bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Significance of A Waves in Acute Inflammatory Demyelinating Polyradiculoneuropathy
Authors: Lakshminarasimhan Sindhuja , Venkatraman Chandramouleeswaran , vellaichamy Kannan , Ranganathan Lakshminarasimhan 
Published: May 2018

Purpose:
A wave is a late response recognized during recording of F waves. Though they might be seen in healthy subjects, their presence assumes significance in a patient presenting with polyradiculoneuropathy.

Methods:
In this prospective study, 75 patients with acute inflammatory demyelinating polyradiculoneuropathy (AIDP) were enrolled. They were divided into two groups based on the presence or absence of A waves. Clinical features, electrophysiological parameters and extent of clinical recovery in short-term follow-up were analyzed.

Results:
A waves were present in 49 out of 75 patients (65%). Most common pattern observed was multiple A waves. Prevalence of A waves was more in lower limb nerves than upper limb nerves. Occurrence of A waves correlated with the presence of conduction block. Patients with A waves had higher Hughes grade (P = 0.003) and lower Medical Research Council sum score at 6 weeks of follow-up (P = 0.04) as compared to patients without A waves.

Conclusions:
A waves are common in acute inflammatory demyelinating polyradiculoneuropathy form of Guillain Barre syndrome and are considered as a marker of demyelination. Long-term follow-up studies are required to ascertain their significance in prognostication and assessing recovery.
A genetically-encoded fluorescent sensor enables rapid and specific detection of dopamine in flies, fish, and mice
Authors: Sun Fangmiao , Zeng Jianzhi , Jing Miao , Zhou Jingheng , Feng Jiesi , Owen Scott F. , Luo Yichen , Li Funing , Yamaguchi Takashi , Yong Zihao , Gao Yijing , Peng Wanling , Wang Lizhao , Zhang Siyu , Du Jiulin , Lin Dayu , Xu Min , Kreitzer Anatol C. , Cui Guohong , Li Yulong 
Published: May 2018

AbstractDopamine (DA) is a central monoamine neurotransmitter involved in many physiological and pathological processes. A longstanding yet largely unmet goal is to measure DA changes reliably and specifically with high spatiotemporal precision, particularly in animals executing complex behaviors. Here we report the development of novel genetically-encoded GPCR-Activation-Based-DA (GRABDA) sensors that enable these measurements. In response to extracellular DA rises, GRABDAsensors exhibit large fluorescence increases (ΔF/F0∼90%) with sub-second kinetics, nanomolar to sub-micromolar affinities, and excellent molecular specificity. Importantly, GRABDA sensors can resolve a single-electrical-stimulus evoked DA release in mouse brain slices, and detect endogenous DA release in the intact brains of flies, fish, and mice. In freely-behaving mice, GRABDA sensors readily report optogenetically-elicited nigrostriatal DA release and depict dynamic mesoaccumbens DA changes during Pavlovian conditioning or during sexual behaviors. Thus, GRABDAsensors enable spatiotemporal precise measurements of DA dynamics in a variety of model organisms while exhibiting complex behaviors.
Antimicrobial exposure in sexual networks drives divergent evolution in modern gonococci
Authors: Sánchez-Busó Leonor , Golparian Daniel , Corander Jukka , Grad Yonatan H. , Ohnishi Makoto , Flemming Rebecca , Parkhill Julian , Bentley Stephen D. , Unemo Magnus , Harris Simon R. 
Published: May 2018

AbstractThe sexually transmitted pathogenNeisseria gonorrhoeaeis regarded as being on the way to becoming an untreatable superbug. Despite its clinical importance, little is known about its emergence and evolution, and how this corresponds with the introduction of antimicrobials. We present a genome-based phylogeographic analysis of 419 gonococcal isolates from across the globe. Results indicate that modern gonococci originated in Europe or Africa as late as the 16thcentury and subsequently disseminated globally. We provide evidence that the modern gonococcal population has been shaped by antimicrobial treatment of sexually transmitted and other infections, leading to the emergence of two major lineages with different evolutionary strategies. The well-described multi-resistant lineage is associated with high rates of homologous recombination and infection in high-risk sexual networks where antimicrobial treatment is frequent. A second, multi-susceptible lineage associated with heterosexual networks, where asymptomatic infection is more common, was also identified, with potential implications for infection control.
Whole genome linkage disequilibrium and effective population size in a coho salmon (Oncorhynchus kisutch) breeding population
Authors: Barría Agustín , Christensen Kris A. , Yoshida Grazyella , Jedlicki Ana , Lhorente Jean P. , Davidson William S. , Yáñez José M. 
Published: May 2018

AbstractThe estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection and for inferring historical events influencing different populations. This work aimed to evaluate the extent and decay of linkage disequilibrium in a coho salmon breeding population using ddRAD genomic markers.Linkage disequilibrium was estimated between a total of 7,505 SNPs found in 62 individuals (33 dams and 29 sires) from the breeding population. The makers encompass all 30 coho salmon chromosomes and comprise 1,655.19 Mb of the genome. The average density of markers per chromosome ranged from 3.45 to 6.11 per 1 Mbp. The minor allele frequency averaged 0.20 (with a range from 0.08 to 0.50). The overall average linkage disequilibrium among SNPs pairs measured as r2was 0.054. The Average r2value decreased with increasing physical distance, with values ranging from 0.37 to 0.054 at distances lower than 1 kb and up to 10 Mb, respectively. An r2threshold of 0.1 was reached at distance of approximately 1.3 Mb. Chromosomes Okis05, Okis15 and Okis28 showed high levels of linkage disequilibrium (> 0.20 at distances lower than 1 Mb). Average r2values were lower than 0.1 for all chromosomes at distances greater than 4 Mb. Linkage disequilibrium values suggest that whole genome association and selection studies could be performed using about 75,000 SNPs in aquaculture populations (depending on the trait under investigation). From the identified SNPs, an effective population size of 100 was estimated for the population 10 generation ago, and 1,000, for 139 generations ago.Based on the extent of r2decay, we suggest that at least 75,000 SNPs would be necessary for an association mapping study. Over 100,000 SNPs would be necessary for a high power study, in the current coho salmon population.
Aedes anphevirus (AeAV): an insect-specific virus distributed worldwide inAedes aegyptimosquitoes that has complex interplays withWolbachiaand dengue virus infection in cells
Authors: Parry Rhys , Asgari Sassan 
Published: May 2018

AbstractInsect specific viruses (ISVs) of the yellow fever mosquitoAedes aegyptihave been demonstrated to modulate transmission of arboviruses such as dengue virus (DENV) and West Nile virus by the mosquito. The diversity and composition of the virome ofAe. aegypti, however, remains poorly understood. In this study, we characterised Aedes anphevirus (AeAV), a negative-sense RNA virus from the orderMononegavirales. AeAV identified fromAedescell lines were infectious to bothAe. aegyptiandAedes albopictuscells, but not to three mammalian cell lines. To understand the incidence and genetic diversity of AeAV, we assembled 17 coding-complete and two partial genomes of AeAV from available RNA-Seq data. AeAV appears to transmit vertically and be present in laboratory colonies, wild-caught mosquitoes and cell lines worldwide. Phylogenetic analysis of AeAV strains indicates that as theAe. aegyptimosquito has expanded into the Americas and Asia-Pacific, AeAV has evolved into monophyletic African, American and Asia-Pacific lineages. The endosymbiotic bacteriumWolbachia pipientisrestricts positive-sense RNA viruses inAe. aegypti. Re-analysis of a small RNA library ofAe. aegypticells co-infected with AeAV andWolbachiaproduces an abundant RNAi response consistent with persistent virus replication. We foundWolbachiaenhances replication of AeAV when compared to a tetracycline cleared cell line, and AeAV modestly reduces DENV replicationin vitro. The results from our study improve understanding of the diversity and evolution of the virome ofAe. aegyptiand adds to previous evidence that showsWolbachiadoes not restrict a range of negative strand RNA viruses.
Biological capacities clearly define a major subdivision in Domain Bacteria
Authors: Méheust Raphaël , Burstein David , Castelle Cindy J. , Banfield Jillian F. 
Published: May 2018

ResumePhylogenetic analyses separate candidate phyla radiation (CPR) bacteria from other bacteria, but the degree to which their proteomes are distinct remains unclear. Here, we leveraged a proteome database that includes sequences from thousands of uncultivated organisms to identify protein families and examine their organismal distributions. We focused on widely distributed protein families that co-occur in genomes, as they likely foundational for metabolism. Clustering of genomes using the protein family presence/absence patterns broadly recapitulates the phylogenetic structure of the tree, suggesting persistence of core sets of protein families after lineage divergence. CPR bacteria group together and away from all other bacteria and archaea, in part due to novel proteins, some of which may be involved in cell-cell interactions. The diversity of combinations of protein families in CPR may exceed that of all other bacteria. Overall, the results extend the phylogeny-based suggestion that the CPR represent a major subdivision within Bacteria.
Identification of a novel tetrameric structure for human apolipoprotein-D
Authors: Kielkopf Claudia S. , Low Jason K.K. , Mok Yee-Foong , Bhatia Surabhi , Palasovski Tony , Oakley Aaron J. , Whitten Andrew E. , Garner Brett , Brown Simon H.J. 
Published: May 2018

ABSTRACTApolipoprotein-D is a 25 kDa glycosylated member of the lipocalin family that folds into an eight-stranded β-barrel with a single adjacent α-helix. Apolipoprotein-D specifically binds a range of small hydrophobic ligands such as progesterone and arachidonic acid and has an antioxidant function that is in part due to the reduction of peroxidised lipids by methionine-93. Therefore, apolipoprotein-D plays multiple roles throughout the body and is protective in Alzheimer’s disease, where apolipoprotein-D overexpression reduces the amyloid-β burden in Alzheimer’s disease mouse models.Oligomerisation is a common feature of lipocalins that can influence ligand binding. The native structure of apolipoprotein-D, however, has not been conclusively defined. Apolipoprotein-D is generally described as a monomeric protein, although it dimerises when reducing peroxidised lipids.Here, we investigated the native structure of apolipoprotein-D derived from plasma, breast cyst fluid (BCF) and cerebrospinal fluid. In plasma and cerebrospinal fluid, apolipoprotein-D was present in high-molecular weight complexes, potentially in association with lipoproteins. In contrast, apolipoprotein-D in BCF formed distinct oligomeric species. We assessed apolipoprotein-D oligomerisation using native apolipoprotein-D purified from BCF and a suite of complementary methods, including multi-angle laser light scattering, analytical ultracentrifugation and small-angle X-ray scattering. Our analyses showed that apolipoprotein-D predominantly forms a ∽95 to ∽100 kDa tetramer. Small-angle X-ray scattering analysis confirmed these findings and provided a structural model for apolipoprotein-D tetramer. These data indicate apolipoprotein-D rarely exists as a free monomer under physiological conditions and provide insights into novel native structures of apolipoprotein-D and into oligomerisation behaviour in the lipocalin family.
Photosynthesis under very high oxygen concentrations in dense microbial mats and biofilms
Authors: de Beer Dirk , Meyer Volker , Klatt Judith , Li Tong 
Published: May 2018

AbstractUsing microsensors O2concentrations were measured in photosynthetically active microbial mats of up to 3 mM, corresponding to a partial pressure of 3 bar. This could damage mats by internal gas formation, and be inhibitory by formation of reactive oxygen species (ROS) and reduced effectivity of RuBisCo. The reliability of the electrochemical microsensors was checked by creating elevated O2concentrations in a water volume placed inside a pressure tank. A microsensor mounted with the tip in the gassed water bath showed a response linearly proportional to 5.5 mM corresponding to 4 bar pure O2pressure. After release of the pressure the O2concentration reduced quickly to 2.5 mM, then stabilized and subsequently reduced slowly over 14 hours to approximately 2 mM. We concluded that the very high O2concentrations measured in phototrophic microbial mats are real and O2oversaturation in mats is a stable phenomenon. As consequence of high O2concentrations, net production of H2O2occurred. The accumulation was, however, limited to the respiratory zone under the photosynthetic layer. Despite the high gas pressure inside mats, no disruption of the mat structure was apparent by bubble formation inside the mats,and bubbles were only observed at mat surfaces. Additions of H2O2to high concentrations in the water column were efficiently removed in the photosynthetically active zone. As the removal rate was linearly proportional to the H2O2influx, this removal occurred possibly not enzymatically but by abiotic processes. Phototrophic microorganisms can produce O2at high rates under strongly elevated O2levels, despite the decreased efficiency due to the unfavorable kinetics of RuBisCo and energy costs for protection. Under non-limiting light conditions, this apparent dilemma is, however, not disadvantageous.ImportanceBiofilms are often used in photobioreactors for production of biomass, food or specialty chemistry. Photosynthesis rates can be limited by high O2levels or high O2/CO2ratios which are especially enhanced in biofilms and mats, due to mass transfer limitations. High O2may lead to reactive O2species (ROS) and reduce the efficiency of RuBisCo. Moreover, gas formation may destabilize their structure. Here we show that extremely high levels of O2are possible in mats and biofilms without ebullition, and while maintaining very high photosynthetic activity.
Disrupting folate metabolism alters the capacity of bacteria in exponential growth to develop persisters to antibiotics
Authors: Morgan Jasmine , Smith Matthew , Mc Auley Mark T. , Salcedo-Sora J. Enrique 
Published: May 2018

AbstractBacteria can survive high doses of antibiotics through stochastic phenotypic diversification.We present initial evidence that folate metabolism could be involved with the formation of persisters. The aberrant expression of the folate enzyme genefauseems to reduce the incidence of persisters to antibiotics. Folate impaired bacteria had a lower generation rate for persisters to both antibiotics ampicillin and ofloxacin. Persister bacteria were detectable from the outset of the exponential growth phase in the complex media. Gene expression analyses showed tentatively distinctive profiles in exponential growth at times when bacteria persisters were observed. Levels of persisters were assessed in bacteria with altered, genetically and pharmacologically, folate metabolism. This work shows that by disrupting folate biosynthesis and usage, bacterial tolerance to antibiotics seems to be diminished. Based on these findings there is a possibility that bacteriostatic antibiotics such as antifolates could have a role to play in clinical settings where the incidence of antibiotic persisters seem to drive recalcitrant infections.
cytometree: a binary tree algorithm for automatic gating in cytometry analysis
Authors: Commenges Daniel , Alkhassim Chariff , Gottardo Raphael , Hejblum Boris , Thiébaut Rodolphe 
Published: May 2018

AbstractMotivationFlow cytometry is a powerful technology that allows the high-throughput quantification of dozens of surface and intracellular proteins at the single-cell level. It has become the most widely used technology for immunophenotyping of cells over the past three decades. Due to the increasing complexity of cytometry experiments (more cells and more markers), traditional manual flow cytometry data analysis has become untenable due to its subjectivity and time-consuming nature.ResultsWe present a new unsupervised algorithm called “cytometree” to perform automated population discovery (aka gating) in flow cytometry. cytometree is based on the construction of a binary tree, the nodes of which are subpopulations of cells. At each node, the marker distributions are modeled by mixtures of normal distribution. Node splitting is done according to a normalized difference of Akaike information criteria (AIC) between the two models. Post-processing of the tree structure and derived populations allows us to complete the annotation of the derived populations. The algorithm is shown to perform better than the state-of-the-art unsupervised algorithms previously proposed on panels introduced by the Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP I) project. The algorithm is also applied to a T-cell panel proposed by the Human Immunology Project Consortium (HIPC) program; it also outperforms the best unsupervised open-source available algorithm while requiring the shortest computation time.AvailabilityAn R package named “cytometree” is available on the CRAN repository.Contactdaniel.commenges@u-bordeaux.fr; rodolphe.thiebaut@u-bordeaux.frSupplementary informationSupplementary data are available.
Ammonium Pretreatment and Addition Improve Stability of Environmental Parameters and Biogas Production under Anaerobic Co-digestion of Rice Straw and Dairy Manure
Authors: Tang Yun , Zou Shuzhen , Kang Di 
Published: May 2018

AbstractThis paper optimized the anaerobic digestion (AD) pretreatment process, identified the relationship between stability of environmental factors and biogas production under ammonium hydroxide (NH3·H2O) pretreatment and analyzed the reason of NH3·H2O pretreatment to increase biogas production. Variable coefficients (CVs) of environmental factors were calculated to study the stability of environmental factors during AD process. The effect of initial AD environment factors on the stability of environmental factors during AD process was analyzed by redundancy analysis. Path analysis was used to analyze the response relationship the stability of environmental factors between and total biogas production (TBP). Results showed that pretreatment at 8% for 4 days, the TBP produced the highest value (302.5mL/g TS) and significantly higher than the other values (P < 0.01). NH3·H2O pretreatment had effect on the initial AD environment factors and the environment factors during AD process. Under the NH3·H2O pretreatment conditions, the stability of environment factors during AD process was affected by initial AD environment factors, while they had direct and indirect influences on the TBP. This research concluded that NH3·H2O pretreatment improved TBP via changing the initial environment of AD and the stability of environment factors during AD process, as well as the response relationship among initial AD environment factors and the stability of environment factors during AD process and biogas production, the changes improved the stability of environmental factors and made the environment more suitable for AD.
Novel RNA aptamers targeting gastrointestinal cancer biomarkers CEA, CA50 and CA72-4 with superior affinity and specificity
Authors: Pan Qing , Law Carmen OK , Yung Mingo MH , Han KC , Pon YL , Lau Terrence CK 
Published: May 2018

ABSTRACTGastric cancer is the third most common cause of death from cancer in the world and it remains difficult to cure in Western countries, primarily because most patients present with advanced disease. Currently, CEA, CA50 and CA72-4 are commonly used as tumor markers for gastric cancer by immunoassays. However, the drawback and conundrum of immunoassay are the unceasing problem in standardization of quality of antibodies and time/effort for the intensive production. Therefore, there is an urgent need for the development of a standardized assay to detect gastric cancer at the early stage.Aptamers are DNA or RNA oligonucleotides with structural domain which recognize ligands such as proteins with superior affinity and specificity when compared to antibodies. In this study, SELEX (Systematic Evolution of Ligands by Exponential enrichment) technique was adopted to screen a random 30mer RNA library for aptamers targeting CEA, CA50 and CA72-4 respectively. Combined with high-throughput sequencing, we identified 6 aptamers which are specifically target for these three biomarkers of gastrointestinal cancer. Intriguingly, the predicted secondary structures of RNA aptamers from each antigen showed significant structural similarity, suggesting the structural recognition between the aptamers and the antigens. Moreover, we determined the dissociation constants of all the aptamers to their corresponding antigens by fluorescence spectroscopy, which further demonstrating high affinities between the aptamers and the antigens. In addition, immunostaining of gastric adenocarcinoma cell line AGS using CEA Aptamer probe showed positive fluorescent signal which proves the potential of the aptamer as a detection tool for gastric cancer. Furthermore, substantially decreased cell viability and growth were observed when human colorectal cell line LS-174T was transfected with each individual aptamers. Taking together, these novel RNA aptamers targeting gastrointestinal cancer biomarker CEA, CA50 and CA72-4 will aid further development and standardization of clinical diagnostic method with better sensitivity and specificity, and potentially future therapeutics development of gastric cancer.
The length distribution and multiple specificity of naturally presented HLA-I ligands
Authors: Gfeller David , Guillaume Philippe , Michaux Justine , Pak Hui-Song , Daniel Roy T. , Racle Julien , Coukos George , Bassani-Sternberg Michal 
Published: May 2018

AbstractHLA-I molecules bind short peptides and present them for recognition by CD8+ T cells. The length of HLA-I ligands typically ranges from 8 to 12 amino acids, but variability is observed across different HLA-I alleles. Here we collected recent in-depth HLA peptidomics data, including 12 newly generated HLA peptidomes (31,896 unique peptides) from human meningioma samples, to analyze the peptide length distribution and multiple specificity across 84 different HLA-I alleles. We observed a clear clustering of HLA-I alleles with distinct peptide length distributions, which enabled us to study the structural basis of peptide length distributions and predict peptide length distributions from HLA-I sequences. We further identified multiple specificity in several HLA-I molecules and validated these observations with binding assays. Explicitly modeling peptide length distribution and multiple specificity improved predictions of naturally presented HLA-I ligands, as demonstrated in an independent benchmarking based on the new human meningioma samples.