bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternatives to vitamin B1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages
Authors: McRose Darcy , Guo Jian , Monier Adam , Sudek Sebastian , Wilken Susanne , Yan Shuangchun , Mock Thomas , Archibald John M , Begley Tadhg P , Reyes-Prieto Adrian , Worden Alexandra Z 
Published: August 2014

Abstract
Vitamin B1 (thiamine pyrophosphate, TPP) is essential to all life but scarce in ocean surface waters. In many bacteria and a few eukaryotic groups thiamine biosynthesis genes are controlled by metabolite-sensing mRNA-based gene regulators known as riboswitches. Using available genome sequences and transcriptomes generated from ecologically important marine phytoplankton, we identified 31 new eukaryotic riboswitches. These were found in alveolate, cryptophyte, haptophyte and rhizarian phytoplankton as well as taxa from two lineages previously known to have riboswitches (green algae and stramenopiles). The predicted secondary structures bear hallmarks of TPP-sensing riboswitches. Surprisingly, most of the identified riboswitches are affiliated with genes of unknown function, rather than characterized thiamine biosynthesis genes. Using qPCR and growth experiments involving two prasinophyte algae, we show that expression of these genes increases significantly under vitamin B1-deplete conditions relative to controls. Pathway analyses show that several algae harboring the uncharacterized genes lack one or more enzymes in the known TPP biosynthesis pathway. We demonstrate that one such alga, the major primary producer Emiliania huxleyi, grows on 4-amino-5-hydroxymethyl-2-methylpyrimidine (a thiamine precursor moiety) alone, although long thought dependent on exogenous sources of thiamine. Thus, overall, we have identified riboswitches in major eukaryotic lineages not known to undergo this form of gene regulation. In these phytoplankton groups, riboswitches are often affiliated with widespread thiamine-responsive genes with as yet uncertain roles in TPP pathways. Further, taxa with ‘incomplete’ TPP biosynthesis pathways do not necessarily require exogenous vitamin B1, making vitamin control of phytoplankton blooms more complex than the current paradigm suggests.
Species specificity of symbiosis and secondary metabolism in ascidians
Authors: Tianero Ma Diarey B , Kwan Jason C , Wyche Thomas P , Presson Angela P , Koch Michael , Barrows Louis R , Bugni Tim S , Schmidt Eric W 
Published: August 2014

Abstract
Ascidians contain abundant, diverse secondary metabolites, which are thought to serve a defensive role and which have been applied to drug discovery. It is known that bacteria in symbiosis with ascidians produce several of these metabolites, but very little is known about factors governing these ‘chemical symbioses’. To examine this phenomenon across a wide geographical and species scale, we performed bacterial and chemical analyses of 32 different ascidians, mostly from the didemnid family from Florida, Southern California and a broad expanse of the tropical Pacific Ocean. Bacterial diversity analysis showed that ascidian microbiomes are highly diverse, and this diversity does not correlate with geographical location or latitude. Within a subset of species, ascidian microbiomes are also stable over time (R=−0.037, P-value=0.499). Ascidian microbiomes and metabolomes contain species-specific and location-specific components. Location-specific bacteria are found in low abundance in the ascidians and mostly represent strains that are widespread. Location-specific metabolites consist largely of lipids, which may reflect differences in water temperature. By contrast, species-specific bacteria are mostly abundant sequenced components of the microbiomes and include secondary metabolite producers as major components. Species-specific chemicals are dominated by secondary metabolites. Together with previous analyses that focused on single ascidian species or symbiont type, these results reveal fundamental properties of secondary metabolic symbiosis. Different ascidian species have established associations with many different bacterial symbionts, including those known to produce toxic chemicals. This implies a strong selection for this property and the independent origin of secondary metabolite-based associations in different ascidian species. The analysis here streamlines the connection of secondary metabolite to producing bacterium, enabling further biological and biotechnological studies.
Comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease
Authors: Endo Akiko , Watanabe Takayasu , Ogata Nachiko , Nozawa Takashi , Aikawa Chihiro , Arakawa Shinichi , Maruyama Fumito , Izumi Yuichi , Nakagawa Ichiro 
Published: August 2014

Abstract
Polymicrobial diseases are caused by combinations of multiple bacteria, which can lead to not only mild but also life-threatening illnesses. Periodontitis represents a polymicrobial disease; Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia, called ‘the red complex’, have been recognized as the causative agents of periodontitis. Although molecular interactions among the three species could be responsible for progression of periodontitis, the relevant genetic mechanisms are unknown. In this study, we uncovered novel interactions in comparative genome analysis among the red complex species. Clustered regularly interspaced short palindromic repeats (CRISPRs) of T. forsythia might attack the restriction modification system of P. gingivalis, and possibly work as a defense system against DNA invasion from P. gingivalis. On the other hand, gene deficiencies were mutually compensated in metabolic pathways when the genes of all the three species were taken into account, suggesting that there are cooperative relationships among the three species. This notion was supported by the observation that each of the three species had its own virulence factors, which might facilitate persistence and manifestations of virulence of the three species. Here, we propose new mechanisms of bacterial symbiosis in periodontitis; these mechanisms consist of competitive and cooperative interactions. Our results might shed light on the pathogenesis of periodontitis and of other polymicrobial diseases.
Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-13C-acetate probing coupled with pyrosequencing
Authors: Ding Long-Jun , Su Jian-Qiang , Xu Hui-Juan , Jia Zhong-Jun , Zhu Yong-Guan 
Published: August 2014

Abstract
Iron reduction is an important biogeochemical process in paddy soils, yet little is known about the microbial coupling between nitrogen and iron reduction. Here, we investigated the shift of acetate-metabolizing iron-reducers under long-term nitrogen fertilization using 13C-acetate-based ribosomal RNA (rRNA)-stable isotope probing (SIP) and pyrosequencing in an incubation experiment, and the shift of putative iron-reducers in original field samples were investigated by 16S rRNA gene-based pyrosequencing. During SIP incubations, in the presence of iron(III) oxyhydroxides, more iron(II) formation and less methane production were detected in nitrogen-fertilized (N) compared with non-fertilized (NF) soil. In 13C-rRNA from microcosms amended with ferrihydrite (FER), Geobacter spp. were the important active iron-reducers in both soils, and labeled to a greater extent in N (31% of the bacterial classified sequences) than NF soils (11%). Pyrosequencing of the total 16S rRNA transcripts from microcosms at the whole community level further revealed hitherto unknown metabolisms of potential FER reduction by microorganisms including Pseudomonas and Solibacillus spp. in N soil, Dechloromonas, Clostridium, Bacillus and Solibacillus spp. in NF soil. Goethite (GOE) amendment stimulated Geobacter spp. to a lesser extent in both soils compared with FER treatment. Pseudomonas spp. in the N soil and Clostridium spp. in the NF soil may also be involved in GOE reduction. Pyrosequencing results from field samples showed that Geobacter spp. were the most abundant putative iron-reducers in both soils, and significantly stimulated by long-term nitrogen fertilization. Overall, for the first time, we demonstrate that long-term nitrogen fertilization promotes iron(III) reduction and modulates iron-reducing bacterial community in paddy soils.
Anthocyanin-rich fractions from red raspberries attenuate inflammation in both RAW264.7 macrophages and a mouse model of colitis
Authors: Li Li , Wang Liyan , Wu Zhiqin , Yao Lijun , Wu Yonghou , Huang Lian , Liu Kan , Zhou Xiang , Gou Deming 
Published: August 2014

AbstractEdible berries have a broad spectrum of biomedical functions, including improving immune responses and reducing risk for chronic diseases. In this study, the anti-inflammatory activities of crude extracts (CEs), anthocyanin-rich fractions (ARFs) and des-anthocyanin fractions (DAFs) from seven berries were evaluated based on their inhibitory effects on nitric oxide (NO) production in lipopolysaccharide (LPS)/IFN-γ-activated RAW264.7 macrophages. ARFs from red raspberries (RR-ARFs) exhibited the highest efficiency in suppressing NO synthesis. The anti-inflammatory properties were also demonstrated by reducing the expression levels of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), interleukin-1 beta (IL-1β) and IL-6 in RAW264.7 cells. The luciferase reporter assay demonstrated that the activities of NF-κB and AP-1 signaling pathways were significantly suppressed by RR-ARFs. Further studies showed that RR-ARFs decreased the phosphorylation of IKK, IκBα, p65 and JNK and the nuclear translocation of p65 in LPS/IFN-γ-stimulated RAW264.7 cells. In a mouse colitis model, dextran sulfate sodium (DSS)-induced weight loss and histological damage were significantly ameliorated by RR-ARFs treatment. Taken together, our results indicate that RR-ARFs attenuate inflammation both in vitro and in vivo primarily by inhibiting the activation of NF-κB and MAPKs. The anti-inflammatory of RR-ARFs could be harnessed and applied in animal agriculture, drug and food industries.
Proton-associated sucrose transport of mammalian solute carrier family 45: an analysis in Saccharomyces cerevisiae
Authors: Bartölke Rabea , Heinisch Jürgen J. , Wieczorek Helmut , Vitavska Olga 
Published: August 2014

The members of the solute carrier 45 (SLC45) family have been implicated in the regulation of glucose homoeostasis in the brain (SLC45A1), with skin and hair pigmentation (SLC45A2), and with prostate cancer and myelination (SLC45A3). However, apart from SLC45A1, a proton-associated glucose transporter, the function of these proteins is still largely unknown, although sequence similarities to plant sucrose transporters mark them as a putative sucrose transporter family. Heterologous expression of the three members SLC45A2, SLC45A3 and SLC45A4 in Saccharomyces cerevisiae confirmed that they are indeed sucrose transporters. [14C]Sucrose-uptake measurements revealed intermediate transport affinities with Km values of approximately 5 mM. Transport activities were best under slightly acidic conditions and were inhibited by the protonophore carbonyl cyanide m-chlorophenylhydrazone, demonstrating an H+-coupled transport mechanism. Na+, on the other hand, had no effect on sucrose transport. Competitive inhibition assays indicated a possible transport also of glucose and fructose. Real-time PCR of mouse tissues confirmed mRNA expression of SLC45A2 in eyes and skin and of SLC45A3 primarily in the prostate, but also in other tissues, whereas SLC45A4 showed a predominantly ubiquitous expression. Altogether the results provide new insights into the physiological significance of SLC45 family members and challenge existing concepts of mammalian sugar transport, as they (i) transport a disaccharide, and (ii) perform secondary active transport in a proton-dependent manner.
Topology assessment for 3 + 3 terminal offshore DC grid considering DC fault management
Authors: Jovcic Dragan , Taherbaneh Mohsen , Taisne Jean Pierre , Nguefeu Samuel 
Published: August 2014

This study assesses four DC grid topologies where each of the terminals can exchange power with any other terminal and a DC fault on any DC cable can be isolated. The DC grids are built using the following components: hybrid DC circuit breakers (CB), mechanical DC CBs, DC/DC converters and DC hubs. The aim is to compare DC fault performance, technical feasibility/readiness, power transfer security, expansion and costs. The base case for comparison are three separate 300 km offshore HVDCs connecting 3 1 GW offshore wind farms with three onshore VSC terminals. The rating of DC CBs is limited by the state of technology and costs which introduces limitation on the length of DC cables (because of communication delays) and on the DC bus fault level (limiting the number of connecting DC lines). DC/DC converters inherently block propagation of DC faults and their rating is not sensitive to DC fault level. DC hubs have considerable cost advantages over multiple DC/DC converters in cases where multiple DC systems are connecting at the same DC station. The cost assumptions for all major components are analysed, including the offshore platform costs. The study concludes that overall DC grid costs are similar (within 8%) for all four topologies. Although power security is similar for all technologies, the expansion options are best with DC/DC converters or DC hubs. DC hubs nevertheless suffer from highest on‐state losses.
Dual band‐notched monopole antenna with enhanced bandwidth for ultra‐wideband wireless communications
Authors: Akbari Mohammad , Rojhani Neda , Saberi Mehdi , Movahedinia Reza 
Published: August 2014

A new configuration of an ultra‐wideband (UWB) dual band‐notched antenna is presented. The designed geometry consists of octagonal radiating patch, a 50 Ω microstrip feed‐line on the front and an asymmetric partial ground on the back. For impedance bandwidth enhancement, a unilateral stepped structure is utilised on the ground. By etching two E‐shaped slots connected to each other on the radiating patch and applying E‐shaped defected ground structure on the back, dual notched bands are achieved. The antenna is printed on a low profile FR4 substrate with a compact size of 25 × 18 × 1 mm3. The experimental results indicate that the antenna has an impedance bandwidth from 2.55 to 21.65 GHz for voltage standing wave ratio ≤2, except the notched bands on worldwide interoperability for microwave access and wireless local area network bands. Moreover, stable radiation patterns and gains within the operating band are shown.
Does money talk, and do languages have price tags? Economic perspectives on English as a global language
Authors: Mair Christian 
Published: August 2014

The rise of English to its present position of the world’s undisputed lingua franca and the role of Global English in a multilingual world are core topics of World Englishes research. However, this does not mean that they have not been of interest to researchers in other disciplines, as well – for example in history, sociology and economics. The present contribution reviews a sample of recent analyses of English in multilingual settings written by economists, arguing that in spite of their methodological blindness to some phenomena important to (socio)linguists they have important things to say to the World Englishes research community. Conversely, taking account of the results of linguistic research on World Englishes would greatly help in refining the econometric models.
The evolutionary trajectory of Cameroonian Creole and its varying sociolinguistic statuses
Authors: Ngefac Aloysius 
Published: August 2014

The different names the contact language spoken in Cameroon has had at different historical points significantly reveal the complex evolutionary itinerary of the language and its varying sociolinguistic statuses. After the Portuguese era (ca. 1469 – 1600), which had Pidgin Portuguese as the main lingua franca, the language has had such names as “Pidgin English”, “Neger Englisch”, “Cameroons Creole”, “Cameroonian”, “Cameroon Pidgin English”, “Kumba English”, “Kamtok”, and “Cameroonian Creole”. This article makes an appraisal of these names in terms of how they reveal sociolinguistic information about the language (history, functions and status) and information about the country where it is spoken.
The Effects and Value of a Resistant Perennial Variety: An Application to Pudrición del Cogollo Disease
Authors: Grogan Kelly A. , Mosquera Mauricio 
Published: August 2014

AbstractThis article develops a forestry model to obtain the optimal control strategy and optimal rotation length after a disease attacks in a perennial variety. Three cases are considered: a benchmark consisting of a disease‐free field, an identical field with the disease present but no resistant variety with which to replant, and an identical field with the disease present and a resistant variety with which to replant. We determine general decision rules and then apply the model to the case of Pudrición del Cogollo, a major disease threat to the Colombian oil palm industry. In the application, we compare the optimal rotation length between the three scenarios and determine the optimal level of control in each period for the disease scenarios. The singular solution involves complete control of the disease, and in the absence of a resistant variety, the presence of the disease increases the rotation length. With these solutions, we then determine the value of developing a resistant variety. This value depends heavily on the age distribution of the current trees and decreases as the average tree age decreases. The value further declines when the resistance variety has negative attributes such as higher replanting and maintenance costs than the original variety.
VSEAMS: a pipeline for variant set enrichment analysis using summary GWAS data identifies IKZF3, BATF and ESRRA as key transcription factors in type 1 diabetes
Authors: Burren Oliver S. , Guo Hui , Wallace Chris 
Published: August 2014

Abstract
Motivation: Genome-wide association studies (GWAS) have identified many loci implicated in disease susceptibility. Integration of GWAS summary statistics (P-values) and functional genomic datasets should help to elucidate mechanisms.
Results: We extended a non-parametric SNP set enrichment method to test for enrichment of GWAS signals in functionally defined loci to a situation where only GWAS P-values are available. The approach is implemented in VSEAMS, a freely available software pipeline. We use VSEAMS to identify enrichment of type 1 diabetes (T1D) GWAS associations near genes that are targets for the transcription factors IKZF3, BATF and ESRRA. IKZF3 lies in a known T1D susceptibility region, while BATF and ESRRA overlap other immune disease susceptibility regions, validating our approach and suggesting novel avenues of research for T1D.
Availability and implementation: VSEAMS is available for download (http://github.com/ollyburren/vseams).
Contact: chris.wallace@cimr.cam.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Parasitic Diseases
Authors: Meunier Yann A. 
Published: August 2014

Abstract
Presentation of the Geographic Distribution, Main Symptoms, Treatment and Preventive Measures of parasitic diseases (1) classified by adult parasite location: Blood and Lymphatic System Diseases, Digestive Tract Diseases, Lung Diseases, Nail and Hair Diseases, Sexual Organ Diseases, Skin and Integumentary System Diseases, Urinary Tract Diseases, and (2) Parasitic Dead-ends and Larval Diseases.
Bacterial, Chlamydial, and Prion Diseases
Authors: Meunier Yann A. 
Published: August 2014

Abstract
Presentation of the Geographic Distribution, Main Symptoms, Treatment and Preventive Measures of bacterial and chlamydial diseases: (1) Bacterial Diseases: Anthrax, Bartonellosis (or Carrion disease), Bejel (or endemic syphilis), Buruli ulcers (or Bairnsdale or Daintree or Mossman or Searls ulcer, or mycoburuli ulcers), Diphtheria, Granuloma inguinale (or Donovan disease), Leprosy (or Hansen disease) Leptospirosis (or Weil disease, or Nanukayami fever), Pertussis (or whooping cough), Pinta (or carate) Yaws (or pian, or parangi, or paru, or frambesia tropica), and (2) Chlamydial Diseases: Lymphogranuloma venereum (or Durand-Nicholas-Favre disease), Urethritis and Cervicitis
Advancing Novel Anesthetics
Authors: Campagna Jason A. , Pojasek Kevin , Grayzel David , Randle John , Raines Douglas E. 
Published: August 2014

Abstract

Background:
Cyclopropyl-methoxycarbonyl metomidate (CPMM, also known as ABP-700) is a second-generation “soft” (i.e., metabolically labile) etomidate analogue. The purpose of this study was to characterize CPMM’s pharmacology in beagle dogs in preparation for potential first in human phase 1 clinical trials.

Methods:
CPMM’s and etomidate’s hypnotic activity and duration of action were assessed using loss of righting reflex and anesthesia score assays in three or four dogs. Their pharmacokinetics were defined after single bolus administration and single bolus followed by 2-h infusion. Adrenocortical recovery times after single bolus followed by 2-h infusion of CPMM, propofol, etomidate, and vehicle were measured using an adrenocorticotropic hormone stimulation test.

Results:
Compared with etomidate, CPMM was half as potent as a hypnotic (ED50 approximately 0.8 mg/kg), was more rapidly metabolized, and had a shorter duration of sedative–hypnotic action. Recovery times after CPMM administration were also independent of infusion duration. After hypnotic infusion, adrenocorticotropic hormone–stimulated plasma cortisol concentrations were 4- to 27-fold higher in dogs that received CPMM versus etomidate. Adrenocortical recovery was faster in dogs after CPMM infusion versus etomidate infusion (half-time: 215 vs. 1,623 min, respectively). Adrenocortical responsiveness assessed 90 min after CPMM infusion was not significantly different from that after propofol infusion.

Conclusion:
The studies in dogs confirm that CPMM has hypnotic and adrenocortical recovery profiles that are superior than those of etomidate, supporting the continued development of CPMM as a clinical sedative–hypnotic to be used as a single bolus and by continuous infusion to induce and maintain general anesthesia or procedural sedation.