bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visual Cues Contribute Differentially to Audiovisual Perception of Consonants and Vowels in Improving Recognition and Reducing Cognitive Demands in Listeners With Hearing Impairment Using Hearing Aids
Authors: Moradi Shahram , Lidestam Björn , Danielsson Henrik , Ng Elaine Hoi Ning , Rönnberg Jerker 
Published: June 2017

Purpose
We sought to examine the contribution of visual cues in audiovisual identification of consonants and vowels—in terms of isolation points (the shortest time required for correct identification of a speech stimulus), accuracy, and cognitive demands—in listeners with hearing impairment using hearing aids.

Method
The study comprised 199 participants with hearing impairment (mean age = 61.1 years) with bilateral, symmetrical, mild-to-severe sensorineural hearing loss. Gated Swedish consonants and vowels were presented aurally and audiovisually to participants. Linear amplification was adjusted for each participant to assure audibility. The reading span test was used to measure participants' working memory capacity.

Results
Audiovisual presentation resulted in shortened isolation points and improved accuracy for consonants and vowels relative to auditory-only presentation. This benefit was more evident for consonants than vowels. In addition, correlations and subsequent analyses revealed that listeners with higher scores on the reading span test identified both consonants and vowels earlier in auditory-only presentation, but only vowels (not consonants) in audiovisual presentation.

Conclusion
Consonants and vowels differed in terms of the benefits afforded from their associative visual cues, as indicated by the degree of audiovisual benefit and reduction in cognitive demands linked to the identification of consonants and vowels presented audiovisually.
Acute Onset Neurological Disorders during Pregnancy: A Literature Review
Authors: Ferraz Zita , Parra Joana , Areia Ana Luísa , Vasco Elsa , Moura Paulo 
Published: June 2017

Objectives To characterize the most common peripheral and central neurological disorders during pregnancy.
Methods Original research and review of the literature on neurological complications during pregnancy. We searched for keywords related to the topic on different databases.
Results Pregnancy involves physiological changes that can trigger peripheral neurological and/or central nervous system pathologies, which can sometimes be associated with hypertensive disorders. A definitive diagnosis of neurological disorders can be made according to the trimester of pregnancy and the clinical findings. Carpal tunnel syndrome and peripheral facial palsy are common peripheral neurological disorders, more frequent in the second half of pregnancy. Central nervous disorders are more complex and a precise diagnosis must be made in order to improve perinatal outcomes, provide correct management and treatment and to prevent acute and long-term complications.
Conclusions It is possible to achieve a precise diagnosis, management and treatment of neurological disorders during pregnancy, but these require a multidisciplinary approach, crucial to improve perinatal outcomes.
White Paper: Interventional MRI: Current Status and Potential for Development Considering Economic Perspectives, Part 1: General Application
Authors: Barkhausen Jörg , Kahn Thomas , Krombach Gabriele , Kuhl Christiane , Lotz Joachim , Maintz David , Ricke Jens , Schönberg Stefan , Vogl Thomas , Wacker Frank ,   German Association of Chairmen in Academic Radiology (KLR)
Published: June 2017

Background MRI is attractive for the guiding and monitoring of interventional procedures due to its high intrinsic soft tissue contrast and the possibility to measure physiologic parameters like flow and cardiac function.
Method The current status of interventional MRI for the clinical routine was analyzed.
Results The effort needed for the development of MR-safe monitoring systems and instruments initially resulted in the application of interventional MRI only for procedures that could not be performed by other means. Accordingly, biopsy of lesions in the breast, which are not detectable by other modalities, has been performed under MRI guidance for decades. Currently, biopsies of the prostate under MRI guidance are established in a similar fashion. At many sites blind biopsy has already been replaced by MR-guided biopsy or at least by the fusion of MR images with ultrasound. Cardiovascular interventions are performed at several centers for ablation as a treatment for atrial fibrillation.
Conclusion Interventional MRI has been established in the clinical routine for a variety of indications. Broader application can be expected in the clinical routine in the future owing to the multiple advantages compared to other techniques.
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Development of a Reference Standard Library of Chloroplast Genome Sequences, GenomeTrakrCP
Authors: Zhang Ning , Ramachandran Padmini , Wen Jun , Duke James , Metzman Helen , McLaughlin William , Ottesen Andrea , Timme Ruth , Handy Sara 
Published: June 2017

AbstractPrecise, species-level identification of plants in foods and dietary supplements is difficult. While the use of DNA barcoding regions (short regions of DNA with diagnostic utility) has been effective for many inquiries, it is not always a robust approach for closely related species, especially in highly processed products. The use of fully sequenced chloroplast genomes, as an alternative to short diagnostic barcoding regions, has demonstrated utility for closely related species. The U. S. Food and Drug Administration (FDA) has also developed species-specific DNA-based assays targeting plant species of interest by utilizing chloroplast genome sequences. Here, we introduce a repository of complete chloroplast genome sequences called GenomeTrakrCP, which will be publicly available at the National Center for Biotechnology Information (NCBI). Target species for inclusion are plants found in foods and dietary supplements, toxin producers, common contaminants and adulterants, and their close relatives. Publicly available data will include annotated assemblies, raw sequencing data, and voucher information with each NCBI accession associated with an authenticated reference herbarium specimen. To date, 40 complete chloroplast genomes have been deposited in GenomeTrakrCP (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA325670/), and this will be expanded in the future.
The relative need for Comparative Translation Studies
Authors: van Doorslaer Luc 
Published: June 2017

Abstract
This article asks to what extent Comparative Translation Studies is needed and realistic to achieve. The difficulties of comparative approaches in other disciplines are related to translation studies, where ‘comparative’ up to now has been used for several levels of analysis. An important difference with most other disciplines is that comparison seems to be more self-evident in a trans-discipline like translation studies, where transfer between two or more sides is always immanently present. The selection of the units of analysis/comparison is a pitfall, particularly when working with larger units at a systemic or sociocultural level when studying cultural (ex)change. It is suggested that existing tools used in translation studies can be helpful in structuring the approach and the methodology: both mixed-method models from descriptive translation studies and existing conceptual maps in the discipline.
Phase I Trial of Radiosurgery Dose Escalation Plus Bevacizumab in Patients With Recurrent/Progressive Glioblastoma
Authors: Abbassy Mahmoud , Missios Symeon , Barnett Gene H , Brewer Cathy , Peereboom David M , Ahluwalia Manmeet , Neyman Gennady , Chao Samuel T , Suh John H , Vogelbaum Michael A 
Published: June 2017

Abstract

BACKGROUND
The effectiveness of stereotactic radiosurgery (SRS) for recurrent glioblastoma (rGBM) remains uncertain. SRS has been associated with a high risk of radionecrosis in gliomas.

OBJECTIVE
To determine the safety of dose escalation of single-fraction radiosurgery for rGBM in the setting of bevacizumab therapy.

METHODS
We conducted a prospective trial to determine the safety and synergistic benefit of higher doses of SRS administered with bevacizumab for rGBM. A single dose of bevacizumab was given prior to SRS and continued until progression. Dose-limiting toxicity was evaluated in successive cohorts of 3 patients.

RESULTS
Seven males and 2 females entered the study. The maximum linear diameter of the enhancing tumor was 2.58 cm (2.04-3.09). Prescription dose was escalated from 18 to 22 Gy. The radiosurgery target was chosen before the first dose of bevacizumab, about 1 wk prior to SRS treatment. Pre-SRS bevacizumab treatment was associated with a reduction of the mean volume of the enhancing lesion from 4.7 to 2.86 cm3 on the day of SRS (P = .103). No patient developed an acute side effect related to SRS treatment. The combination of SRS and bevacizumab resulted in a partial response in 3 patients and stable disease in 6 patients. Median progression-free and overall survival were 7.5 and 13 mo, respectively.

CONCLUSION
A single dose of bevacizumab prior to SRS permitted safe prescription dose escalation up to 22 Gy for rGBM. Further evaluation of the efficacy of SRS for rGBM should be performed in the setting of bevacizumab treatment.
The independent influences of age and education on functional brain networks and cognition in healthy older adults
Authors: Perry Alistair , Wen Wei , Kochan Nicole A. , Thalamuthu Anbupalam , Sachdev Perminder S. , Breakspear Michael 
Published: June 2017

AbstractHealthy ageing is accompanied by a constellation of changes in cognitive processes and alterations in functional brain networks. The relationships between brain networks and cognition during ageing in later life are moderated by demographic and environmental factors, such as prior education, in a poorly understood manner. Using multivariate analyses, we identify three latent patterns (or modes) linking resting-state functional connectivity to demographic and cognitive measures in 101 cognitively-normal elders. The first mode (p=0.00043) captures an opposing association between age and core cognitive processes such as attention and processing speed on functional connectivity patterns. The functional subnetwork expressed by this mode links bilateral sensorimotor and visual regions through key areas such as the parietal operculum. A strong, independent association between years of education and functional connectivity loads onto a second mode (p=0.012), characterised by the involvement of key hub-regions. A third mode (p=0.041) captures weak, residual brain-behaviour relations. Our findings suggest that circuits supporting lower-level cognitive processes are most sensitive to the influence of age in healthy older adults. Education, and to a lesser extent, executive functions, load independently onto functional networks - suggesting that the moderating effect of education acts upon networks distinct from those vulnerable with ageing. This has important implications in understanding the contribution of education to cognitive reserve during healthy ageing.
Molecular evolution, diversity and adaptation of H7N9 influenza A viruses in China
Authors: Lu Jing , Raghwani Jayna , Wu Jie , Pryce Rhys , Bowden Thomas A. , Thézé Julien , Huang Shanqian , Song Yingchao , Zou Lirong , Liang Lijun , Bai Ru , Jin Yi , Zhou Pingping , Kang Min , Yi Lina , Pybus Oliver G. , Ke Changwen 
Published: June 2017

SummaryA novel H7N9 avian influenza virus has caused five human epidemics in China since 2013. The substantial increase in prevalence and the emergence of antigenically divergent or highly pathogenic (HP) H7N9 strains during the current outbreak raises concerns about the epizootic-potential of these viruses. Here, we investigate the evolution and adaptation of H7N9 by combining publicly available data with newly generated virus sequences isolated in Guangdong between 2015-2017. Phylogenetic analyses show that currently-circulating H7N9 viruses belong to distinct lineages with differing spatial distributions. Using ancestral sequence reconstruction and structural modelling we have identified parallel amino-acid changes on multiple separate lineages. Furthermore, we infer mutations in HA primarily occur at sites involved in receptor-recognition and/or antigenicity. We also identify seven new HP strains, which likely emerged from viruses circulating in eastern Guangdong around March 2016 and is further associated with a high rate of adaptive molecular evolution.
A rate threshold mechanism regulates MAPK stress signaling and survival
Authors: Johnson Amanda N. , Li Guoliang , Jashnsaz Hossein , Thiemicke Alexander , Kesler Benjamin K. , Rogers Dustin C. , Neuert Gregor 
Published: June 2017

AbstractCells are exposed to changes in extracellular stimulus concentration that vary as a function of rate. However, the effect of stimulation rate on cell behavior and signaling remains poorly understood. Here, we examined how varying the rate of stress application alters budding yeast cell viability and mitogen-activated protein kinase (MAPK) signaling at the single-cell level. We show that cell survival and signaling depend on a rate threshold that operates in conjunction with a concentration threshold to determine the timing of MAPK signaling during rate-varying stimulus treatments. We also discovered that the stimulation rate threshold is sensitive to changes in the expression levels of the Ptp2 phosphatase, but not of another phosphatase that similarly regulates osmostress signaling during switch-like treatments. Our results demonstrate that stimulation rate is a regulated determinant of signaling output and provide a paradigm to guide the dissection of major stimulation rate-dependent mechanisms in other systems.
Buffering Agent Induced Lactose Content Increases via Growth Hormone-Mediated Activation of Gluconeogenesis in Lactating Goats
Authors: Li Lin , He MeiLin , Liu Ying , Zhang Yuanshu 
Published: June 2017

AbstractDairy goats are often fed a high-concentrate (HC) diet to meet lactation demands; however, long-term concentrate feeding is unhealthy and decreases milk yield and lactose content. Therefore, we tested whether a buffering agent increases the output of glucose in the liver and influences of lactose synthesis. In this study, sixteen lactating goats were randomly assigned to two groups: one group received a HC diets (Concentrate: Forage = 6:4, HG), and the other group received the same diet with a buffering agent added (0.2% NaHCO3, 0.1% MgO, BG) as a treatment for 19-weeks experimental period. The results showed that the total volatile fatty acids and lipopolysaccharide (LPS) declined in the rumen leading to the rumen pH was stabilized in the BG group. Milk yield and lactose content increased. The alanine aminotransferase, aspartate transaminase, alkaline phosphatase, pro-inflammatory cytokines, LPS and lactate content in the plasma was significantly decreased, whereas prolactin and growth hormone levels were increased. The hepatic vein content of glucose was increased. In addition, the expression of pyruvate carboxylase (PC), phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6PC) in the liver was significantly up-regulated. In mammary gland, the glucose transporter type-1, 8, 12 and sodium-glucose cotransporter-1 levels were increased. Cumulatively, the buffering agent treatment increased blood concentrations of glucose via the gluconeogenes and promoting their synthesis in the liver. It may contribute to the increase in milk yield and lactose synthesis of lactating goats.
PARP mediated chromatin unfolding is coupled to long-range enhancer activation
Authors: Benabdallah Nezha S. , Williamson Iain , Illingworth Robert S. , Boyle Shelagh , Grimes Graeme R. , Therizols Pierre , Bickmore Wendy A. 
Published: June 2017

AbstractEnhancers are critical regulators of gene expression and can be located far from their target gene. It is widely assumed that mechanisms of enhancer action involve reorganization of three-dimensional chromatin architecture, but this is poorly understood. Here we identify a novel mechanism of long-range enhancer associated chromatin reorganization. At the Sonic hedgehog (Shh) locus we observe large-scale decompaction of chromatin betweenShhand its brain enhancers in neural progenitor cells. We show that the chromatin unfolding is dependent on activation of the enhancers, not the promoter, is impeded by chromatin-bound proteins located between the enhancer and promoter, and is mediated by the recruitment of Poly (ADP-Ribose) Polymerase 1. We suggest that large-scale chromatin decompaction, analogous to the inducible puffs inDrosophilapolytene chromosomes, represents a new mechanism of chromatin reorganization coupled to long-range gene activation from mammalian enhancers and that seems incompatible with a chromatin-looping model of enhancer-promoter communication
Adsorption and conformations of lysozyme andα-lactalbumin at a water-octane interface
Authors: Cheung David L. 
Published: June 2017

AbstractAs they contain both hydrophobic and hydrophilic amino acids proteins will readily adsorb onto interfaces between water and hydrophobic fluids such as oil. This adsorption normally causes changes in protein structure, which can result in a loss of protein function and irreversible adsorption, leading to the formation of protein interfacial films. While this can be advantageous in some applications (e.g. food technology) in most cases it limits our ability to exploit protein functionality at interfaces. To understand and control protein interfacial adsorption and function it is necessary to understand the microscopic conformation of proteins at liquid interfaces. In this paper molecular dynamics simulations are used to investigate the adsorption and conformation of two similar proteins, lysozyme andα-lactalbumin, at a water-octane interface. While they both adsorb onto the interfaceα-lactalbumin does so in a specific orientation, mediated by two amphipathic helices, while lysozyme adsorbs in a non-specific manner. Using replica exchange simulations both proteins are found to possess a number of distinct interfacial conformations, with compact states similar to the solution conformation being most common for both proteins. Decomposing the different contributions to the protein energy at oil-water interfaces, suggests that conformational change forα-lactalbumin, unlike lysozyme, is driven by favourable protein-oil interactions. Revealing these differences between the factors that govern conformational change at interfaces in otherwise similar proteins can give insight into the control of protein interfacial adsorption, aggregation, and function.
Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants
Authors: Awad Sherine , Irber Luiz , Brown C. Titus 
Published: June 2017

AbstractWe evaluate the performance of three metagenome assemblers, IDBA, MetaSPAdes, and MEGAHIT, on short-read sequencing of a defined “mock” community containing 64 genomes (Shakya et al. (2013)). We update the reference metagenome for this mock community and detect several additional genomes in the read data set. We show that strain confusion results in significant loss in assembly of reference genomes that are otherwise completely present in the read data set. In agreement with previous studies, we find that MEGAHIT performs best computationally; we also show that MEGAHIT tends to recover larger portions of the strain variants than the other assemblers.
A trapped double bond-photoisomerization intermediate in a bacterial photoreceptor
Authors: Xu Xiuling , Höppner Astrid , Zhao Kai-Hong , Gärtner Wolfgang 
Published: June 2017

AbbreviationsASUasymmetric unitBV, PCB, PVB (bilin compounds serving as chromophores)biliverdin Ixα, phycocyanobilin, phycoviolobilinCAPSON-cyclohexyl-2-hydroxyl-3-aminopropanesulfonic acidCBCRcyanobacteriochromeGAF (protein domain)cGMP-specific phosphodiesterasesadenylyl cyclases andFhlAIMACimmobilized metal-affinity chromatographyMRmolecular replacementPAS (protein domain)Per-Arnt-SimPHY (protein domain)phytochrome-specificPfr, Pg, Prfar red-, green-, and red-absorbing states of phytochromes and CBCRsSummaryThe GAF3 domain of cyanobacteriochrome Slr1393 (SynechocystisPCC6803) with anin vivoassembled phycocyanobilin (PCB) chromophore has been crystallized in parental state (1.8 Å) and photoproduct state (1.86 Å), identified by 15-Zand 15-Echromophore configuration. Comparison of both structures for the same protein allows precise determination of structural changes after photo-activation. The chromophore photoisomerization causes an outward movement and partial helix formation of a formerly unstructured loop. A tryptophan residue located in this loop, in π-π stacking distance to PCB in the dark state, moves away by 14 Å opening the binding cleft for the entry of water molecules. Also thein vitroassembled protein (chromophore addition to apo-protein) has been crystallized (1.6 Å resolution). Most importantly, an intermediate structure was solved (2.1 Å) with the protein in photoproduct conformation and the chromophore already isomerized into the parental 15-Zconfiguration, thereby giving insight into chromophore-initiated conformational protein changes.Impact StatementThis manuscript presents crystal structures of a photochromic protein in both states, before (1.6 Å) and after (1.9 Å) the light induced photochemical event with sufficient resolution to allow detailed description of conformational changes of chromophore and protein. The light driven reaction, double bond photoisomerization of a covalently bound bilin chromophore is presented here for the first time. Our results allow determining the impact of the chromophore photochemistry on the protein conformation. In addition, we succeeded in trapping an intermediate carrying the chromophore already in isomerized state with the protein still in unchanged conformation. Absorption spectra of this intermediate clearly demonstrate a color change, thus allowing conclusion that the absorption of phytochromes is predominantly determined by the chromophore conformation alone with only moderate effect of the surrounding protein.Authors’ ContributionsXX, KHZ, and WG designed the experiment. XX generated the protein. AH performed crystallization trials, collected the X-ray diffraction data and solved the structure. All authors contributed in preparing the manuscript.
Enhancing plant diversity in a novel grassland using seed addition
Authors: Zamin Tara J. , Jolly Alex , Sinclair Steve , Morgan John W. , Moore Joslin L. 
Published: June 2017

Abstract

Restoration of novel ecosystems to a historical benchmark may not always be possible or advisable. Novel ecosystems may be managed by targeting specific components and accepting the novelty of other ecosystem attributes. The feasibility of this component‐wise management of novel ecosystems has rarely been tested.

In a novel grassland, where C3 grasses have replaced C4 grasses, nutrients have been elevated, and diversity has been lost due to a history of agricultural land use, we aimed to return diversity using seed addition, without altering the dominant grass matrix or nutrient status. Using direct seeding, with and without soil disturbance, we assessed the ability of 10 species of native forbs to establish.

Eight of the 10 seeded species established in the first year. Soil disturbance increased establishment success by 50%, while high levels of exotic cover decreased it by 24%. Establishment was inversely related to total plant cover at sowing, with a 10% increase in initial plant cover decreasing establishment by 47%.

By the third year, six of the eight species persisted and five were flowering. Survival and reproduction in the third year was not associated with the soil disturbance treatment or plant cover.

Synthesis and applications. We show that native plant species can be re‐established in grasslands where abiotic and biotic conditions are novel relative to their reference state. This suggests that the conservation value of novel ecosystems can be enhanced using simple restoration tools that target specific ecosystem components.