bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Academic Spoken Word List
Authors: Dang Thi Ngoc Yen , Coxhead Averil , Webb Stuart 
Published: September 2017

AbstractThe linguistic features of academic spoken English are different from those of academic written English. Therefore, for this study, an Academic Spoken Word List (ASWL) was developed and validated to help second language (L2) learners enhance their comprehension of academic speech in English‐medium universities. The ASWL contains 1,741 word families with high frequency and wide range in an academic spoken corpus totaling 13 million words. The list, which features vocabulary from 24 subjects across four equally sized disciplinary subcorpora, is graded into four levels according to Nation's British National Corpus and Corpus of Contemporary American English lists, and each level is divided into sublists of function words and lexical words. Depending on their vocabulary levels, language learners may reach 92–96% coverage of academic speech with the aid of the ASWL.Open PracticesThis article has been awarded Open Materials and Open Data badges. The composition of the corpora, the Academic Spoken Word List, and sublists are publicly accessible via the Open Science Framework at https://osf.io/gwk45 and the IRIS digital repository at http://www.iris‐database.org. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.
The unusual S locus of Leavenworthia is composed of two sets of paralogous loci
Authors: Chantha Sier‐Ching , Herman Adam C. , Castric Vincent , Vekemans Xavier , Marande William , Schoen Daniel J. 
Published: September 2017

Summary

The Leavenworthia self‐incompatibility locus (S locus) consists of paralogs (Lal2, SCRL) of the canonical Brassicaceae S locus genes (SRK, SCR), and is situated in a genomic position that differs from the ancestral one in the Brassicaceae. Unexpectedly, in a small number of Leavenworthia alabamica plants examined, sequences closely resembling exon 1 of SRK have been found, but the function of these has remained unclear.

BAC cloning and expression analyses were employed to characterize these SRK‐like sequences.

An SRK‐positive Bacterial Artificial Chromosome clone was found to contain complete SRK and SCR sequences located close by one another in the derived genomic position of the Leavenworthia S locus, and in place of the more typical Lal2 and SCRL sequences. These sequences are expressed in stigmas and anthers, respectively, and crossing data show that the SRK/SCR haplotype is functional in self‐incompatibility. Population surveys indicate that < 5% of Leavenworthia S loci possess such alleles.

An ancestral translocation or recombination event involving SRK/SCR and Lal2/SCRL likely occurred, together with neofunctionalization of Lal2/SCRL, and both haplotype groups now function as Leavenworthia S locus alleles. These findings suggest that S locus alleles can have distinctly different evolutionary origins.
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives
Authors: Tedersoo Leho , Tooming‐Klunderud Ave , Anslan Sten 
Published: September 2017

Summary

Second‐generation, high‐throughput sequencing methods have greatly improved our understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) provide limited taxonomic and phylogenetic information for species discrimination and taxonomic assignment.

Here, we utilized the third‐generation Pacific Biosciences (PacBio) RSII and Sequel instruments to evaluate the suitability of full‐length internal transcribed spacer (ITS) barcodes and longer rRNA gene amplicons for metabarcoding Fungi, Oomycetes and other eukaryotes in soil samples.

Metabarcoding revealed multiple errors and biases: Taq polymerase substitution errors and mis‐incorporating indels in sequencing homopolymers constitute major errors; sequence length biases occur during PCR, library preparation, loading to the sequencing instrument and quality filtering; primer–template mismatches bias the taxonomic profile when using regular and highly degenerate primers.

The RSII and Sequel platforms enable the sequencing of amplicons up to 3000 bp, but the sequence quality remains slightly inferior to Illumina sequencing especially in longer amplicons. The full ITS barcode and flanking rRNA small subunit gene greatly improve taxonomic identification at the species and phylum levels, respectively. We conclude that PacBio sequencing provides a viable alternative for metabarcoding of organisms that are of relatively low diversity, require > 500‐bp barcode for reliable identification or when phylogenetic approaches are intended.
Stationary Expansion Shocks for a Regularized Boussinesq System
Authors: El Gennady A. , Hoefer Mark A. , Shearer Michael 
Published: September 2017

AbstractStationary expansion shocks have been identified recently as a new type of solution to hyperbolic conservation laws regularized by nonlocal dispersive terms that naturally arise in shallow‐water theory. These expansion shocks were studied previously for the Benjamin‐Bona‐Mahony (BBM) equation using matched asymptotic expansions. In this paper, we extend the BBM analysis to the regularized Boussinesq system by using Riemann invariants of the underlying dispersionless shallow‐water equations. The extension for a system is nontrivial, requiring a combination of small amplitude, long‐wave expansions with high order matched asymptotics. The constructed asymptotic solution is shown to be in excellent agreement with accurate numerical simulations of the Boussinesq system for a range of appropriately smoothed Riemann data.
Comparison of one commercial and two in‐house TaqMan multiplex real‐time PCR assays for detection of enteropathogenic, enterotoxigenic and enteroaggregative Escherichia coli
Authors: Hahn Andreas , Luetgehetmann Marc , Landt Olfert , Schwarz Norbert Georg , Frickmann Hagen 
Published: September 2017

AbstractObjectiveEnteropathogenic, enterotoxigenic and enteroaggregative Escherichia coli (EPEC, ETEC, EAEC) are among the most frequent causes of diarrhoea during travel or on military deployments. Cost‐efficient and reliable real‐time multiplex PCR (mPCR) assays are desirable for surveillance or point prevalence studies in remote and resource‐limited tropical settings. We compared one commercial PCR kit and two in‐house assays without using a gold standard to estimate sensitivity and specificity of each assay.MethodsResidual materials from nucleic acid extractions of stool samples from two groups with presumably different prevalences and increased likelihood of being infected or colonised by diarrhoeagenic E. coli were included in the assessment. One group comprised samples from returnees from tropical deployments, the second group was of migrants and study participants from high‐endemicity settings. Each sample was assessed with all of the PCR assays. Cycle threshold (Ct) values were descriptively compared.ResultsThe calculated sensitivities for the commercial test vs. the in‐house tests were for EPEC 0.84 vs. 0.89 and 0.96, for ETEC 0.83 vs. 0.76 and 0.61, and for EAEC 0.69 vs. 0.54 and 0.69. False positive results were rare – specificity was 0.94 and 0.97 for two EPEC tests and 1.0 for all other tests. Most positive samples had late Ct values corresponding to low quantities of pathogens. Discordant test results were associated with late Ct values.ConclusionsAs commercial and in‐house assays showed comparable results, in‐house tests can be assumed to be safe while affording considerable savings, making them a valuable alternative for surveillance testing in resource‐limited tropical areas.
Cryopreserved platelets demonstrate reduced activation responses and impaired signaling after agonist stimulation
Authors: Waters Lauren , Padula Matthew P. , Marks Denese C. , Johnson Lacey 
Published: September 2017

BACKGROUNDRoom temperature–stored (20‐24°C) platelets (PLTs) have a shelf life of 5 days, making it logistically challenging to supply remote medical centers with PLT products. Cryopreservation of PLTs in dimethyl sulfoxide (DMSO) and storage at –80°C enables an extended shelf life up to 2 years. Although cryopreserved PLTs have been widely characterized under resting conditions, their ability to undergo agonist‐induced activation is yet to be fully explored.STUDY DESIGN AND METHODSBuffy coat PLTs were cryopreserved at –80°C with 5% to 6% DMSO and sampled before freezing and after thawing. PLTs were analyzed under resting conditions and after agonist stimulation with adenosine diphosphate, collagen, or thrombin receptor–activating peptide‐6. The expression of activation markers, microparticle formation, and calcium mobilization were analyzed by flow cytometry. Soluble PLT proteins present in the PLT supernatant were examined by enzyme‐linked immunosorbent assay. Protein phosphorylation was investigated with Western blotting.RESULTSAfter cryopreservation, PLTs displayed increased surface activation markers and higher basal calcium levels. Cryopreserved PLTs demonstrated diminished aggregation responses. Additionally, cryopreserved PLTs showed a limited ability to become activated (as measured by CD62P and phosphatidylserine exposure and cytokine release) after agonist stimulation. A reduction in the abundance and phosphorylation of key signaling proteins (Akt, Src, Lyn, ERK, and p38) was seen in cryopreserved PLTs.CONCLUSIONSCryopreservation of PLTs induces dramatic changes to the basal PLT phenotype and renders them largely nonresponsive to agonist stimulation, likely due to the alterations in signal transduction. Therefore, further efforts are required to understand how cryopreserved PLTs achieve their hemostatic effect once transfused.
Transmission and immunopathology of the avian influenza virus A/Anhui/1/2013 (H7N9) human isolate in three commonly commercialized avian species
Authors: Vidaña B. , Dolz R. , Busquets N. , Ramis A. , Sánchez R. , Rivas R. , Valle R. , Cordón I. , Solanes D. , Martínez J. , Majó N. 
Published: September 2017

SummaryH7N9 virus infection is a global concern, given that it can cause severe infection and mortality in humans. However, the understanding of H7N9 epidemiology, animal reservoir species and zoonotic risk remains limited. This work evaluates the pathogenicity, transmissibility and local innate immune response of three avian species harbouring different respiratory distribution of α2,6 and α2,3 SA receptors. Muscovy ducks, European quails and SPF chickens were intranasally inoculated with 105 embryo infectious dose (EID)50 of the human H7N9 (A/Anhui/1/2013) influenza isolate. None of the avian species showed clinical signs or macroscopic lesions, and only mild microscopic lesions were observed in the upper respiratory tract of quail and chickens. Quail presented more severe histopathologic lesions and avian influenza virus (AIV) positivity by immunohistochemistry (IHC), which correlated with higher IL‐6 responses. In contrast, Muscovy ducks were resistant to disease and presented higher IFNα and TLR7 response. In all species, viral shedding was higher in the respiratory than in the digestive tract. Higher viral shedding was observed in quail, followed by chicken and ducks, which presented similar viral titres. Efficient transmission was observed in all contact quail and half of the Muscovy ducks, while no transmission was observed between chicken. All avian species showed viral shedding in drinking water throughout infection.
Reviewer Acknowledgements
Authors: Smith Robert 
Published: September 2017

Journal of Education and Training Studies (JETS) would like to acknowledge the following reviewers for their assistance with peer review of manuscripts for this issue. Many authors, regardless of whether JETS publishes their work, appreciate the helpful feedback provided by the reviewers. Their comments and suggestions were of great help to the authors in improving the quality of their papers. Each of the reviewers listed below returned at least one review for this issue.Reviewers for Volume 5, Number 9Angel H. Y. Lai, Hong Kong Baptist University, Hong KongCengiz Alyilmaz, TurkeyCharlotte Alverson, University of Oregon, USAChris Prince Udochukwu Njoku, University of Nigeria, NigeriaCynthia M. Compton, Wingate University, USAEbru Temiz, Niğde Ömer Halis Demir University, TurkeyElena Jerves, University of Cuenca, EcuadorErkan Atalmış, Kahramanmaras Imam University, TurkeyErkut Tutkun, TurkeyFethi Kayalar, Erzincan University, TurkeyHalide Nur Ozudogru Erdogan, Abant Izzet Baysal University, TurkeyHalil Erdem Çocuk, Mersin University, TurkeyHatice Irem Ozteke Kozan, Necmettin Erbakan University, TurkeyIbrahim Can, TurkeyIoannis Syrmpas, University of Thessaly, GreeceJohn Cowan, Edinburgh Napier University, UKJosé D Badia, University of Valencia, SpainKun-Hsi Liao, Taiwan Shoufu University, TaiwanKürşad Çağrı Bozkirli, TurkeyLaima Kyburiene, Kaunas University of Applied Sciences, LithuaniaLisa Marie Portugal, Grand Canyon University, USALorna T. Enerva, Polytechnic University of the Philippines, PhilippinesM. Fatih Karahuseyinoglu, Firat Universitesi, TurkeyMan-fung Lo, The Hong Kong Polytechnic University, Hong KongMarcie Zaharee, The MITRE Corporation, USAMarco Antonio Catussi Paschoalotto, University of São Paulo, BrazilMehmet Akif Ziyagil, TurkeyMehmet Inan, Marmara University, TurkeyMeral Seker, Alanya Alaaddin Keykubat University, TurkeyMichail Kalogiannakis, University of Crete, GreeceMin Gui, Wuhan University, ChinaMustafa Çakır, Marmara Üniversity, TurkeyMustafa Önder, Şekeroğlu-Muş Alparslan University, TurkeyNele Kampa, Leibniz-Institute for Science and Mathematics Education (IPN), GermanyNerina Fernanda Sarthou, Universidad Nacional del Centro de la Provincia de Buenos Aires, ArgentinaNurşat Biçer, TurkeyÖnder Dağlıoğlu, TurkeyÖzgür Ulubey, Muğla Sıtkı Koçman University, TurkeyRichard H. Martin, Mercer University, USARichard Penny, University of Washington Bothell, USARui Manuel Carreteiro, National Institute of Psychology and Neurosciences, PortugalSadia Batool, Preston University Islamabad, PakistanSelloane Pitikoe, University of Kwazulu-Natal, South AfricaSenem Seda Şahenk Erkan, Marmara University, TurkeyStamatis Papadakis, University of Crete, GreeceThomas K. F. Chiu, The University of Hong Kong, Hong KongYakup Koç, Erzincan University, TurkeyYi Lu, American Institute for Research, USAZeki Coskuner, Firat Universitesi, Turkey Robert SmithEditorial AssistantOn behalf of,The Editorial Board of Journal of Education and Training StudiesRedfame Publishing9450 SW Gemini Dr. #99416Beaverton, OR 97008, USAURL: http://jets.redfame.com
Heteromeric α/β glycine receptors regulate excitability in parvalbumin‐expressing dorsal horn neurons through phasic and tonic glycinergic inhibition
Authors: Gradwell M. A. , Boyle K. A. , Callister R. J. , Hughes D. I. , Graham B. A. 
Published: September 2017

Key points
Spinal parvalbumin‐expressing interneurons have been identified as a critical source of inhibition to regulate sensory thresholds by gating mechanical inputs in the dorsal horn.
This study assessed the inhibitory regulation of the parvalbumin‐expressing interneurons, showing that synaptic and tonic glycinergic currents dominate, blocking neuronal or glial glycine transporters enhances tonic glycinergic currents, and these manipulations reduce excitability.
Synaptically released glycine also enhanced tonic glycinergic currents and resulted in decreased parvalbumin‐expressing interneuron excitability.
Analysis of the glycine receptor properties mediating inhibition of parvalbumin neurons, as well as single channel recordings, indicates that heteromeric α/β subunit‐containing receptors underlie both synaptic and tonic glycinergic currents.
Our findings indicate that glycinergic inhibition provides critical control of excitability in parvalbumin‐expressing interneurons in the dorsal horn and represents a pharmacological target to manipulate spinal sensory processing.
AbstractThe dorsal horn (DH) of the spinal cord is an important site for modality‐specific processing of sensory information and is essential for contextually relevant sensory experience. Parvalbumin‐expressing inhibitory interneurons (PV+ INs) have functional properties and connectivity that enables them to segregate tactile and nociceptive information. Here we examine inhibitory drive to PV+ INs using targeted patch‐clamp recording in spinal cord slices from adult transgenic mice that express enhanced green fluorescent protein in PV+ INs. Analysis of inhibitory synaptic currents showed glycinergic transmission is the dominant form of phasic inhibition to PV+ INs. In addition, PV+ INs expressed robust glycine‐mediated tonic currents; however, we found no evidence for tonic GABAergic currents. Manipulation of extracellular glycine by blocking either, or both, the glial and neuronal glycine transporters markedly decreased PV+ IN excitability, as assessed by action potential discharge. This decreased excitability was replicated when tonic glycinergic currents were increased by electrically activating glycinergic synapses. Finally, we show that both phasic and tonic forms of glycinergic inhibition are mediated by heteromeric α/β glycine receptors. This differs from GABAA receptors in the dorsal horn, where different receptor stoichiometries underlie phasic and tonic inhibition. Together these data suggest both phasic and tonic glycinergic inhibition regulate the output of PV+ INs and contribute to the processing and segregation of tactile and nociceptive information. The shared stoichiometry for phasic and tonic glycine receptors suggests pharmacology is unlikely to be able to selectively target each form of inhibition in PV+ INs.
An investigation into the variability between different shear wave elastography systems in muscle
Authors: Alfuraih Abdulrahman M. , O'Connor Philip , Tan Ai Lyn , Hensor Elizabeth , Emery Paul , Wakefield Richard J. 
Published: September 2017

Aims: The reliability and agreement between shear wave elastography (SWE) systems using different acquisition methods in muscles is not yet established. The objectives were to determine the reliability of a new SWE system on normal resting muscles using different acquisition methods and to compare its performance to an established state-of-the-art system.Material and methods: Small, medium and large ROI sizes in addition to longitudinal, oblique and transverse orientations over five different locations within the rectus femoris muscle were tested using the new system. Results were compared to the established system to test for inter-system reproducibility.Results: Lowest within-subject coefficient of variance (4.3%) andshear wave velocity (1.83 m/s) were associated with the medium ROI and longitudinal orientation from the lateral location. This combination resulted in a strong internal agreement of intra-class correlation of 0.76 (0.57–0.89) for the new system and an almost perfect agreement of 0.92 (0.82–0.97) for the established. Inter-system reproducibility for the best combination was 0.71 (0.48–1) with a mean velocity difference ±95% limits of agreement of 0.07±0.49 m/s.Conclusions: Altering SWE acquisition methods can produce variable results. The new system produced reliable results that are comparable with but not as reliable as the established.
The form and function of channelrhodopsin
Authors: Deisseroth Karl , Hegemann Peter 
Published: September 2017

From biophysics to neuroscience tools
The channelrhodopsins and their distinctive light-activated ion channels have emerged as major tools in modern biological research. Deisseroth and Hegemann review the structural and functional properties of these protein photoreceptors. Mutagenesis and modeling studies, coupled with the reintroduction of modified channels into living systems, offer a profound understanding of how these channels work. The insights into the underlying basic science provide foundations for developing further applications in biology and medicine.

Science
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Characterization of Antigenic Relatedness between GII.4 and GII.17 Noroviruses by Use of Serum Samples from Norovirus-Infected Patients
Authors: Dai Ying-Chun , Xia Ming , Huang Qiong , Tan Ming , Qin Lin , Zhuang Ya-Li , Long Yan , Li Jian-Dong , Jiang Xi , Zhang Xu-Fu 
Published: September 2017

ABSTRACT
A novel GII.17 norovirus variant caused major gastroenteritis epidemics in China in 2014 to 2016. To explore the host immune factors in selection of the emergence of this new variant, we characterized its antigenic relatedness with the GII.4 noroviruses that have dominated in China for decades. Through an enzyme-linked immunosorbent assay (ELISA) and a histo-blood group antigen (HBGA) blocking assay using sera from GII.4 and the GII.17 variant-infected patients, respectively, we observed limited cross-immune reactivity by the ELISA but little reactivity by the HBGA blocking assay between GII.4 norovirus and the new GII.17 variant. Our data suggest that, among other possible factors, GII.4-specific herd immunity had little role in the emergence of the new GII.17 variant. Thus, GII.17 may be an important active antigenic type or immunotype that needs to be considered for future vaccine strategies against human noroviruses.
Finegoldia magna Isolated from Orthopedic Joint Implant-Associated Infections
Authors: Söderquist Bo , Björklund Sanna , Hellmark Bengt , Jensen Anders , Brüggemann Holger 
Published: September 2017

ABSTRACT

The anaerobic Gram-positive coccus
Finegoldia magna
is a rare cause of infections of bone and joints. The aim of this study was to describe the microbiological and clinical characteristics of orthopedic implant-associated infections caused by
F. magna
. We retrospectively analyzed samples consisting of anaerobic Gram-positive cocci and samples already identified as
F. magna
from patients with orthopedic infections. The isolates found were determined to the species level using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). The antibiotic susceptibility pattern was determined by Etest. Whole-genome sequencing (WGS) was performed. Clinical data were extracted from each patient's journal. In nine patients, orthopedic joint implant-associated infections were identified as being caused by
F. magna
. The isolates were susceptible to most of the antibiotics tested, with the exception of rifampin and moxifloxacin in a few cases. Five of the nine infections were monomicrobial. The most common antibiotic used to treat the infection was penicillin V, but five of the nine patients received a combination of antibiotics. Eight patients underwent surgical treatment, with extraction of the implant performed in seven cases and reimplantation in only two cases. The WGS showed a relatively small core genome, with 126,647 single nucleotide polymorphisms identified within the core genome. A phylogenomic analysis revealed that the isolates clustered into two distinct clades. Orthopedic implant-associated infections caused by
F. magna
are rare, but the bacteria are generally susceptible to antibiotics. Despite this, surgical treatment combined with long-term antibiotics is often necessary. The WGS analysis revealed a high heterogeneity and suggested the existence of at least two different
Finegoldia
species.