bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards OED3: 1989–
Authors: Gilliver Peter
Published: September 2016

This chapter describes the progress of the OED project since the publication of OED2, down to the retirement of John Simpson as Chief Editor in 2013. The 1990s saw the publication of three OED Additions volumes, containing entries for new words, and the development of editorial policy and plans for the next phase of work on the Dictionary, namely the revision of its entire text. Work on revision began in 1994 and has continued ever since; the work has, however, had to be replanned several times in the light of various developments, most significantly the emergence of the World Wide Web as a medium that made it possible for revised portions of the Dictionary to be published online on a regular basis. Online publication of OED3 began in 2000; the chapter concludes with a brief survey of significant events since then.
The Islamic Lineage of American Literary Culture
Authors: Einboden Jeffrey
Published: September 2016

The Islamic Lineage of American Literary Culture maps the Middle Eastern interiors and interiority of New World authorship, tracing neglected genealogies of Islamic source reception from the Revolution to Reconstruction. Privileging informal engagements and intimate exchanges, the book uncovers Islam’s formative impact on U.S. literary origins, excavating personal and private appeals to the Qur’ān, ḥadīth, and Sufi poetry by pivotal authors of early American literature, spanning the nation’s century of self-definition, from the 1770s to the 1870s. Domesticated in a double sense, literal and literary, Muslim sources are seen to permeate the home lives and household labors of five primary American figures—Ezra Stiles, William Bentley, Washington Irving, Lydia Maria Child, and Ralph Waldo Emerson—with Islamic traditions woven into the familiar fabric of their letters and sermons, journals and journalism, memoirs and marginalia. Distinct from foregoing treatments, the book emphasizes the materiality of early American appeals to Islam, publishing images from neglected manuscripts that witness U.S. engagement with the Muslim world, exhibiting the Arabic literacy and Islamic learning cultivated by the nation’s earliest authors. The book argues that the identities and idioms of foundational American figures were catalyzed through creative, and occasionally covert, acts of Islamic engagement, with Muslim sources and Middle Eastern languages acting as vehicles of artistic reflection, religious contemplation, and political liberation.
The effects of a 50-Hz magnetic field on the cardiovascular system in rats
Authors: Zhou Ling , Wan Baoquan , Liu Xingfa , Zhang Yemao , Lai Jinsheng , Ruan Guoran , He Mengying , Chen Chen , Wang Dao Wen
Published: September 2016

A 50-Hz magnetic field (MF) is a potential health-risk factor. Its effects on the cardiovascular system have not been fully investigated. This study was conducted to explore the effects of long-term exposure to a 50-Hz MF on the cardiovascular system. In the study, an exposure system was constructed, and the distribution of the 50-Hz MF was determined. Sixty-four Sprague-Dawley (SD) rats were exposed to a 50-Hz MF at 100 μT for 24 weeks, 20 h per day, while another 64 rats were sham exposed. During the exposure, blood pressure was measured every 4 weeks. After 24 weeks, echocardiography, cardiac catheterization and electrocardiography were performed. Moreover, heart and body weight were recorded, and haematoxylin–eosin staining and real-time PCR were conducted. The results showed that compared with the sham group, exposure to a 50-Hz MF did not exert any effects on blood pressure, pulse rate, heart rate or cardiac rhythm. Furthermore, echocardiography and cardiac catheterization showed that there were no significant differences in the cardiac morphology or haemodynamics. In addition, histopathological examination showed that exposure to a 50-Hz MF had no effects on the structure of the heart. Finally, expression of the cardiac hypertrophy–related genes did not show any significant differences between the 50-Hz MF exposure group and the sham group. Taken together, in SD rats, exposure to a 50-Hz/100 μT MF for 24 weeks did not show any obvious effects on the cardiovascular system.
Postsplenectomy Prophylaxis: A Persistent Failure to Meet Standard?
Authors: Jones Alexander David , Khan Mashuk , Cheshire James , Bowley Douglas
Published: September 2016

A retrospective case review of patients that underwent emergency splenectomy or splenic preservation from May 2003 to April 2014 was undertaken at a single center. The results highlight failures in administration of postsplenectomy vaccination for emergency splenectomy patients. In this study, we highlight methods to improve postsplenectomy care.
The Role of Antimicrobial Stewardship in the Clinical Microbiology Laboratory: Stepping Up to the Plate
Authors: MacVane Shawn H. , Hurst John M. , Steed Lisa L.
Published: September 2016

We report the development of a collaborative relationship between antimicrobial stewardship and clinical microbiology that incorporates stewardship practices into daily laboratory rounds. Antimicrobial stewardship involvement on rounds was a welcomed and effective initiative with substantial rates of intervention. New opportunities to positively impact use of antimicrobials and laboratory resources were realized.
Appropriateness of Language Used in Patient Educational Materials from 24 National Anesthesiology Associations
Authors: Govender Denira , Villafranca Alexander , Hamlin Colin , Hiebert Brett , Parveen Divya , Jacobsohn Eric
Published: September 2016

Background

Patient education materials produced by national anesthesiology associations could be used to facilitate patient informed consent and promote the discipline of anesthesiology. To achieve these goals, materials must use language that most adults can understand. Health organizations recommend that materials be written at the grade 8 level or less to ensure that they are understood by laypersons. The authors, therefore, investigated the language of educational materials produced by anesthesiology associations.

Methods

Educational materials were downloaded from the Web sites of 24 national anesthesiology associations, as available. Materials were divided into eight topics, resulting in 112 separate passages. Linguistic measures were calculated using Coh-Metrix (version 3.0; Memphis, USA) linguistic software. The authors compared the measures to a grade 8 standard and examined the influence of both passage topic and country of origin using multivariate ANOVA.

Results

The authors found that 67% of associations provided online educational materials. None of the passages had all linguistic measures at or below the grade 8 level. Linguistic measures were influenced by both passage topic (F = 3.64; P < 0.0001) and country of origin (F = 7.26; P < 0.0001). Contrast showed that passages describing the role of anesthesiologists in perioperative care used language that was especially inappropriate.

Conclusions

Those associations that provided materials used words that were long and abstract. The language used was especially inappropriate for topics that are critical to facilitating patient informed consent and promoting the discipline of anesthesiology. Anesthesiology associations should simplify their materials and should consider screening their materials with linguistic software before making them public.
Brain basis of childhood speech and language disorders: are we closer to clinically meaningful MRI markers?
Authors: Morgan Angela , Bonthrone Alexandra , Liégeois Frédérique J.
Published: September 2016

Purpose of review

Developmental speech and language disorders are common, seen in one in 20 preschool children, in the absence of frank neurological deficits or intellectual impairment. They are a key reason parents seek help from paediatricians. Complex neurogenetic and environmental contributions underpin the disorders, yet few specific causes are known. With the advent of quantitative brain imaging, a growing number of studies have investigated neural contributions. Here, we discuss current MRI approaches and recent findings (January 2014–June 2016) in the field.

Recent findings

Five relevant studies were identified (n = 3 – speech disorder and n = 2 – language disorder). Significant variability in MRI approaches and heterogeneity of participant phenotypes was seen. Children with speech disorder had structural and functional anomalies in the left supramarginal gyrus and functional anomalies in the posterior cerebellum bilaterally – regions critical for sensory–motor integration or feedback. Children with language disorder showed increased mean and radial diffusivity of the left arcuate fasciculus, although a widespread cortical and subcortical network of regions was implicated.

Limited evidence exists for specific regional brain anomalies in this population. MRI prognostic markers of speech and language ability are not currently available at an individual level. Further work is required to disentangle neurobiological contributions to speech and language disorders for affected children.
Characteristics of EEG Interpreters Associated With Higher Interrater Agreement
Authors: Halford Jonathan J. , Arain Amir , Kalamangalam Giridhar P. , LaRoche Suzette M. , Leonardo Bonilha , Basha Maysaa , Azar Nabil J. , Kutluay Ekrem , Martz Gabriel U. , Bethany Wolf J. , Waters Chad G. , Dean Brian C.
Published: September 2016

Purpose:

The goal of the project is to determine characteristics of academic neurophysiologist EEG interpreters (EEGers), which predict good interrater agreement (IRA) and to determine the number of EEGers needed to develop an ideal standardized testing and training data set for epileptiform transient (ET) detection algorithms.

Methods:

A three-phase scoring method was used. In phase 1, 19 EEGers marked the location of ETs in two hundred 30-second segments of EEG from 200 different patients. In phase 2, EEG events marked by at least 2 EEGers were annotated by 18 EEGers on a 5-point scale to indicate whether they were ETs. In phase 3, a third opinion was obtained from EEGers on any inconsistencies between phase 1 and phase 2 scoring.

Results:

The IRA for the 18 EEGers was only fair. A select group of the EEGers had good IRA and the other EEGers had low IRA. Board certification by the American Board of Clinical Neurophysiology was associated with better IRA performance but other board certifications, years of fellowship training, and years of practice were not. As the number of EEGers used for scoring is increased, the amount of change in the consensus opinion decreases steadily and is quite low as the group size approaches 10.

Conclusions:

The IRA among EEGers varies considerably. The EEGers must be tested before use as scorers for ET annotation research projects. The American Board of Clinical Neurophysiology certification is associated with improved performance. The optimal size for a group of experts scoring ETs in EEG is probably in the 6 to 10 range.
Occipito-Frontal Sharp Waves—An Under-Recognized Electroencephalogram Pattern in Self-Limited Idiopathic Childhood Focal Epilepsy
Authors: Wyllie Elaine , Moosa Ahsan N. V.
Published: September 2016

We report four children who highlight the potentially under-recognized electroencephalogram pattern of bilaterally synchronous occipito-frontal sharp waves, which may occur in children with Panayiotopoulos type self-limited childhood epilepsy but may be easily confused with the patterns of symptomatic generalized epilepsy. Our patients were young, healthy children who had infrequent, predominantly nocturnal, fairly prolonged seizures characterized by altered consciousness, vomiting, and autonomic features, or in one case nocturnal secondary generalized tonic-clonic convulsion. Their electroencephalograms showed stereotyped abundant sleep-activated sharp waves with maximum negativity in bilateral occipital and frontal greater than centro-temporo-parietal regions. On a “double-banana” bipolar montage, the sharp waves had upward deflections in frontal electrodes, downward deflections at occipital electrodes, and a positive phase reversal in the middle of each chain. The lower-amplitude occipital discharges slightly preceded the frontal discharges, consistent with posterior-to-anterior propagation likely originating from mesial occipital regions. In the proper clinical context, recognizing the electroencephalogram pattern of bilateral occipito-frontal sharp waves affords confidence in a favorable prognosis, presents the option to possibly defer daily treatment with antiepileptic medication, and shifts the emphasis to rescue medication for isolated seizures.
The outer membrane phospholipase A is essential for membrane integrity and type III secretion in
Shigella flexneri
Authors: Wang Xia , Jiang Feng , Zheng Jianhua , Chen Lihong , Dong Jie , Sun Lilian , Zhu Yafang , Liu Bo , Yang Jian , Yang Guowei , Jin Qi
Published: September 2016

Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in
Escherichia coli
and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in
Shigella flexneri
, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the
ΔpldA
mutant strain. Furthermore, the
ΔpldA
mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support that PldA, which is widespread across Gram-negative bacteria, is an important factor for the bacterial life cycle, particularly in human pathogens.
A role for the p53 tumour suppressor in regulating the balance between homologous recombination and non-homologous end joining
Authors: Moureau Sylvie , Luessing Janna , Harte Emma Christina , Voisin Muriel , Lowndes Noel Francis
Published: September 2016

Loss of p53, a transcription factor activated by cellular stress, is a frequent event in cancer. The role of p53 in tumour suppression is largely attributed to cell fate decisions. Here, we provide evidence supporting a novel role for p53 in the regulation of DNA double-strand break (DSB) repair pathway choice. 53BP1, another tumour suppressor, was initially identified as p53 Binding Protein 1, and has been shown to inhibit DNA end resection, thereby stimulating non-homologous end joining (NHEJ). Yet another tumour suppressor, BRCA1, reciprocally promotes end resection and homologous recombination (HR). Here, we show that in both human and mouse cells, the absence of p53 results in impaired 53BP1 focal recruitment to sites of DNA damage induced by ionizing radiation. This effect is largely independent of cell cycle phase and the extent of DNA damage. In p53-deficient cells, diminished localization of 53BP1 is accompanied by a reciprocal increase in BRCA1 recruitment to DSBs. Consistent with these findings, we demonstrate that DSB repair via NHEJ is abrogated, while repair via homology-directed repair (HDR) is stimulated. Overall, we propose that in addition to its role as an ‘effector’ protein in the DNA damage response, p53 plays a role in the regulation of DSB repair pathway choice.
GWAS for serum galactose-deficient IgA1 implicates critical genes of theO-glycosylation pathway
Authors: Kiryluk Krzysztof , Li Yifu , Moldoveanu Zina , Suzuki Hitoshi , Reily Colin , Hou Ping , Xie Jingyuan , Mladkova Nikol , Prakash Sindhuri , Fischman Clara , Shapiro Samantha , LeDesma Robert A. , Bradbury Drew , Ionita-Laza Iuliana , Eitner Frank , Rauen Thomas , Maillard Nicolas , Berthoux Francois , Floege Jürgen , Chen Nan , Zhang Hong , Scolari Francesco , Wyatt Robert J. , Julian Bruce A. , Gharavi Ali G. , Novak Jan
Published: September 2016

AberrantO-glycosylation of serum immunoglobulin A1 (IgA1) represents a heritable pathogenic defect in IgA nephropathy, the most common form of glomerulonephritis worldwide, but specific genetic factors involved in its determination are not known. We performed a quantitative GWAS for serum levels of galactose-deficient IgA1 (Gd-IgA1) in 2,633 subjects of European and East Asian ancestry and discovered two genome-wide significant loci, inC1GALT1(rs13226913,P= 3.2 × 10−11) andC1GALT1C1(rs5910940,P= 2.7 × 10−8). These genes encode molecular partners essential for enzymaticO-glycosylation of IgA1. We demonstrated that these two loci explain approximately 7% of variability in circulating Gd-IgA1 in Europeans, but only 2% in East Asians. Notably, the Gd-IgA1-increasing allele of rs13226913 is common in Europeans, but rare in East Asians. Moreover, rs13226913 represents a strong cis-eQTL forC1GALT1,which encodes the key enzyme responsible for the transfer of galactose toO-linked glycans on IgA1. Byin vitrosiRNA knock-down studies, we confirmed that mRNA levels of bothC1GALT1andC1GALT1C1determine the rate of secretion of Gd-IgA1 in IgA1-producing cells. Our findings provide novel insights into the genetic regulation ofO-glycosylation and are relevant not only to IgA nephropathy, but also to other complex traits associated withO-glycosylation defects, including inflammatory bowel disease, hematologic disease, and cancer.

Author Summary

O-glycosylation is a common type of post-translational modification of proteins; specific abnormalities in the mechanism ofO-glycosylation have been implicated in cancer, inflammatory and blood diseases. However, the molecular basis of abnormalO-glycosylation in these complex disorders is not known. We studied the genetic basis of defectiveO-glycosylation of serum Immunoglobulin A1 (IgA1), which represents the key pathogenic defect in IgA nephropathy, the most common form of primary glomerulonephritis worldwide. We report our results of the first genome-wide association study for this trait using serum assays in 2,633 individuals of European and East Asian ancestry. In our genome scan, we observed two significant signals with large effects, on chromosomes 7p21.3 and Xq24, jointly explaining about 7% of trait variability. These signals implicate two genes that encode molecular partners essential for enzymaticO-glycosylation of IgA1 and mucins, and represent potential new targets for therapy.
Nuclear pore-like structures in a compartmentalized bacterium
Authors: Sagulenko Evgeny , Nouwens Amanda , Webb Richard I. , Green Kathryn , Yee Benjamin , Morgan Garry , Leis Andrew , Lee Kuo-Chang , Butler Margaret K. , Chia Nicholas , Phuong Pham Uyen Thi , Lindgreen Stinus , Catchpole Ryan , Poole Anthony M. , Fuerst John A
Published: September 2016

Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomyceteGemmata obscuriglobuscontains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes ofG.obscuriglobusand that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of theG. obscuriglobusproteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immuno-gold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to theG. obscuriglobuspore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.
Neural correlates of early sound encoding and their relationship to speech in noise perception
Authors: Coffey Emily B.J. , Chepesiuk Alexander M.P. , Herholz Sibylle C. , Baillet Sylvain , Zatorre Robert J.
Published: September 2016

Speech-in-noise (SIN) perception is a complex cognitive skill that affects social, vocational, and educational activities. Poor SIN ability particularly affects young and elderly populations, yet varies considerably even among healthy young adults with normal hearing. Although SIN skills are known to be influenced by top-down processes that can selectively enhance lower-level sound representations, the complementary role and of feed-forward mechanisms and their relationship to musical training is poorly understood. Using a paradigm that eliminates the main top-down factors that have been implicated in SIN performance, we aimed to better understand how robust encoding of periodicity in the auditory system (as measured by the frequency-following response) contributes to SIN perception. Using magnetoencephalograpy, we found that the strength of encoding at the fundamental frequency in the brainstem, thalamus, and cortex is correlated with SIN accuracy, as was the amplitude of the slower cortical P2 wave, and these enhancements were related to the extent and timing of musicianship. These results are consistent with the hypothesis that basic feed-forward sound encoding affects SIN perception by providing better information to later processing stages, and that modifying this process may be one mechanism through which musical training might enhance the auditory networks that subserve both musical and language functions.

Highlights

–

Enhancements in periodic sound encoding are correlated with speech-in-noise ability

–

This effect is observed in the absence of contextual cues and task demands

–

Better encoding is observed throughout the auditory system and is right-lateralized

–

Stronger encoding is related to stronger subsequent secondary auditory cortex activity

–

Musicianship is related to both speech-in-noise perception and enhanced MEG signals
shinyheatmap: ultra fast low memory heatmap web interface for big data genomics
Authors: Khomtchouk Bohdan B. , Hennessy James R. , Wahlestedt Claes
Published: September 2016

Background

Transcriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics. For example, rendering interactive heatmaps from large input datasets (e.g., 100k+ rows) has been computationally infeasible on both desktop computers and web browsers. In addition to memory requirements, programming skills and knowledge have frequently been barriers-to-entry for creating highly customizable heatmaps.

Results

We propose shinyheatmap: an advanced user-friendly heatmap software suite capable of efficiently creating highly customizable static and interactive biological heatmaps in a web browser. shinyheatmap is a low memory footprint program, making it particularly well-suited for the interactive visualization of extremely large datasets that cannot typically be computed in-memory due to size restrictions. Also, shinyheatmap features a built-in high performance web plug-in, fastheatmap, for rapidly plotting interactive heatmaps of datasets as large as 105− 107rows within seconds, effectively shattering previous performance benchmarks of heatmap rendering speed.

Conclusions

shinyheatmap is hosted online as a freely available web server with an intuitive graphical user interface:http://shinyheatmap.com. The methods are implemented in R, and are available as part of the shinyheatmap project at:https://github.com/Bohdan-Khomtchouk/shinyheatmap. Users can access fastheatmap directly from within the shinyheatmap web interface, and all source code has been made publicly available on Github:https://github.com/Bohdan-Khomtchouk/fastheatmap.
Frontal cortex function derives from hierarchical predictive coding
Authors: Alexander William H , Brown Joshua W
Published: September 2016

The frontal lobes are essential for human volition and goal-directed behavior, yet their function remains unclear. While various models have highlighted working memory, reinforcement learning, and cognitive control as key functions, a single framework for interpreting the range of effects observed in prefrontal cortex has yet to emerge. Here we show that a simple computational motif based on predictive coding can be stacked hierarchically to learn and perform arbitrarily complex goal-directed behavior. The resulting Hierarchical Error Representation (HER) model simulates a wide array of findings from fMRI, ERP, single-units, and neuropsychological studies of both lateral and medial prefrontal cortex. Additionally, the model compares favorably with current machine learning approaches, learning more rapidly and with comparable performance, while self-organizing representations into efficient hierarchical groups and managing working memory storage. By reconceptualizing lateral prefrontal activity as anticipating prediction errors, the HER model provides a novel unifying account of prefrontal cortex function with broad implications both for understanding the frontal cortex and building more powerful machine learning applications.
In vitroprofiling of endocrine cell death using UCHL1 and GAD65 as soluble biomarkers
Authors: Brackeva Benedicte , Roels Sarah , Stangé Geert , Ates Gamze , Costa Olivier R. , Ling Zhidong , Gorus Frans K. , Martens Geert A.
Published: September 2016

BACKGROUND

Pancreatic islet grafts are culturedin vitroprior to transplantation and this is associated to a variable degree of beta cell loss. Optimization of culture conditions is currently hampered by the lack of a specific and sensitivein vitroindicator of beta cell death.

METHODS

We developed a high-sensitivity duplex bead-based immunoassay for two protein-type biomarkers of beta cell destruction, GAD65 and UCHL1, and investigated its proficiency forin vitrotoxicity profiling on rodent and human beta cells, as compared to a semi-automatic and manual image-based assessment of beta cell death, andin vivoafter intraportal islet transplantation.

RESULTS

Both GAD65 and UCHL1 were discharged by necrotic and apoptotic beta cells proportionate to the number of dead beta cells as counted by microscopic methods.In vitro, UCHL1 was superior to GAD65, in terms of biomarker stability providing more sensitive detection of low grade beta cell death.In vivo, however, GAD65 was consistently detected after islet transplantation while UCHL1 remained undetectable.

CONCLUSION

The use of soluble biomarkers represents a fast, selective and sensitive method for beta cell toxicity profilingin vitro. UCHL1 is superior to GAD65in vitrobut notin vivo.
Probabilistic inference of bifurcations in single-cell data using a hierarchical mixture of factor analysers
Authors: Campbell Kieran R. , Yau Christopher
Published: September 2016

Modelling bifurcations in single-cell transcriptomics data has become an increasingly popular field of research. Several methods have been proposed to infer bifurcation structure from such data but all rely on heuristic non-probabilistic inference. Here we propose the first generative, fully probabilistic model for such inference based on a Bayesian hierarchical mixture of factor analysers. Our model exhibits competitive performance on large datasets despite implementing full MCMC sampling and its unique hierarchical prior structure enables automatic determination of genes driving the bifurcation process.
Reading positional codes with fMRI: Problems and solutions
Authors: Kalm Kristjan , Norris Dennis
Published: September 2016

Neural mechanisms which bind items into sequences have been investigated in a large body of research in animal neurophysiology and human neuroimaging. However, a major problem in interpreting this data arises from a fact that several unrelated processes, such as memory load, sensory adaptation, and reward expectation, also change in a consistent manner as the sequence unfolds. In this paper we show that the problem of extracting neural data about the structure of a sequence is especially acute for fMRI, which is almost exclusively the modality used in human experiments. We show that such fMRI results must be treated with caution and in many cases the assumed neural representation might actually reflect unrelated processes.
Parasitic Infection byPseudocapillaria tomentosais Associated with a Longitudinal Restructuring of the Zebrafish Gut Microbiome
Authors: Gaulke Christopher A. , Martins Mauricio L , Watral Virginia , Kent Michael L. , Sharpton Thomas J.
Published: September 2016

Helminth parasites represent a significant threat to wild, domesticated, and research animal health.Pseudocapillaria tomentosais a common intestinal nematode parasite and an important source of infection in zebrafish. Symptoms of the infection vary widely from no clinical signs to sever emaciation and mortality, however, the reasons underpinning these disparate outcomes are unclear. Components of the microbiome may interact with parasites to influence their success in the gut while parasite infections are also known to influence the composition of the gut microbiome. In this study we evaluated the longitudinal changes in the gut microbiome structure and gut physiology during experimentalP. tomentosainfection in adult 5D line zebrafish. We observed less severe signs of infection and less mortality in these fish than previously described in AB line fish. However, inflammation and epithelial hyperplasia in the intestine was still observed in infected 5D line fish. The composition of the microbiome changed rapidly during the infection and these changes were associated with parasite stage of development and burden. Individual taxa covaried with parasite abundance in the intestine intimating the gut microbiome may influence parasite burden. Associations between taxa and parasite abundance in some cases appeared to be phylogenetically patterned. Strong positive associations were observed between OTUs phylotyped to Proteobacteria and abundance of adult parasites and parasite eggs. Together these experiments demonstrate thatP. tomentosainfection results in a rapid and temporally dynamic disruption of the zebrafish gut microbiome and clarify how interactions between the gut microbiome and intestinal parasites may impact fish populations.
Data Aggregation at the Level of Molecular Pathways Improves Stability of Experimental Transcriptomic and Proteomic Data
Authors: Borisov Nicolas , Suntsova Maria , Garazha Andrew , Lezhnina Ksenia , Kovalchuk Olga , Aliper Alexander , Ilnitskaya Elena , Sorokin Maxim , Korzinkin Mihkail , Saenko Vyacheslav , Saenko Yury , Sokov Dmitry G. , Gaifullin Nurshat M. , Kashintsev Kirill , Shirokorad Valery , Shabalina Irina , Zhavoronkov Alex , Mishra Bhubaneswar , Cantor Charles R. , Buzdin Anton
Published: September 2016

High throughput technologies opened a new era in biomedicine by enabling massive analysis of gene expression at both RNA and protein levels. Unfortunately, expression data obtained in different experiments are often poorly compatible, even for the same biological samples. Here, using experimental and bioinformatic investigation of major experimental platforms, we show that aggregation of gene expression data at the level of molecular pathways helps to diminish cross- and intra-platform bias otherwise clearly seen at the level of individual genes. We created a mathematical model of cumulative suppression of data variation that predicts the ideal parameters and the optimal size of a molecular pathway. We compared the abilities to aggregate experimental molecular data for the five alternative methods, also evaluated by their capacity to retain meaningful features of biological samples. The bioinformatic method OncoFinder showed optimal performance in both tests and should be very useful for future cross-platform data analyses.
PDGF signaling directs cardiomyocyte movement toward the midline during heart tube assembly
Authors: Bloomekatz Joshua , Singh Reena , Prall Owen W.J. , Dunn Ariel C. , Vaughan Megan , Loo Chin-San , Harvey Richard P. , Yelon Deborah
Published: September 2016

Communication between neighboring tissues plays a central role in guiding organ morphogenesis. During heart tube assembly, interactions with the adjacent endoderm control the medial movement of cardiomyocytes, a process referred to as cardiac fusion. However, the molecular underpinnings of this endodermal-myocardial relationship remain unclear. Here, we show an essential role for platelet-derived growth factor receptor alpha (Pdgfra) in directing cardiac fusion. In both zebrafish and mouse, mutation ofpdgfrainhibits cardiac fusion and can lead to cardia bifida. Timelapse analysis of individual cardiomyocyte trajectories reveals misdirected cells in zebrafishpdgframutants, suggesting that PDGF signaling steers cardiomyocytes toward the midline. Intriguingly, the ligandpdgfaais expressed in the endoderm medial to thepdgfra-expressing myocardial precursors. Ectopic expression ofpdgfaainterferes with cardiac fusion, consistent with an instructive role for PDGF signaling. Together, these data uncover a novel mechanism through which endodermal-myocardial communication guides the cell movements that initiate cardiac morphogenesis.

IMPACT STATEMENT

Studies in zebrafish and mouse implicate the PDGF signaling pathway in the communication between the endoderm and the myocardium that drives medial myocardial movement and thereby initiates cardiac morphogenesis.
Layout validation and re-configuration in Plug&Produce systems
Authors: Neves Pedro , Ribeiro Luis , Dias-Ferreira João , Onori Mauro , Barata Oliveira José
Published: September 2016

Purpose

This paper aims to provide a method and decision support tool to enhance swift reconfiguration of Plug&Produce (P&P) systems in the presence of continuously changing production orders.

Design/methodology/approach

The paper reviews different production scenarios and system design and configuration methods and more particularly specifies the need of decision support tools for P&P systems that integrate configuration and planning activities. This problem is then addressed by proposing a method that helps reduce the solution space of the reconfiguration problem and allows the timely selection of the most promising reconfiguration alternative.

Findings

The proposed method was found to be helpful in reducing the reconfiguration alternatives that need to be considered and in selecting the most promising one for different orders. The advantages and limitations of this method are identified, and an illustrative test case of the approach is presented, corroborating the method applicability in the absence of large queues in the system.

Originality/value

This paper addresses a less explored domain within the P&P systems research field, which is the system reconfiguration. It proposed a method to support system validation and reconfiguration jointly with an illustrative test case. This represents an original contribution to the P&P research field, and it can have impact in improving agility and decreasing the complexity of reconfiguration activities to cope with constantly changing production orders.
An automated assembly technology for large mobile radar antenna
Authors: Peng Gaoliang , Sun Yu , Han Rui , Li Chuanhao
Published: September 2016

Purpose

Large-scale mobile radars are still erected manually by using lifting equipment, which often fails to meet the requirements on precision, quality and efficiency in the erecting process. This paper aims to introduce techniques for automatic assembly of large mobile radar antenna.

Design/methodology/approach

A large-scale metrology system for accurate identification of the positions and orientation of the radar antenna components is presented. A novel three-degree-of-freedom parallel mechanism is designed to realize orientation adjustment of three axes synchronous, and, thus guarantees the efficiency and accuracy of positioning process.

Findings

The system described in this paper is practicable in outdoor environment and provides a holistic solution that gives full consideration of the operation conditions and the environmental influences. In performance evaluation tests, the measured absolute accuracy is less than ±1 mm and repeatability is less than ±0.5 mm in the positioning task for 10 × 3 m large antenna.

Originality/value

This paper presents a new concept of an automatic assembly technology for the large radar antenna application.
Method of estimation of corrosion stability of multicomponent alloys using equilibrium and polarization potential – pH diagrams
Authors: Tyurin Aleksandr Georgievich , Manannikov Dmitriy Andreevich , Parshukov Vladimir Pavlovich , Antonova Anna Valeryevna , Nikolaychuk Pavel Anatolyevich
Published: September 2016

Purpose

The purpose of this study is to develop a method of thermodynamic and kinetic evaluation of corrosion properties of alloys.

Design/methodology/approach

Method of estimation of corrosion-electrochemical behaviour of multicomponent alloys is proposed. The method takes into account both thermodynamic and kinetic data and is based on mutual construction of equilibrium and polarization potential – pH diagrams. The usage of the proposed method is illustrated in the example of the structural steel 20KT.

Findings

Passivation of steel 20KT is determined by formation of oxide film based on magnetite (Fe3O4); silicon, manganese and copper oxides as well as manganese sulphides can be locally included into the inner side of the passivation layer. An experimental potential – pH diagram of steel 20KT is constructed. Interpreting the results of polarization measurements revealed good agreement between equilibrium and polarization potential – pH diagrams.

Originality/value

It is shown in the example of structural steel 20KT that for interpretation of experimental potential – pH diagrams, one should compare them with corresponding equilibrium diagrams for multicomponent alloys rather than with Pourbaix diagrams for pure metals. The corrosion properties of steel 20KT are estimated using equilibrium and polarization potential – pH diagrams.
Averting risk or embracing opportunity? Exploring the impact of ambidextrous capabilities on innovation of Chinese firms in internationalization
Authors: Zhou Yu , Lu Lu , Chang Xiaoxi
Published: September 2016

Purpose

The purpose of this paper is to examine the impacts of ambidextrous capabilities, explorative capability and exploitative capability on product innovation performance in the context of internationalization and cross-cultural environment; and to examine the moderating effects of CEO’s preference of risks and opportunities in the international market on the relationship between ambidextrous capabilities and multinational enterprises’ (MNEs) product innovation performance.

Design/methodology/approach

Data were collected from 189 MNEs located in China, which develop international business through export, outsourcing, foreign equity investment or foreign direct investment. Measurement reliability and validity were examined and hierarchical linear regression was used to test the hypotheses.

Findings

Results indicated that both explorative and exploitative capability are positively related to MNEs’ new product development and commercialization of Chinese MNEs; and CEO’s preference of risks and opportunities in international market plays a significant moderating role in the two phases of product innovation.

Research limitations/implications

This study extends organizational ambidextrous capabilities theory to better understand the effects of explorative capability and exploitative capability on innovation performance in the context of internationalization and national cultural differences. Sample constitution is a possible limitation.

Practical implications

MNEs, especially those from emerging economies, should develop both explorative and exploitative capability to be flexible and competitive in dealing with cultural differences. fully take risks and opportunities should be taken into consideration regarding the international market and national cultural differences, and take an effective contingency strategy, driven by the ambidextrous capabilities toward new product innovation development and commercialization.

Originality/value

An empirical examination of how ambidextrous capabilities impact on Chinese MNEs’ new product development and commercialization connects the organizational ambidexterity theory to the innovation and characteristics of upper echelons.
Managing digital records in a global environment
Authors: Katuu Shadrack
Published: September 2016

Purpose

This paper aims to widen as well as deepen the discussion on standards and good practice guidelines beyond just local or regional efforts and include international developments.

Design/methodology/approach

An extensive review of literature was used to develop an outline of existing standards and good practice guidelines that are used by records management professionals to manage digital records.

Findings

The analysis reveals that there has been a long tradition in standards and good practice guidelines development dating back to the 1980s. The study also reveals that there are two broad categories of standards and good practice guidelines, those with assessment mechanisms and those without such mechanisms. The choice of whether to have an assessment mechanism depends on the purpose for which a standard or good practice guideline is developed.

Originality/value

The paper explores an extensive array of standards and good practice guidelines, their utility and their geographical coverage. It demonstrates how different terms such as Electronic Records Management Systems, Electronic Document Management Systems, Electronic Document and Records Management Systems and Enterprise Content Management have been used without much clarity on how these terms relate to each other, and proposes a clarification framework.
The status of open access library and information science journals in SSCI
Authors: Chen Ming , Du Yunfei
Published: September 2016

Purpose

The main purpose of this paper is to measure the status and quality of library and information science (LIS) open-access (OA) journals in the Social Science Citation Index (SSCI).

Design/methodology/approach

The study selected 86 source journals of LIS in the SSCI as a sample and measured their status of open access. Analytic hierarchy process (AHP) was used to analyze 36 OA journals of 86 source journals, especially their production capability, academic influence and network communication ability.

Findings

The results indicate that OA journals have become an increasingly important part of LIS journals. Production capability, academic influence and network communication ability are important factors affecting the quality of OA journals. These three evaluation indicators of LIS OA journals are high, but many still have room for improvement.

Research limitations/implications

As the paper is limited by collecting data, the indicators of OA journals’ quality are not all-around. So, they cannot reflect the quality of LIS OA journals. In the selection of the evaluation method, the evaluation results are limited because only one AHP method is used.

Practical implications

The research on evaluation of OA journals can help library and scientific research personnel use OA journals effectively. Identifying key factors on evaluation can help researchers to construct OA journals better.

Social implications

The research on OA journals’ quality can also promote the study on OA process in academic circles and promote the communication, development and utilization of academic information. Such research can also enrich the theory of OA, and provide some new perspectives for the study of journals’ evaluation.

Originality/value

This paper measures the quality of LIS OA journals by analyzing production capability, academic influence and network communication ability. Rather than the traditional research methods, the focus of this study is on the value of the Web as a source of impact indices. It contributes to the scholarly impact measurements of OA journals.
I feel like a hypocrite: a beginning teacher’s disconnect between beliefs and practice
Authors: Knotts Michelle
Published: September 2016

Purpose

This study aims to examine the lived experiences of a beginning teacher to understand the constraints and possibilities she faces in moving from a critically minded preservice teacher toward a critical educator during her first year of teaching secondary English Language Arts at a public high school in the Southwestern USA.

Design/methodology/approach

This research was conducted as a qualitative case study. The data set was collected through interviews, documents and observations. Data were analyzed inductively using open coding techniques and grounded theory in order to establish themes.

Findings

The research describes three themes: losing a sense of self, losing hope and losing sight. These themes explore in order to illustrate the participant’s sense of loss, the disconnect between her stated beliefs and practice and how contextual factors contribute to her experiences.

Practical implications

The paper includes recommendations for teacher induction and undergraduate initial teacher education.

Originality/value

This research contributes to the literature about beginning teachers and their challenges to realize their stated beliefs in practice. It extends this body of literature with a specific focus on criticality and an exploration of how the current corporate reform paradigm impacts beginning teachers and how these topics can be taken up in teacher education.
Grab those teachable moments! (On teacher identities and student learning)
Authors: Keranova Hristina
Published: September 2016

Purpose

This study aims to use the works of Bakhtin and theorists who further developed his ideas to show the struggle teachers go through in trying to balance different identities in the classroom and the effect of that process on student learning.

Design/methodology/approach

The author-transcribed observations and interviews are analyzed using ATLAS.ti qualitative research software, and narrative vignettes are used for data representation.

Findings

It gives a glimpse of the difficulty in making choices when professional identities, based on established criteria for professionalism and determining self-esteem, are at stake. The two vignettes used to represent the data blend the informative with the evocative and dramatize the readers’ perception by giving voice to the participants.

Originality/value

The study illustrates the importance of adapting fossilized teacher identities to the specificity of each classroom to support student learning.