bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Dexmedetomidine for Prophylactic Analgesia and Sedation in Patients With Delayed Extubation After Craniotomy: A Randomized Controlled Trial
Authors: Zhao Li-Hong , Shi Zhong-Hua , Chen Guang-Qiang , Yin Ning-Ning , Chen Han , Yuan Yuan , Cao Wei , Xu Ming , Hao Jing-Jing , Zhou Jian-Xin 
Published: December 2015

Background:
We conducted a randomized trial to evaluate the efficacy and safety of dexmedetomidine for prophylactic analgesia and sedation in patients with delayed extubation after craniotomy.

Methods:
From June 2012 to July 2014, 150 patients with delayed extubation after craniotomy were randomized 1:1 and were assigned to the dexmedetomidine group that received a continuous infusion of 0.6 μg/kg/h (10 μg/mL) or the control group that received a maintenance infusion of 0.9% sodium chloride for injection. The mean percentage of time under optimal sedation (SAS3-4), the percentage of patients who required rescue with propofol/fentanyl, and the total dose of propofol/fentanyl required throughout the course of drug infusion, as well as VAS, HR, MAP, and SpO2 were recorded.

Results:
The percentage of time under optimal sedation was significantly higher in the dexmedetomidine group than in the control group (98.4%±6.7% vs. 93.0%±16.2%, P=0.008). The VAS was significantly lower in the dexmedetomidine group than in the control group (1.0 vs. 4.0, P=0.000). The HR and mean BP were significantly lower in the dexmedetomidine group than in the control group at all 3 time points (before endotracheal suctioning, immediately after extubation, and 30 min after extubation). No significant difference in SpO2 was observed between the 2 groups. For hemodynamic adverse events, patients in the dexmedetomidine group were more likely to develop bradycardia (5.3% vs. 0%, P=0.043) but had a lower likelihood of tachycardia (2.7% vs. 18.7%, P=0.002).

Conclusions:
Dexmedetomidine may be an effective prophylactic agent to induce sedation and analgesia in patients with delayed extubation after craniotomy. The use of dexmedetomidine (0.6 μg/kg/h) infusion does not produce respiratory depression, but may increase the incidence of bradycardia.
Unraveling the Genetic Architecture of Cryptic Genetic Variation
Authors: Yadav Anupama , Dhole Kaustubh , Sinha Himanshu 
Published: December 2015

ABSTRACTCryptic genetic variation (CGV), hidden under most conditions, is the repressed genetic potential that can facilitate adaptation and evolution. The conditional manifestation of CGV has been claimed to explain the background dependence of causal loci as well as missing heritability. However, despite being proposed over 60 years ago, the genetic architecture and regulation of CGV and its contribution towards regulation of complex traits remains unclear. Using linkage mapping of mean and variance effects, we have identified loci that regulate phenotypic manifestation of standing genetic variation in a previously published dataset of biparentalSaccharomyces cerevisiaepopulation grown in 34 diverse environments. Based on our results we propose the existence of a gradient of buffering states for a population determined by the environment. Most environments show a tight buffering with additive, independent causal loci with little epistasis. However, as this buffering is disrupted, the underlying highly interconnected environment-specific genetic interactome is revealed such that each causal locus is a part of this network. Interspersed within these networks are generalist capacitors that regulate CGV across multiple environments, with one allele behaving as a capacitor and the other as a potentiator. Our study demonstrates the connecting link between architecture of hidden and visible genetic variation and uncovers the genetic networks which potentially underlie all complex traits. Our study establishes CGV as a significant contributor to phenotypic variation, and provides evidence for a predictable pattern underlying gene-gene and gene-environment interactions that can explain background dependence and missing heritability in complex traits and diseases.SUMMARYThe phenotypic effects of cryptic genetic variation (CGV) are mostly hidden and manifested only under certain rare conditions and have the potential to facilitate adaptation. However, little is understood about its genetic regulation. We performed variance QTL mapping to understand the regulation of phenotypic manifestation of standing genetic variation in a biparental yeast population. We propose a model describing the connecting link between visible variation and CGV. We identify generalist capacitors and environment-specific networks that potentially underlie all phenotypes. This fresh approach of mapping causal loci can solve the long-standing mystery of missing heritability in complex traits and diseases.
Classical metapopulation dynamics and eco-evolutionary feedbacks in dendritic networks
Authors: Fronhofer Emanuel A. , Altermatt Florian 
Published: December 2015

AbstractEco-evolutionary dynamics are now recognized to be highly relevant for population and community dynamics. However, the impact of evolutionary dynamics on spatial patterns, such as the occurrence of classical metapopulation dynamics, is less well appreciated. Here, we analyse the evolutionary consequences of spatial network connectivity and topology for dispersal strategies and quantify the eco-evolutionary feedback in terms of altered classical metapopulation dynamics. We find that network properties, such as topology and connectivity, lead to predictable spatio-temporal correlations in fitness expectations. These spatio-temporally stable fitness patterns heavily impact evolutionarily stable dispersal strategies and lead to eco-evolutionary feedbacks on landscape level metrics, such as the number of occupied patches, the number of extinctions and recolonizations as well as metapopulation extinction risk and genetic structure. Our model predicts that classical metapopulation dynamics are more likely to occur in dendritic networks, and especially in riverine systems, compared to other types of landscape configurations. As it remains debated whether classical metapopulation dynamics are likely to occur in nature at all, our work provides an important conceptual advance for understanding the occurrence of classical metapopulation dynamics which has implications for conservation and management of spatially structured populations.
Putting value in context: A role for context memory in decisions for reward
Authors: Bornstein Aaron M. , Norman Kenneth A. 
Published: December 2015

AbstractHow does experience inform decisions? In episodic sampling, decisions are guided by a few episodic memories of past choices. This process can yield choice patterns similar to model-free Reinforcement Learning (RL); however, samples can vary from trial to trial, causing decisions to vary. Here, we show that context retrieved during episodic sampling can cause choice behavior to deviate sharply from the predictions of RL. Specifically, we show that, when a given memory is sampled, choices (in the present) are influenced by the properties of other decisions made in the same context as the sampled event. This effect is mediated by fMRI measures of context retrieval on each trial, suggesting a mechanism whereby cues trigger retrieval of context, which then triggers retrieval of other decisions from that context. This result establishes a new avenue by which experience can guide choice, and as such has broad implications for the study of decisions.
Factorbook Motif Pipeline: Ade novomotif discovery and filtering web server for ChIP-seq peaks
Authors: Kim Bong-Hyun , Zhuang Jiali , Wang Jie , Weng Zhiping 
Published: December 2015

ABSTRACTSummaryHigh-throughput sequencing technologies such as ChIP-seq have deepened our understanding in many biological processes.De novomotif search is one of the key downstream computational analysis following the ChIP-seq experiments and several algorithms have been proposed for this purpose. However, most web-based systems do not perform independent filtering or enrichment analyses to ensure the quality of the discovered motifs. Here, we developed a web server Factorbook Motif Pipeline based on an algorithm used in analyzing ENCODE consortium ChIP-seq datasets. It performs comprehensive analysis on the set of peaks detected from a ChIP-seq experiments: (i)de novomotif discovery; (ii) independent composition and bias analyses and (iii) matching to the annotated motifs. The statistical tests employed in our pipeline provide a reliable measure of confidence as to how significant are the motifs reported in the discovery step.AvailabilityFactorbook Motif Pipeline source code is accessible through the following URL.https://github.com/joshuabhk/factorbook-motif-pipeline
The Development of Requests by L2 Learners of Modern Standard Arabic: A Longitudinal and Cross‐Sectional Study
Authors: Al‐Gahtani Saad , Roever Carsten 
Published: December 2015

AbstractThis study examined the development of requests made by second language (L2) learners of Modern Standard Arabic at four levels of L2 ability. The study used longitudinal and cross‐sectional data collection to investigate how learners' performance of requests developed over a five‐month period and differed as a function of ability level. The results indicated U‐shaped development, with learners initially decreasing their use of direct requests and increasing their use of indirect requests as their overall language ability increased. However, at higher ability levels, learners approximated native speaker norms by reverting to direct requests. This developmental pattern demonstrated the constraining effect of learners' sociopragmatic competence on their pragmalinguistic performance. In addition, the findings highlighted the nonuniversality of developmental stages proposed by Kasper and Rose (2002), showing that developmental trajectories differ between languages with a preference for indirect requests (such as English and Greek) and those with a preference for direct requests (such as Arabic).
Using Speaking Test Data to Define the Advanced Proficiency Level for L2 Arabic Speakers
Authors: Loomis Summer 
Published: December 2015

AbstractReaching the Advanced level of proficiency in speaking is a common goal of second language learners, but data on advanced learners of less commonly taught languages such as Arabic are scarce. This mixed‐methods study reports words‐per‐minute and type‐token ratios for three ACTFL levels—10 Intermediate Mid, 10 Advanced Mid, and 8 Superior—obtained from full‐length OPIs. Independent‐samples t tests revealed a significant difference between Intermediate Mid and Advanced Mid speakers on both measures, but no significant difference between Advanced Mid and Superior speakers was found. Qualitative observations on the distinctive features of Advanced learners' speech are also shared.
Cytoplasmic CopZ-Like Protein and Periplasmic Rusticyanin and AcoP Proteins as Possible Copper Resistance Determinants in Acidithiobacillus ferrooxidans ATCC 23270
Authors: Navarro Claudio A. , von Bernath Diego , Martínez-Bussenius Cristóbal , Castillo Rodrigo A. , Jerez Carlos A. 
Published: December 2015

ABSTRACT

Acidophilic organisms, such as
Acidithiobacillus ferrooxidans
, possess high-level resistance to copper and other metals.
A. ferrooxidans
contains canonical copper resistance determinants present in other bacteria, such as CopA ATPases and RND efflux pumps, but these components do not entirely explain its high metal tolerance. The aim of this study was to find other possible copper resistance determinants in this bacterium. Transcriptional expression of
A. ferrooxidans
genes coding for a cytoplasmic CopZ-like copper-binding chaperone and the periplasmic copper-binding proteins rusticyanin and AcoP, which form part of an iron-oxidizing supercomplex, was found to increase when the microorganism was grown in the presence of copper. All of these proteins conferred more resistance to copper when expressed heterologously in a copper-sensitive
Escherichia coli
strain. This effect was absent when site-directed-mutation mutants of these proteins with altered copper-binding sites were used in this metal sensitivity assay. These results strongly suggest that the three copper-binding proteins analyzed here are copper resistance determinants in this extremophile and contribute to the high-level metal resistance of this industrially important biomining bacterium.
N
-Glycosylation Improves the Pepsin Resistance of Histidine Acid Phosphatase Phytases by Enhancing Their Stability at Acidic pHs and Reducing Pepsin's Accessibility to Its Cleavage Sites
Authors: Niu Canfang , Luo Huiying , Shi Pengjun , Huang Huoqing , Wang Yaru , Yang Peilong , Yao Bin 
Published: December 2015

ABSTRACT

N
-Glycosylation can modulate enzyme structure and function. In this study, we identified two pepsin-resistant histidine acid phosphatase (HAP) phytases from
Yersinia kristensenii
(YkAPPA) and
Yersinia rohdei
(YrAPPA), each having an
N
-glycosylation motif, and one pepsin-sensitive HAP phytase from
Yersinia enterocolitica
(YeAPPA) that lacked an
N
-glycosylation site. Site-directed mutagenesis was employed to construct mutants by altering the
N
-glycosylation status of each enzyme, and the mutant and wild-type enzymes were expressed in
Pichia pastoris
for biochemical characterization. Compared with those of the
N
-glycosylation site deletion mutants and
N
-deglycosylated enzymes, all
N
-glycosylated counterparts exhibited enhanced pepsin resistance. Introduction of the
N
-glycosylation site into YeAPPA as YkAPPA and YrAPPA conferred pepsin resistance, shifted the pH optimum (0.5 and 1.5 pH units downward, respectively) and improved stability at acidic pH (83.2 and 98.8% residual activities at pH 2.0 for 1 h). Replacing the pepsin cleavage sites L197 and L396 in the immediate vicinity of the
N
-glycosylation motifs of YkAPPA and YrAPPA with V promoted their resistance to pepsin digestion when produced in
Escherichia coli
but had no effect on the pepsin resistance of
N
-glycosylated enzymes produced in
P. pastoris
. Thus,
N
-glycosylation may improve pepsin resistance by enhancing the stability at acidic pH and reducing pepsin's accessibility to peptic cleavage sites. This study provides a strategy, namely, the manipulation of
N
-glycosylation, for improvement of phytase properties for use in animal feed.
Mechanism of Sporicidal Activity for the Synergistic Combination of Peracetic Acid and Hydrogen Peroxide
Authors: Leggett Mark J. , Schwarz J. Spencer , Burke Peter A. , McDonnell Gerald , Denyer Stephen P. , Maillard Jean-Yves 
Published: December 2015

ABSTRACT

There is still great interest in controlling bacterial endospores. The use of chemical disinfectants and, notably, oxidizing agents to sterilize medical devices is increasing. With this in mind, hydrogen peroxide (H
2
O
2
) and peracetic acid (PAA) have been used in combination, but until now there has been no explanation for the observed increase in sporicidal activity. This study provides information on the mechanism of synergistic interaction of PAA and H
2
O
2
against bacterial spores. We performed investigations of the efficacies of different combinations, including pretreatments with the two oxidizers, against wild-type spores and a range of spore mutants deficient in the spore coat or small acid-soluble spore proteins. The concentrations of the two biocides were also measured in the reaction vessels, enabling the assessment of any shift from H
2
O
2
to PAA formation. This study confirmed the synergistic activity of the combination of H
2
O
2
and PAA. However, we observed that the sporicidal activity of the combination is largely due to PAA and not H
2
O
2
. Furthermore, we observed that the synergistic combination was based on H
2
O
2
compromising the spore coat, which was the main spore resistance factor, likely allowing better penetration of PAA and resulting in the increased sporicidal activity.
Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an
In Vivo
Competition Assay
Authors: Jin Zhao , Di Rienzi Sara C. , Janzon Anders , Werner Jeff J. , Angenent Largus T. , Dangl Jeffrey L. , Fowler Douglas M. , Ley Ruth E. 
Published: December 2015

ABSTRACT

Metagenomes derived from environmental microbiota encode a vast diversity of protein homologs. How this diversity impacts protein function can be explored through selection assays aimed to optimize function. While artificially generated gene sequence pools are typically used in selection assays, their usage may be limited because of technical or ethical reasons. Here, we investigate an alternative strategy, the use of soil microbial DNA as a starting point. We demonstrate this approach by optimizing the function of a widely occurring soil bacterial enzyme, 1-aminocyclopropane-1-carboxylate (ACC) deaminase. We identified a specific ACC deaminase domain region (ACCD-DR) that, when PCR amplified from the soil, produced a variant pool that we could swap into functional plasmids carrying ACC deaminase-encoding genes. Functional clones of ACC deaminase were selected for in a competition assay based on their capacity to provide nitrogen to
Escherichia coli
in vitro
. The most successful ACCD-DR variants were identified after multiple rounds of selection by sequence analysis. We observed that previously identified essential active-site residues were fixed in the original unselected library and that additional residues went to fixation after selection. We identified a divergent essential residue whose presence hints at the possible use of alternative substrates and a cluster of neutral residues that did not influence ACCD performance. Using an artificial ACCD-DR variant library generated by DNA oligomer synthesis, we validated the same fixation patterns. Our study demonstrates that soil metagenomes are useful starting pools of protein-coding-gene diversity that can be utilized for protein optimization and functional characterization when synthetic libraries are not appropriate.
Direct Image-Based Enumeration of Clostridium phytofermentans Cells on Insoluble Plant Biomass Growth Substrates
Authors: Alvelo-Maurosa Jesús G. , Lee Scott J. , Hazen Samuel P. , Leschine Susan B. 
Published: December 2015

ABSTRACT

A dual-fluorescent-dye protocol to visualize and quantify
Clostridium phytofermentans
ISDg (ATCC 700394) cells growing on insoluble cellulosic substrates was developed by combining calcofluor white staining of the growth substrate with cell staining using the nucleic acid dye Syto 9. Cell growth, cell substrate attachment, and fermentation product formation were investigated in cultures containing either Whatman no. 1 filter paper, wild-type
Sorghum bicolor
, or a reduced-lignin
S. bicolor
double mutant (
bmr-6 bmr-12
double mutant) as the growth substrate. After 3 days of growth, cell numbers in cultures grown on filter paper as the substrate were 6.0- and 2.2-fold higher than cell numbers in cultures with wild-type sorghum and double mutant sorghum, respectively. However, cells produced more ethanol per cell when grown with either sorghum substrate than with filter paper as the substrate. Ethanol yields of cultures were significantly higher with double mutant sorghum than with wild-type sorghum or filter paper as the substrate. Moreover, ethanol production correlated with cell attachment in sorghum cultures: 90% of cells were directly attached to the double mutant sorghum substrate, while only 76% of cells were attached to wild-type sorghum substrate. With filter paper as the growth substrate, ethanol production was correlated with cell number; however, with either wild-type or mutant sorghum, ethanol production did not correlate with cell number, suggesting that only a portion of the microbial cell population was active during growth on sorghum. The dual-staining procedure described here may be used to visualize and enumerate cells directly on insoluble cellulosic substrates, enabling in-depth studies of interactions of microbes with plant biomass.
Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes
Authors: Becraft Eric D. , Dodsworth Jeremy A. , Murugapiran Senthil K. , Ohlsson J. Ingemar , Briggs Brandon R. , Kanbar Jad , De Vlaminck Iwijn , Quake Stephen R. , Dong Hailiang , Hedlund Brian P. , Swingley Wesley D. 
Published: December 2015

ABSTRACT

The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This “microbial dark matter” represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum “
Calescamantes
” (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract
Calescamantes
bins from all metagenomes with abundant
Calescamantes
populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that
Calescamantes
are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate
Calescamantes
populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O
2
, or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs.
An Environmental Shiga Toxin-Producing Escherichia coli O145 Clonal Population Exhibits High-Level Phenotypic Variation That Includes Virulence Traits
Authors: Carter Michelle Qiu , Quinones Beatriz , He Xiaohua , Zhong Wayne , Louie Jacqueline W. , Lee Bertram G. , Yambao Jaszemyn C. , Mandrell Robert E. , Cooley Michael B. 
Published: December 2015

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC) serotype O145 is one of the major non-O157 serotypes associated with severe human disease. Here we examined the genetic diversity, population structure, virulence potential, and antimicrobial resistance profiles of environmental O145 strains recovered from a major produce production region in California. Multilocus sequence typing analyses revealed that sequence type 78 (ST-78), a common ST in clinical strains, was the predominant genotype among the environmental strains. Similarly, all California environmental strains belonged to H28, a common H serotype in clinical strains. Although most environmental strains carried an intact
fliC
gene, only one strain retained swimming motility. Diverse
stx
subtypes were identified, including
stx
1a
,
stx
2a
,
stx
2c
, and
stx
2e
. Although no correlation was detected between the
stx
genotype and Stx1 production, high Stx2 production was detected mainly in strains carrying
stx
2a
only and was correlated positively with the cytotoxicity of Shiga toxin. All environmental strains were capable of producing enterohemolysin, whereas only 10 strains were positive for anaerobic hemolytic activity. Multidrug resistance appeared to be common, as nearly half of the tested O145 strains displayed resistance to at least two different classes of antibiotics. The core virulence determinants of enterohemorrhagic
E. coli
were conserved in the environmental STEC O145 strains; however, there was large variation in the expression of virulence traits among the strains that were highly related genotypically, implying a trend of clonal divergence. Several cattle isolates exhibited key virulence traits comparable to those of the STEC O145 outbreak strains, emphasizing the emergence of hypervirulent strains in agricultural environments.