection of severe acute respiratory syndrome, middle east respiratory syndrome, and related bat coronaviruses by real-time reverse transcription pcr. | since severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers) coronaviruses (covs) share similar characteristics with respect to clinical signs, etiology, and transmission, methods for a rapid and accurate differential diagnosis are important. therefore, the aim of this study was to develop a duplex real-time reverse transcription (rt)-pcr method for the simultaneous detection of these viruses. primers and probes that target the conserved spike s2 region of human sar ... | 2017 | 28220326 |
| the comparison of hydrochloric acid and phosphoric acid treatments in the preparation of montmorillonite catalysts for rna synthesis. | the treatment of clay minerals with a preliminary acid wash and titration to ph 7 has proven to generate catalysts for the most interesting of oligomerization reactions in which activated rna-nucleotides generate oligomers up to 40-mers. significantly, not all clay minerals become catalytic following this treatment and none are catalytic in the absence of such treatment. the washing procedure has been modified and explored further using phosphoric acid and the outcomes are compared to those obta ... | 2017 | 28210992 |
| adsorption of dna binding proteins to functionalized carbon nanotube surfaces with and without dna wrapping. | we examined the adsorption of dna binding proteins on functionalized, single-walled carbon nanotubes (swnts). when swnts were functionalized with polyethylene glycol (peg-swnt), moderate adsorption of protein molecules was observed. in contrast, nanotubes functionalized with conh2 groups (conh2-swnt) exhibited very strong interactions between the conh2-swnt and dna binding proteins. instead, when these swnt surfaces were wrapped with dna molecules (thymine 30-mers), protein binding was a little ... | 2017 | 28204854 |