bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial distribution of emergency obstetric and newborn care services in Ghana: Using the evidence to plan interventions
Authors: Bosomprah Samuel , Tatem Andrew J. , Dotse‐Gborgbortsi Winfred , Aboagye Patrick , Matthews Zoe
Published: December 2015

Objective

To provide clear policy directions for gaps in the provision of signal function services and sub‐regions requiring priority attention using data from the 2010 Ghana Emergency Obstetric and Newborn Care (EmONC) survey.

Methods

Using 2010 survey data, the fraction of facilities with only one or two signal functions missing was calculated for each facility type and EmONC designation. Thematic maps were used to provide insight into inequities in service provision.

Results

Of 1159 maternity facilities, 89 provided all the necessary basic or comprehensive EmONC signal functions 3 months prior to the 2010 survey. Only 21% of facility‐based births were in fully functioning EmONC facilities, but an additional 30% occurred in facilities missing one or two basic signal functions—most often assisted vaginal delivery and removal of retained products. Tackling these missing signal functions would extend births taking place in fully functioning facilities to over 50%. Subnational analyses based on estimated total pregnancies in each district revealed a pattern of inequity in service provision across the country.

Conclusion

Upgrading facilities missing only one or two signal functions will allow Ghana to meet international standards for availability of EmONC services. Reducing maternal deaths will require high national priority given to addressing inequities in the distribution of EmONC services.
The Importance of Data Set Provenance for Science
Authors: Hills Denise , Downs Robert R. , Duerr Ruth , Goldstein Justin , Parsons Mark , Ramapriyan Hampapuram
Published: December 2015

Data do not exist in a vacuum. To be useful, data must be accompanied by context on how they are captured, processed, analyzed, and validated and other information that enables interpretation and use.
Tackling the Poster Hall
Authors: Watson Kelsey
Published: December 2015

Here are some tips for going to a poster session, from knowing where to start to connecting with presenters—even if they're nowhere to be seen.
Paris Climate Talks Could Spur Energy Sector Action
Authors: Showstack Randy
Published: December 2015

A robust climate pact from the United Nations meeting in Paris could urge nations and energy investors toward lower-emissions energy generation, the head of a global energy agency suggests.
Directed evolution of Tau class glutathione transferases reveals a site that regulates catalytic efficiency and masks co-operativity
Authors: Axarli Irine , Muleta Abdi W. , Vlachakis Dimitrios , Kossida Sophia , Kotzia Georgia , Maltezos Anastasios , Dhavala Prathusha , Papageorgiou Anastassios C. , Labrou Nikolaos E.
Published: December 2015

A library of Tau class GSTs (glutathione transferases) was constructed by DNA shuffling using the DNA encoding the Glycine max GSTs GmGSTU2-2, GmGSTU4-4 and GmGSTU10-10. The parental GSTs are >88% identical at the sequence level; however, their specificity varies towards different substrates. The DNA library contained chimaeric structures of alternated segments of the parental sequences and point mutations. Chimaeric GST sequences were expressed in Escherichia coli and their enzymatic activities towards CDNB (1-chloro-2,4-dinitrobenzene) and the herbicide fluorodifen (4-nitrophenyl α,α,α-trifluoro-2-nitro-p-tolyl ether) were determined. A chimaeric clone (Sh14) with enhanced CDNB- and fluorodifen-detoxifying activities, and unusual co-operative kinetics towards CDNB and fluorodifen, but not towards GSH, was identified. The structure of Sh14 was determined at 1.75 Å (1 Å=0.1 nm) resolution in complex with S-(p-nitrobenzyl)-glutathione. Analysis of the Sh14 structure showed that a W114C point mutation is responsible for the altered kinetic properties. This was confirmed by the kinetic properties of the Sh14 C114W mutant. It is suggested that the replacement of the bulky tryptophan residue by a smaller amino acid (cysteine) results in conformational changes of the active-site cavity, leading to enhanced catalytic activity of Sh14. Moreover, the structural changes allow the strengthening of the two salt bridges between Glu66 and Lys104 at the dimer interface that triggers an allosteric effect and the communication between the hydrophobic sites.
The regulation of function, growth and survival of GLP-1-producing L-cells
Authors: Kuhre Rune E. , Holst Jens J. , Kappe Camilla
Published: December 2015

Glucagon-like peptide-1 (GLP-1) is a peptide hormone, released from intestinal L-cells in response to hormonal, neural and nutrient stimuli. In addition to potentiation of meal-stimulated insulin secretion, GLP-1 signalling exerts numerous pleiotropic effects on various tissues, regulating energy absorption and disposal, as well as cell proliferation and survival. In Type 2 Diabetes (T2D) reduced plasma levels of GLP-1 have been observed, and plasma levels of GLP-1, as well as reduced numbers of GLP-1 producing cells, have been correlated to obesity and insulin resistance. Increasing endogenous secretion of GLP-1 by selective targeting of the molecular mechanisms regulating secretion from the L-cell has been the focus of much recent research. An additional and promising strategy for enhancing endogenous secretion may be to increase the L-cell mass in the intestinal epithelium, but the mechanisms that regulate the growth, survival and function of these cells are largely unknown. We recently showed that prolonged exposure to high concentrations of the fatty acid palmitate induced lipotoxic effects, similar to those operative in insulin-producing cells, in an in vitro model of GLP-1-producing cells. The mechanisms inducing this lipototoxicity involved increased production of reactive oxygen species (ROS). In this review, regulation of GLP-1-secreting cells is discussed, with a focus on the mechanisms underlying GLP-1 secretion, long-term regulation of growth, differentiation and survival under normal as well as diabetic conditions of hypernutrition.
Electrically programmable-erasable In-Ga-Zn-O thin-film transistor memory with atomic-layer-deposited Al2O3/Pt nanocrystals/Al2O3 gate stack
Authors: Qian Shi-Bing , Zhang Wen-Peng , Liu Wen-Jun , Ding Shi-Jin
Published: December 2015

Amorphous indium-gallium-zinc oxide (a-IGZO) thin-film transistor (TFT) memory is very promising for transparent and flexible system-on-panel displays; however, electrical erasability has always been a severe challenge for this memory. In this article, we demonstrated successfully an electrically programmable-erasable memory with atomic-layer-deposited Al2O3/Pt nanocrystals/Al2O3 gate stack under a maximal processing temperature of 300 oC. As the programming voltage was enhanced from 14 to 19 V for a constant pulse of 0.2 ms, the threshold voltage shift increased significantly from 0.89 to 4.67 V. When the programmed device was subjected to an appropriate pulse under negative gate bias, it could return to the original state with a superior erasing efficiency. The above phenomena could be attributed to Fowler-Nordheim tunnelling of electrons from the IGZO channel to the Pt nanocrystals during programming, and inverse tunnelling of the trapped electrons during erasing. In terms of 0.2-ms programming at 16 V and 350-ms erasing at −17 V, a large memory window of 3.03 V was achieved successfully. Furthermore, the memory exhibited stable repeated programming/erasing (P/E) characteristics and good data retention, i.e., for 2-ms programming at 14 V and 250-ms erasing at −14 V, a memory window of 2.08 V was still maintained after 103 P/E cycles, and a memory window of 1.1 V was retained after 105 s retention time.
Chaos control for the output-constrained system by using adaptive dynamic surface technology and application to the brushless DC motor
Authors: Luo Shaohua , Hou Zhiwei , Chen Zhong
Published: December 2015

In this paper, chaos control is proposed for the output- constrained system with uncertain control gain and time delay and is applied to the brushless DC motor. Using the dynamic surface technology, the controller overcomes the repetitive differentiation of backstepping and boundedness hypothesis of pre-determined control gain by incorporating radial basis function neural network and adaptive technology. The tangent barrier Lyapunov function is employed for time-delay chaotic system to prevent constraint violation. It is proved that the proposed control approach can guarantee asymptotically stable in the sense of uniformly ultimate boundedness without constraint violation. Finally, the effectiveness of the proposed approach is demonstrated on the brushless DC motor example.
Trapping study of nanofluids in an annulus with cilia
Authors: Nadeem S. , Sadaf Hina
Published: December 2015

The main purpose of this article is to present a mathematical model of ciliary motion in an annulus. In this analysis, two dimensional flow of a viscous nanofluid is observed in an annulus with ciliated tips. The current theoretical model may be supposed as mathematical illustration to the movement of ciliary motion in the presence of an endoscopic tube (or catheter tube). The inner tube is rigid, while the outer tube takes a metachronal wave. The features of ciliary structures are determined by the dominance of viscous effects over inertial effects using the long-wavelength approximation. Exact solutions have been established for both velocity and temperature profiles, which include nanoparticle effects. The features of the ciliary motion are analyzed by plotting graphs and discussed in detail.
Analysis of longitudinal vibration band gaps in periodic carbon nanotube intramolecular junctions using finite element method
Authors: Li Jiaqian , Shen Haijun
Published: December 2015

The longitudinal vibration band gaps in periodic (n, 0)–(2n, 0) single-walled carbon nanotube(SWCNT) intramolecular junctions(IMJs) are investigated based on the finite element calculation. The frequency ranges of band gaps in frequency response functions(FRF) simulated by finite element method (FEM) show good agreement with those in band structure obtained by simple spring-mass model. Moreover, a comprehensive parametric study is also conducted to highlight the influences of the geometrical parameters such as the size of unit cell, component ratios of the IMJs and diameters of the CNT segments as well as geometric imperfections on the first band gap. The results show that the frequency ranges and the bandwidth of the gap strongly depend on the geometrical parameters. Furthermore, the influences of geometrical parameters on gaps are nuanced in IMJs with different topological defects. The existence of vibration band gaps in periodic IMJs lends a new insight into the development of CNT-based nano-devices in application of vibration isolation.
Measurement of field-free molecular alignment by balanced weak field polarization technique
Authors: Peng Peng , Bai Ya , Li Na , Liu Peng
Published: December 2015

We demonstrate the measurement of field-free molecular alignment of air can be realized by combining the weak field polarization technique (WFPT) with a balanced detection system. The measured signal is proportional to the alignment parameter. Periodic revival structures of the transient alignment and permanent alignment between revivals can be detected clearly by a single measurement with high sensitivity. Fourier transform spectrum of the measured signal agrees well with the calculation result and provides information of the populations of different J states in the rotational wave packet.
Big picture of relativistic molecular quantum mechanics
Authors: Liu Wenjian
Published: December 2015

Any quantum mechanical calculation on electronic structure ought to choose first an appropriate Hamiltonian H and then an Ansatz for parameterizing the wave function Ψ, from which the desired energy/property E(λ) can finally be calculated. Therefore, the very first question is: what is the most accurate many-electron Hamiltonian H? It is shown that such a Hamiltonian i.e. effective quantum electrodynamics (eQED) Hamiltonian, can be obtained naturally by incorporating properly the charge conjugation symmetry when normal ordering the second quantized fermion operators. Taking this eQED Hamiltonian as the basis, various approximate relativistic many-electron Hamiltonians can be obtained based entirely on physical arguments. All these Hamiltonians together form a complete and continuous ‘Hamiltonian ladder’, from which one can pick up the right one according to the target physics and accuracy. As for the many-electron wave function Ψ, the most intriguing questions are as follows. (i) How to do relativistic explicit correlation? (ii) How to handle strong correlation? Both general principles and practical strategies are outlined here to handle these issues. Among the electronic properties E(λ) that sample the electronic wave function nearby the nuclear region, nuclear magnetic resonance (NMR) shielding and nuclear spin-rotation (NSR) coupling constant are especially challenging: they require body-fixed molecular Hamiltonians that treat both the electrons and nuclei as relativistic quantum particles. Nevertheless, they have been formulated rigorously. In particular, a very robust ‘relativistic mapping’ between the two properties has been established, which can translate experimentally measured NSR coupling constants to very accurate absolute NMR shielding scales that otherwise cannot be obtained experimentally. Since the most general and fundamental issues pertinent to all the three components of the quantum mechanical equation HΨ = EΨ (i.e. Hamiltonian H, wave function Ψ, and energy/property E(λ)) have fully been understood, the big picture of relativistic molecular quantum mechanics can now be regarded as established.
Surgical and Patient Risk Factors for Severe Arterial Line Complications in Adults
Authors: Nuttall Gregory , Burckhardt Jennifer , Hadley Anita , Kane Sarah , Kor Daryl , Marienau Mary Shirk , Schroeder Darrell R. , Handlogten Kathryn , Wilson Gregory , Oliver William C.
Published: December 2015

AbstractAbstract

In a series of 57,787 patients receiving arterial cannulation, 21 patients were identified as having experienced vascular complications or nerve injuries, resulting in a very low complication rate of 3.4/10,000. The rate of complications differed significantly (P < 0.001) across the three most common catheter sizes (2.7/10,000 for 20 gauge, 17.2/10,000 for 18 gauge, and 9.4/10,000 for 5 French). Given the low frequency of complications observed, the current study does not have sufficient statistical power to make definitive conclusions regarding the risk factors (listed in the appendix).

Background

Prior research has provided inconsistent data regarding the risk factors associated with complications from arterial cannulation. The goal of this study was to clearly define the incidence and risks factors associated with arterial cannulation complications.

Methods

After obtaining institutional review board approval, all patients requiring arterial line placement with documentation were included in this retrospective study between January 1, 2006, and December 31, 2012. Leveraging two robust data warehouses, the Perioperative DataMart and the Mayo Clinic Life Silences System, the authors cross-matched arterial line cannulation with a documented vascular consult, neurologic consult, infection, or return to surgery within 30 days in order to identify the initial patient population.

Results

A total of 62,626 arterial lines were placed in 57,787 patients, and 90.1% of the catheters placed were 20-gauge catheters. The radial artery was cannulated in 94.5% of patients. A total of 21 patients were identified as having experienced vascular complications or nerve injuries, resulting in a complication rate of 3.4 per 10,000 (95% CI, 2.1 to 5.1). Cardiac surgery had the largest number of catheters placed (n = 15,419) with 12 complications (complication rate = 7.8 per 10,000; 95% CI, 4.0 to 13.6). The rate of complications differed significantly (P < 0.001) across the three most common catheter sizes (2.7 per 10,000 [95% CI, 1.5 to 4.4] for 20 gauge, 17.2 per 10,000 [95% CI, 4.7 to 43.9] for 18 gauge, and 9.4 per 10,000 [95% CI, 1.1 to 34.1] for 5 French).

Conclusion

In a large retrospective study, the authors document a very low rate of complications with arterial line placement.
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.
Intervention trial of previous nonattender invitation for breast screening
Authors: Fleming Padraic , Mooney Therese , Wilson Linda , Fitzpatrick Patricia
Published: December 2015

BreastCheck, the National Breast Screening Programme in the Republic of Ireland, invites women aged between 50 and 64 years biennially. A pilot intervention trial of invitation for screening of women not attending the previous appointment [previous nonattender (PNA)] was carried out that aimed at maximizing the efficiency of resources in terms of radiographer workload and scheduled appointment slots. The trial was conducted during screening round 5 at two of the regional units. The intervention arm implemented an alternative process for inviting PNA women, in which they were sent a letter inviting them to phone their screening unit to make an appointment at a convenient date/time. The control arm continued usual practice – that is, all PNA women were sent a single invitation letter with a scheduled appointment slot at a predetermined date/time. In the intervention arm, fewer PNAs took up their appointments (15.5%) compared with the control arm (18.3%; P<0.001). Uptake among PNAs fell in both arms between screening rounds 4 and 5 (intervention arm: 22.0% OSR 4, 15.5% OSR 5; control arm: 21.4% OSR 4, 18.3% OSR 5). There was a significant increase in mobile unit screening days saved because of the intervention and a significant improvement in the percentage of women reinvited for screening within 27 months in the intervention arm (85.5%). PNA recall and cancer detection rates were significantly higher compared with the general screened population. This trial showed an improvement in the efficiency of resource use. However, there was a higher cancer detection rate in PNA women. This trial provides important evidence for invitation policy for screening.
Unraveling the Genetic Architecture of Cryptic Genetic Variation
Authors: Yadav Anupama , Dhole Kaustubh , Sinha Himanshu
Published: December 2015

Cryptic 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.

The 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

Eco-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

How 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

High-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.

Availability

Factorbook Motif Pipeline source code is accessible through the following URL.https://github.com/joshuabhk/factorbook-motif-pipeline
FANCJ suppresses microsatellite instability and lymphomagenesis independent of the Fanconi anemia pathway
Authors: Matsuzaki Kenichiro , Borel Valerie , Adelman Carrie A. , Schindler Detlev , Boulton Simon J.
Published: December 2015

Microsatellites are short tandem repeat sequences that are highly prone to expansion/contraction due to their propensity to form non-B-form DNA structures, which hinder DNA polymerases and provoke template slippage. Although error correction by mismatch repair plays a key role in preventing microsatellite instability (MSI), which is a hallmark of Lynch syndrome, activities must also exist that unwind secondary structures to facilitate replication fidelity. Here, we report that Fancj helicase-deficient mice, while phenotypically resembling Fanconi anemia (FA), are also hypersensitive to replication inhibitors and predisposed to lymphoma. Whereas metabolism of G4-DNA structures is largely unaffected in Fancj−/− mice, high levels of spontaneous MSI occur, which is exacerbated by replication inhibition. In contrast, MSI is not observed in Fancd2−/− mice but is prevalent in human FA-J patients. Together, these data implicate FANCJ as a key factor required to counteract MSI, which is functionally distinct from its role in the FA pathway.
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

This 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

Reaching 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.
Promotion Signals, Experience, and Education
Authors: Bognanno Michael , Melero Eduardo
Published: December 2015

This paper uses a nation‐wide representative survey of employees to examine whether more informative job promotions carry larger wage increases. In job assignment models with asymmetric information, unexpected promotions send a signal to the external labor market to revise upward their assessment of a worker's ability. The employing firm must then increase wages to prevent the worker from being bid away. Less educated workers are assumed to come from a group with lower average ability. Their promotion is hypothesized to induce a larger positive update of the assessment of their ability than the promotion of more educated workers. Promotions of less experienced workers, with less known about their abilities, should also result in strong signaling effects. We obtain regression results consistent with our hypotheses, although the size and significance of the estimates hinge on the promotion definition. Inexperienced workers gain more from promotions that entail new managerial responsibilities, whereas less educated workers gain more from nonmanagerial promotions. This sensitivity to the definition of promotion suggests that promotions reveal information on different dimensions of ability for different types of workers.
PRMT8 as a phospholipase regulates Purkinje cell dendritic arborization and motor coordination
Authors: Kim Jun-Dal , Park Kyung-Eui , Ishida Junji , Kako Koichiro , Hamada Juri , Kani Shuichi , Takeuchi Miki , Namiki Kana , Fukui Hajime , Fukuhara Shigetomo , Hibi Masahiko , Kobayashi Makoto , Kanaho Yasunori , Kasuya Yoshitoshi , Mochizuki Naoki , Fukamizu Akiyoshi
Published: December 2015

PRMT8 directly hydrolyzes phosphatidylcholine, which is important for brain functions.
Regulation of gene transcription by Polycomb proteins
Authors: Aranda Sergi , Mas Gloria , Di Croce Luciano
Published: December 2015

New findings extend the functionality of mammalian Polycomb protein complexes on gene regulation and 3D chromatin conformation.
Glacier maxima in Baffin Bay during the Medieval Warm Period coeval with Norse settlement
Authors: Young Nicolás E. , Schweinsberg Avriel D. , Briner Jason P. , Schaefer Joerg M.
Published: December 2015

The Baffin Bay region was relatively cool during the Medieval Warm Period coinciding with the period of Norse settlement.
Vortex and half-vortex dynamics in a nonlinear spinor quantum fluid
Authors: Dominici Lorenzo , Dagvadorj Galbadrakh , Fellows Jonathan M. , Ballarini Dario , De Giorgi Milena , Marchetti Francesca M. , Piccirillo Bruno , Marrucci Lorenzo , Bramati Alberto , Gigli Giuseppe , Szymańska Marzena H. , Sanvitto Daniele
Published: December 2015

Two-dimensional fluid of polaritons sheds light on quantum vortex dynamics.
From tunable core-shell nanoparticles to plasmonic drawbridges: Active control of nanoparticle optical properties
Authors: Byers Chad P. , Zhang Hui , Swearer Dayne F. , Yorulmaz Mustafa , Hoener Benjamin S. , Huang Da , Hoggard Anneli , Chang Wei-Shun , Mulvaney Paul , Ringe Emilie , Halas Naomi J. , Nordlander Peter , Link Stephan , Landes Christy F.
Published: December 2015

Redox electrochemistry was used to reversibly tune the optical properties of plasmonic core-shell nanoparticles and dimers.
Earthquake detection through computationally efficient similarity search
Authors: Yoon Clara E. , O’Reilly Ossian , Bergen Karianne J. , Beroza Gregory C.
Published: December 2015

Data mining techniques applied to continuous waveforms reveal many previously unknown small earthquakes.
The crystal structure of the global anaerobic transcriptional regulator FNR explains its extremely fine-tuned monomer-dimer equilibrium
Authors: Volbeda Anne , Darnault Claudine , Renoux Oriane , Nicolet Yvain , Fontecilla-Camps Juan C.
Published: December 2015

The dimerization of the O
2
sensor FNR is regulated by extremely fine-tuned interactions.
Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR
Authors: Shi Chaowei , Fricke Pascal , Lin Lin , Chevelkov Veniamin , Wegstroth Melanie , Giller Karin , Becker Stefan , Thanbichler Martin , Lange Adam
Published: December 2015

The first atomic structure of a member of a recently discovered class of cytoskeletal proteins was revealed.
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

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

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

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

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

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

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

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.