bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of Movement to Surgical Stimulation by the Pupillary Dilatation Reflex Amplitude Evoked by a Standardized Noxious Test
Authors: Guglielminotti Jean , Grillot Nicolas , Paule Marine , Mentré France , Servin Fréderique , Montravers Philippe , Longrois Dan 
Published: February 2015

AbstractAbstract
Seventy-six women scheduled for an operative procedure requiring cervical dilation were anesthetized with a target propofol effect-site concentration of 4 μg/ml with a randomly assigned remifentanil effect-site concentration of 0, 1, 3, or 5 ng/ml. Pupillary dilatation reflex amplitude in response to a standardized noxious test predicted movement response on cervical dilation as accurately as the estimated remifentanil effect-site concentration.

Background:
Individual assessment of the amplitude of a physiologic reflex evoked by a standardized noxious test (SNT) before surgical stimulation has been suggested to predict movement upon the forthcoming surgical stimulation. This study aimed to compare the ability of pupillary dilatation reflex amplitude (PDRA) evoked by an SNT and estimated remifentanil effect-site concentration (Ce) to predict movement upon surgical stimulation.

Methods:
Eighty female patients were anesthetized for vacuum aspiration with propofol (Ce 4 μg/ml) and remifentanil. Remifentanil Ce was randomized to 0, 1, 3, or 5 ng/ml. SNT was a 60-mA, 5-s, 100-Hz tetanus applied on median nerve before cervix dilatation. PDRA was calculated as the difference in pupillary diameter after and before SNT. Movement upon cervix dilatation was recorded by an independent observer. Ability of PDRA and estimated remifentanil Ce to discriminate movers from non-movers during cervix dilatation was measured as the area under the receiver operating characteristics curve.

Results:
Twenty-one of the 76 patients analyzed moved during cervix dilatation. Mean PDRA (±1 SD) evoked by SNT was 2.0 ± 1.2 mm in movers and 0.6 ± 0.7 in non-movers (P < 0.0001). Remifentanil Ce was 0.2 ± 0.4 ng/ml in movers and 3.0 ± 1.7 in non-movers (P < 0.0001). Area under the receiver operating characteristics curve for PDRA was 0.90 (95% CI, 0.83 to 0.96) and for remifentanil Ce 0.94 (0.89 to 0.98), without any significant difference between the two areas.

Conclusions:
PDRA evoked by an SNT is as accurate as the estimated remifentanil Ce to predict movement upon cervix dilatation. PDRA could be valuable when estimated opioid Ce is not available or reliable.
A Patient-centered Approach to Evaluate the Information Needs of Women With Ductal Carcinoma In Situ
Authors: Lo Andrea C. , Olson Robert , Feldman-Stewart Deb , Truong Pauline T. , Aquino-Parsons Christina , Bottorff Joan L. , Carolan Hannah 
Published: February 2015

Objective:To evaluate the information needs of ductal carcinoma in situ (DCIS) patients.Methods:Four focus groups involving 24 previously treated DCIS patients were conducted to develop a comprehensive list of questions they felt were important to have answered at the time of diagnosis. Using a survey, a separate group of patients treated for DCIS then rated the importance of having each of these questions addressed before treatment decision making. Response options were “essential,” “desired,” “not important,” “no opinion,” and “avoid.” For each essential/desired question, respondents specified how addressing it would help them: “understand,” “decide,” “plan,” “not sure,” or “other.”Results:Focus group participants generated 117 questions used in the survey. Fifty-seven patients completed the survey (55% response rate). Respondents rated a median of 66 questions as essential. The most commonly cited reason for rating a question essential was to “understand,” followed by to “decide.” The top questions women deemed essential to help them understand were disease specific, whereas the top questions deemed essential to help women decide were predominantly treatment specific, pertaining to available options, recurrence and survival outcomes, and timelines to decide and start treatment.Conclusions:DCIS patients want a large number of questions answered, mostly for understanding, and also for deciding and planning. A core set of questions that most patients consider essential for decision making has been formulated and may be used in the clinical setting and in research to develop educational resources and decision-making tools specific to DCIS.
Analog nitrogen sensing inEscherichia colienables high fidelity information processing
Authors: Komorowski M. , Schumacher J. , Behrends V. , Jetka T. , Bennett Mark H. , Ale A. , Filippi S. , Pinney J.W. , Bundy J.G. , Buck M. , Stumpf M.P.H. 
Published: February 2015

AbstractThe molecular reaction networks that coordinate the response of an organism to changing environmental conditions are central for survival and reproduction.Escherchia coliemploys an accurate and flexible signalling system that is capable of processing ambient nitrogen availability rapidly and with high accuracy. Carefully orchestrated post-translational modifications of PII and the glutamine synthetase allowE. colito trace nitrogen availability in a continuous, decidedly non-digital fashion. We measure the dynamic proteomic and metabolomic responses to trace the analog computations, and use an information theoretical framework to characterize the information capacity ofE. coli’s nitrogen sensing network: we find that this system can transmit up to 9bits of information about the nitrogen state. This allows cells to respond rapidly and accurately even to small differences in metabolite concentrations.
Speciation inHeliconiusButterflies: Minimal Contact Followed by Millions of Generations of Hybridisation
Authors: Martin Simon H. , Eriksson Anders , Kozak Krzysztof M. , Manica Andrea , Jiggins Chris D. 
Published: March 2015

AbstractDocumenting the full extent of gene flow during speciation poses a challenge, as species ranges change over time and current rates of hybridisation might not reflect historical trends. Theoretical work has emphasized the potential for speciation in the face of ongoing hybridisation, and the genetic mechanisms that might facilitate this process. However, elucidating how the rate of gene flow between species may have changed over time has proved difficult. Here we use Approximate Bayesian Computation (ABC) to fit a model of speciation between the Neotropical butterfliesHeliconius melpomeneandHeliconius cydno. These species are ecologically divergent, rarely hybridize and display female hybrid sterility. Nevertheless, previous genomic studies suggests pervasive gene flow between them, extending deep into their past, and potentially throughout the speciation process. By modelling the rates of gene flow during early and later stages of speciation, we find that these species have been hybridising for hundreds of thousands of years, but have not done so continuously since their initial divergence. Instead, it appears that gene flow was rare or absent for as long as a million years in the early stages of speciation. Therefore, by dissecting the timing of gene flow between these species, we are able to reject a scenario of purely sympatric speciation in the face of continuous gene flow. We suggest that the period of minimal contact early in speciation may have allowed for the accumulation of genomic changes that later enabled these species to remain distinct despite a dramatic increase in the rate of hybridisation.
Chemical integration of proteins in signaling and development
Authors: Dick Jeffrey M. 
Published: March 2015

ABSTRACTIn developing embryos of eukaryotes, varying concentrations and/or duration of exposure to morphogens induce and repress transcription factors (TFs) in a regular order, thereby acting as signals for cell differentiation. I present a chemical thermodynamic model for the formation and degradation of the morphogen Sonic hedgehog (Shh) and the major TFs involved in dorsal-ventral patterning of the vertebrate neural tube. This two-stage model first considers introduction of Shh into a chemically defined (oxidizing) environment. As the system is driven away from metastable equilibrium, the TFs progressively become more stable than Shh, as indicated by comparison of the calculated overall energies of formation (chemical affinity). In the second stage, a gradual return to metastable equilibrium with Shh drives transitions in the relative stabilities of the TFs that follow the experimental patterns of TF expression. At the intracellular level, the major proteins in the signal transduction network show a metastability progression among reactions of Shh and its cell-surface receptor and the intracellular Gli proteins that act as activators and repressors of transcription. If the endocytosis and degradation of receptor-ligand complexes are coupled to localized protein translation, the consequent thermodynamic constraints may represent a high-level source of specificity that coexists with molecular mechanisms of signal transduction.
Coordinated Rates of Evolution between Interacting Plastid and Nuclear Genes in Geraniaceae
Authors: Zhang Jin , Ruhlman Tracey A. , Sabir Jamal , Blazier J. Chris , Jansen Robert K. 
Published: February 2015

Abstract
Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae.
Regulation of plasmid‐encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle
Authors: Crombie Andrew T. , Khawand Myriam El , Rhodius Virgil A. , Fengler Kevin A. , Miller Michael C. , Whited Gregg M. , McGenity Terry J. , Murrell J. Colin 
Published: February 2015

SummaryEmissions of biogenic volatile organic compounds (VOCs) form an important part of the global carbon cycle, comprising a significant proportion of net ecosystem productivity. They impact atmospheric chemistry and contribute directly and indirectly to greenhouse gases. Isoprene, emitted largely from plants, comprises one third of total VOCs, yet in contrast to methane, which is released in similar quantities, we know little of its biodegradation. Here, we report the genome of an isoprene degrading isolate, Rhodococcus sp. AD45, and, using mutagenesis shows that a plasmid‐encoded soluble di‐iron centre isoprene monooxygenase (IsoMO) is essential for isoprene metabolism. Using RNA sequencing (RNAseq) to analyse cells exposed to isoprene or epoxyisoprene in a substrate‐switch time‐course experiment, we show that transcripts from 22 contiguous genes, including those encoding IsoMO, were highly upregulated, becoming among the most abundant in the cell and comprising over 25% of the entire transcriptome. Analysis of gene transcription in the wild type and an IsoMO‐disrupted mutant strain showed that epoxyisoprene, or a subsequent product of isoprene metabolism, rather than isoprene itself, was the inducing molecule. We provide a foundation of molecular data for future research on the environmental biological consumption of this important, climate‐active compound.
Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla
Authors: Emerson Joanne B. , Thomas Brian C. , Alvarez Walter , Banfield Jillian F. 
Published: February 2015

SummaryResearch on geologic carbon sequestration raises questions about potential impacts of subsurface microbiota on carbon cycling and biogeochemistry. Subsurface, high‐CO2 systems are poorly biologically characterized, partly because of difficulty accessing high‐volume, uncontaminated samples. CO2‐driven Crystal Geyser (CG, Utah, USA), an established geologic carbon sequestration analogue, provides high volumes of deep (∼ 200–500 m) subsurface fluids. We explored microbial diversity and metabolic potential in this high‐CO2 environment by assembly and analysis of metagenomes recovered from geyser water filtrate. The system is dominated by neutrophilic, iron‐oxidizing bacteria, including ‘marine’ Mariprofundus (Zetaproteobacteria) and ‘freshwater’ Gallionellales, sulfur‐oxidizing Thiomicrospira crunogena and Thiobacillus‐like Hydrogenophilales. Near‐complete genomes were reconstructed for these bacteria. CG is notably populated by a wide diversity of bacteria and archaea from phyla lacking isolated representatives (candidate phyla) and from as‐yet undefined lineages. Many bacteria affiliate with OD1, OP3, OP9, PER, ACD58, WWE3, BD1‐5, OP11, TM7 and ZB2. The recovery of nearly 100 genes encoding ribulose‐1,5 bisphosphate carboxylase‐oxygenase subunit proteins of the Calvin cycle and AMP salvage pathways suggests a strong biological role in high‐CO2 subsurface carbon cycling. Overall, we predict microbial impacts on subsurface biogeochemistry via iron, sulfur, and complex carbon oxidation, carbon and nitrogen fixation, fermentation, hydrogen metabolism, and aerobic and anaerobic respiration.
Decoupled distance–decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate‐reducing bacteria
Authors: Angermeyer Angus , Crosby Sarah C. , Huber Julie A. 
Published: March 2015

SummaryIn many habitats, microorganisms exhibit significant distance–decay patterns as determined by analysis of the 16S rRNA gene and various other genetic elements. However, there have been few studies that examine how the similarities of both taxonomic and functional genes co‐vary over geographic distance within a group of ecologically related microbes. Here, we determined the biogeographic patterns of the functional dissimilatory sulfite reductase gene (dsrA) and the 16S rRNA gene in sulfate‐reducing bacterial communities of US East Coast salt marsh sediments. Distance–decay, ordination and statistical analyses revealed that the distribution of 16S rRNA genes is strongly influenced by geographic distance and environmental factors, whereas the dsrA gene is not. Together, our results indicate that 16S rRNA genes are likely dispersal limited and under environmental selection, whereas dsrA genes appear randomly distributed and not selected for by any expected environmental variables. Selection, drift, dispersal and mutation are all factors that may help explain the decoupled biogeographic patterns for the two genes. These data suggest that both the taxonomic and functional elements of microbial communities should be considered in future studies of microbial biogeography to aid in our understanding of the diversity, distribution and function of microorganisms in the environment.
Physiological and genetic analyses reveal a mechanistic insight into the multifaceted lifestyles of Pseudoalteromonas sp. SM9913 adapted to the deep‐sea sediment
Authors: Mi Zi‐Hao , Yu Zi‐Chao , Su Hai‐Nan , Wang Lei , Chen Xiu‐Lan , Pang Xiuhua , Qin Qi‐Long , Xie Bin‐Bin , Zhang Xi‐Ying , Zhou Bai‐Cheng , Zhang Yu‐Zhong 
Published: March 2015

SummaryAlthough bacteriobenthos play a major role in the degradation of particulate organic matter in marine sediment, knowledge of the sediment‐adapted lifestyles of bacteriobenthos is still scarce. Here, the particle‐associated, swimming and swarming lifestyles of the benthonic bacterium Pseudoalteromonas sp. SM9913 (SM9913) were illustrated. SM9913 had a clay particle‐associated lifestyle, and its exopolysaccharide played an important role in this lifestyle. SM9913 also had swimming and swarming motilities, indicating that it may have swimming and swarming lifestyles in the sediment. The lateral flagella were responsible for the swarming motility, and the polar flagella were responsible for the swimming motility. Iron limitation was an indispensable inductive signal of the swarming motility. An analysis of the motilities of SM9913 and its mutants in clay demonstrated that SM9913 moved in clay by both swimming and swarming motilities. Genomic analysis suggests that having two flagella systems is most likely a common adaptation of some bacteriobenthos to the sediment environment. Our results reveal the lifestyles of benthonic SM9913, providing a better understanding of the environmental adaptation of benthonic bacteria.
Disruption of photoautotrophic intertidal mats by filamentous fungi
Authors: Carreira Cátia , Staal Marc , Falkoski Daniel , de Vries Ronald P. , Middelboe Mathias , Brussaard Corina P. D. 
Published: February 2015

SummaryRing‐like structures, 2.0–4.8 cm in diameter, observed in photosynthetic microbial mats on the Wadden Sea island Schiermonnikoog (the Netherlands) showed to be the result of the fungus Emericellopsis sp. degrading the photoautotrophic top layer of the mat. The mats were predominantly composed of cyanobacteria and diatoms, with large densities of bacteria and viruses both in the top photosynthetic layer and in the underlying sediment. The fungal attack cleared the photosynthetic layer; however, no significant effect of the fungal lysis on the bacterial and viral abundances could be detected. Fungal‐mediated degradation of the major photoautotrophs could be reproduced by inoculation of non‐infected mat with isolated Emericellopsis sp., and with an infected ring sector. Diatoms were the first re‐colonizers followed closely by cyanobacteria that after about 5 days dominated the space. The study demonstrated that the fungus Emericellopsis sp. efficiently degraded a photoautotrophic microbial mat, with potential implications for mat community composition, spatial structure and productivity.
Identification of 2‐(ethylamino)‐1‐(4‐methylphenyl)‐1‐pentanone (4‐MEAP), a New “Legal High” Sold by an Internet Vendor as 4‐Methyl Pentedrone
Authors: Hamby Danielle , Burnett Annessa , Jablonsky Michael , Twamley Brendan , Kavanagh Pierce V. , Gardner Elizabeth A. 
Published: February 2015

AbstractOnline vendors are offering a new legal high, 4‐methylpentedrone (4‐MPD). Information for potential users provided by internet vendors of 4‐MPD includes incorrect structures and nonexistent CAS numbers. A sample of 4‐MPD was obtained and analyzed using GC‐MS, NMR, and LC‐EIS. The fragmentation data from the GC‐MS and LC‐EIS produced an M‐1 ion that suggested the molecular mass was 219 amu, rather than 205 amu as calculated for 4‐methylpentedrone. The difference in molecular mass corresponded to the addition of a methyl group. Based on the mass and fragmentation pattern, two standards were synthesized, 2‐(ethylamino)‐1‐(4‐methylphenyl)‐1‐pentanone and 1‐(4‐methylphenyl)‐2‐(propylamino)‐1‐butanone. The synthesis involved bromination of the appropriate ketone followed by the reaction with ethylamine or propylamine. Based on the NMR data and unique fragmentation patterns produced by these molecules, the sample was identified as 2‐(ethylamino)‐1‐(4‐methylphenyl)‐1‐pentanone, not 4‐methylpentedrone.
Isolated ventriculomegaly on prenatal ultrasound: What does fetal MRI add?
Authors: Kandula Tejaswi , Fahey Michael , Chalmers Rebecca , Edwards Andrew , Shekleton Paul , Teoh Mark , Clark Jenni , Goergen Stacy K. 
Published: March 2015

AbstractIntroductionCerebral ventriculomegaly is one of the most commonly detected fetal anomalies at the midtrimester ultrasound. Current evidence suggests that magnetic resonance imaging (MRI) is indicated when the isolated ventriculomegaly (IVM) on ultrasound is severe (>15 mm), but there is less agreement when IVM is mild or moderate (10–15 mm). The current study aimed to determine the frequency and nature of additional findings on MRI in IVM and their relationship to the severity of VM and gestational age.MethodsData were gathered prospectively from all pregnant women with ultrasound‐diagnosed IVM referred for MRI between November 2006 and February 2013. Cases with IVM and no other suspected cranial abnormality on a tertiary ultrasound performed at our institution, at or after 20 weeks gestation, were included.ResultsOf the 59 fetuses with unilateral or bilateral IVM, additional findings were seen on MRI in 10 cases (17%) and half of these findings were identified in fetuses with mild IVM. Five of 40 (12.5%) fetuses with mild IVM had additional findings and 3/5 (60%) were potentially clinically significant. No additional abnormalities were identified in fetuses less than or equal to 24 weeks gestation with mild or moderate IVM. There was no statistically significant relationship between gestational age and additional findings on MRI in mild IVM. Callosal and septum pellucidum lesions, periventricular abnormalities and malformations of cortical development accounted for all of the significant additional findings.ConclusionThis study helps to inform referral of pregnant women with a fetus who has IVM for prenatal MRI.
Early‐life establishment of the swine gut microbiome and impact on host phenotypes
Authors: Mach Núria , Berri Mustapha , Estellé Jordi , Levenez Florence , Lemonnier Gaëtan , Denis Catherine , Leplat Jean‐Jacques , Chevaleyre Claire , Billon Yvon , Doré Joël , Rogel‐Gaillard Claire , Lepage Patricia 
Published: March 2015

SummaryEarly bacterial colonization and succession within the gastrointestinal tract has been suggested to be crucial in the establishment of specific microbiota composition and the shaping of host phenotype. Here, the composition and dynamics of faecal microbiomes were studied for 31 healthy piglets across five age strata (days 14, 36, 48, 60 and 70 after birth) together with their mothers. Faecal microbiome composition was assessed by 16S rRNA gene 454‐pyrosequencing. Bacteroidetes and Firmicutes were the predominant phyla present at each age. For all piglets, luminal secretory IgA concentration was measured at day 70, and body weight was recorded until day 70. The microbiota of suckling piglets was mainly represented by Bacteroides, Oscillibacter, Escherichia/Shigella, Lactobacillus and unclassified Ruminococcaceae genera. This pattern contrasted with that of Acetivibrio, Dialister, Oribacterium, Succinivibrio and Prevotella genera, which appeared increased after weaning. Lactobacillus fermentum might be vertically transferred via breast milk or faeces. The microbiota composition coevolved with their hosts towards two different clusters after weaning, primarily distinguished by unclassified Ruminococcaceae and Prevotella abundances. Prevotella was positively correlated with luminal secretory IgA concentrations, and body weight. Our study opens up new possibilities for health and feed efficiency manipulation via genetic selection and nutrition in the agricultural domain.