bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the anisotropy and tortuosity of permeable pathways in clay-rich mudstones using models based on X-ray tomography
Authors: Backeberg Nils R. , Iacoviello Francesco , Rittner Martin , Mitchell Thomas M. , Jones Adrian P. , Day Richard , Wheeler John , Shearing Paul R. , Vermeesch Pieter , Striolo Alberto 
Published: October 2017

AbstractThe permeability of shales is important, because it controls where oil and gas resources can migrate to and where in the Earth hydrocarbons are ultimately stored. Shales have a well-known anisotropic directional permeability that is inherited from the depositional layering of sedimentary laminations, where the highest permeability is measured parallel to laminations and the lowest permeability is perpendicular to laminations. We combine state of the art laboratory permeability experiments with high-resolution X-ray computed tomography and for the first time can quantify the three-dimensional interconnected pathways through a rock that define the anisotropic behaviour of shales. Experiments record a physical anisotropy in permeability of one to two orders of magnitude. Two- and three-dimensional analyses of micro- and nano-scale X-ray computed tomography illuminate the interconnected pathways through the porous/permeable phases in shales. The tortuosity factor quantifies the apparent decrease in diffusive transport resulting from convolutions of the flow paths through porous media and predicts that the directional anisotropy is fundamentally controlled by the bulk rock mineral geometry. Understanding the mineral-scale control on permeability will allow for better estimations of the extent of recoverable reserves in shale gas plays globally.
The Prevalence of Double Eyelid and the 3D Measurement of Orbital Soft Tissue in Malays and Chinese
Authors: Lu Ting Yin , Kadir Kathreena , Ngeow Wei Cheong , Othman Siti Adibah 
Published: October 2017

AbstractThis study aimed to determine the prevalence of double eyelid among two main Mongoloid ethnicities, the Malays and Chinese who reside in Malaysia. We also measured their periorbital tissue parameters for application in anthropology, optometry, ophthalmology, oculoplastic surgery and maxillofacial trauma surgery. The images of the 103 Malay and 97 Chinese volunteers were captured using indirect 3D photogrammetry, and quantitative measurement was obtained using the software provided by the manufacturer. All Malays and 70.1% of Chinese in this cross section population had double eyelid on both eyes. The mean pretarsal skin height was 3.99 mm for the Malays and 2.29 mm for the Chinese. The Malays appeared to have shorter eyebrow height (11.10 mm) compared to the Chinese (11.79 mm). An opposite pattern could be seen in the measurement of upper eyelid crease height between the Malays (8.33 mm) and the Chinese (4.91 mm). Of note, the intercanthal distance of the Chinese (IDC = 35.85 mm) was wider and their interpupillary distance was narrower (IPD = 62.85 mm) compared to the Malays’ (ICD = 34.21 mm; IPD = 64.04 mm). In conclusion, there were significant differences in the prevalence of double eyelid and periorbital tissue measurements between the Malays and Chinese.
Analysis of the CRISPR-Cas system in bacteriophages active on epidemic strains of Vibrio cholerae in Bangladesh
Authors: Naser Iftekhar Bin , Hoque M. Mozammel , Nahid M. Ausrafuggaman , Tareq Tokee M. , Rocky M. Kamruzzaman , Faruque Shah M. 
Published: October 2017

AbstractCRISPR-Cas (clustered regularly interspersed short palindromic repeats-CRISPR-associated proteins) are microbial nuclease systems involved in defense against phages. Bacteria also resist phages by hosting phage-inducible chromosomal islands (PICI) which prevent phage reproduction. Vibrio cholerae which causes cholera epidemics, interacts with numerous phages in the environment and in cholera patients. Although CRISPR-Cas systems are usually carried by bacteria and archea, recently V. cholerae specific ICP1 phages were found to host a CRISPR-Cas system that inactivates PICI-like elements (PLE) in V. cholerae. We analyzed a collection of phages and V. cholerae isolated during seasonal cholera epidemics in Bangladesh, to study the distribution, and recent evolution of the phage-encoded CRISPR-Cas system. Five distinct but related phages carrying the CRISPR-Cas system, and possible CRISPR-Cas negative progenitor phages were identified. Furthermore, CRISPR arrays in the phages were found to have evolved by acquisition of new spacers targeting diverse regions of PLEs carried by the V. cholerae strains, enabling the phages to efficiently grow on PLE positive strains. Our results demonstrate a continuing arms-race involving genetic determinants of phage-resistance in V. cholerae, and the phage-encoded CRISPR-Cas system in the co-evolution of V. cholerae and its phages, presumably fostered by their enhanced interactions during seasonal epidemics of cholera.
Dynamic changes in binding interaction networks of sex steroids establish their non-classical effects
Authors: Bálint Mónika , Jeszenői Norbert , Horváth István , Ábrahám István M. , Hetényi Csaba 
Published: October 2017

AbstractNon-classical signaling in the intracellular second messenger system plays a pivotal role in the cytoprotective effect of estradiol. Estrogen receptor is a common target of sex steroids and important in mediating estradiol-induced neuroprotection. Whereas the mechanism of genomic effects of sex steroids is fairly understood, their non-classical effects have not been elucidated completely. We use real time molecular dynamics calculations to uncover the interaction network of estradiol and activator estren. Besides steroid interactions, we also investigate the co-activation of the receptor. We show how steroid binding to the alternative binding site of the non-classical action is facilitated by the presence of a steroid in the classical binding site and the absence of the co-activator peptide. Uncovering such dynamic mechanisms behind steroid action will help the structure-based design of new drugs with non-classical responses and cytoprotective potential.
Progressive and Prognosis Value of Notch Receptors and Ligands in Hepatocellular Carcinoma: A Systematic Review and Meta-analysis
Authors: Zhang Yingshi , Li Dandan , Feng Fan , An Li , Hui Fuhai , Dang Dasheng , Zhao Qingchun 
Published: October 2017

AbstractHepatocellular carcinoma (HCC) is not sensitive to radiotherapy and chemotherapy and experiences postoperative relapse extremely easy, which is the major cause of the high mortality rate. The Notch signaling pathway is expected to become a new target for the biological treatment of HCC. We searched databases for studies that evaluated the expression of Notch receptors and/or ligands in human HCC tissue. The search yielded 15 studies that enrolled 1643 patients. Compared with non-HCC tissues, Notch 1 was associated with a higher expression level (odds risk 1.59, 95% confidence interval 0.34 to 7.45), as well as Notch 3 (2.63, 0.69 to 10.02), Notch 4 (1.33, 0.74 to 2.38) and Jagged 1 (1.47, 0.23 to 9.53); however, Notch 2 showed the opposite result (0.60, 0.30 to 1.20). Larger tumor size (>5 cm), metastasis positive, and micro vascular invasion positive were features that were associated with over-expression in Notch 1 according to the clinicopathological features. The expression levels of Notch 1, 3, 4 and Jagged 1 were associated with higher expression in HCC tissues, while Notch 2 had the opposite result. This study is registered with PROSPERO (CRD42017055782).
The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface
Authors: Helliwell J. R. , Sturrock C. J. , Mairhofer S. , Craigon J. , Ashton R. W. , Miller A. J. , Whalley W. R. , Mooney S. J. 
Published: October 2017

AbstractThe rhizosphere is the zone of soil influenced by a plant root and is critical for plant health and nutrient acquisition. All below ground resources must pass through this dynamic zone prior to their capture by plant roots. However, researching the undisturbed rhizosphere has proved very challenging. Here we compare the temporal changes to the intact rhizosphere pore structure during the emergence of a developing root system in different soils. High resolution X-ray Computed Tomography (CT) was used to quantify the impact of root development on soil structural change, at scales relevant to individual micro-pores and aggregates (µm). A comparison of micro-scale structural evolution in homogenously packed soils highlighted the impacts of a penetrating root system in changing the surrounding porous architecture and morphology. Results indicate the structural zone of influence of a root can be more localised than previously reported (µm scale rather than mm scale). With time, growing roots significantly alter the soil physical environment in their immediate vicinity through reducing root-soil contact and crucially increasing porosity at the root-soil interface and not the converse as has often been postulated. This ‘rhizosphere pore structure’ and its impact on associated dynamics are discussed.
The characterisation of shellac resin by flow injection and liquid chromatography coupled with electrospray ionisation and mass spectrometry
Authors: Tamburini Diego , Dyer Joanne , Bonaduce Ilaria 
Published: October 2017

AbstractA strategy based on electrospray ionisation (ESI) in negative mode coupled with quadrupole-time of flight (Q-ToF) detection techniques was adopted to characterise some samples of shellac resin. Flow injection analysis (FIA) was used to investigate the distribution of the components of the resin. Eight groups of compounds with increasing masses were detected and assigned to free acids, esters and polyesters with up to eight units. High pressure liquid chromatography (HPLC) enabled the compounds to be chromatographically separated. Accurate molecular masses and tandem mass (MS/MS) spectra interpretation were used to characterise the different compounds, assigning and/or suggesting molecular structures. In some cases, highly detailed information about the ester linkages was provided by the MS/MS spectra, enabling the different isomers to be distinguished. Oxidation products were also identified in the samples and differences were observed in terms of hydrolysis and oxidation. In addition to providing the first characterisation of shellac by HPLC-ESI-Q-ToF and an atlas of MS/MS spectra of shellac components, this work demonstrates the suitability of the proposed strategy for characterising the resin, and provides the identification of previously unknown degradation products and minor components. This represents a significant step forward in the chemical knowledge of this material.
A Method for Quantifying Molecular Interactions Using Stochastic Modelling and Super-Resolution Microscopy
Authors: Bermudez-Hernandez Keria , Keegan Sarah , Whelan Donna R. , Reid Dylan A. , Zagelbaum Jennifer , Yin Yandong , Ma Sisi , Rothenberg Eli , Fenyö David 
Published: October 2017

AbstractWe introduce the Interaction Factor (IF), a measure for quantifying the interaction of molecular clusters in super-resolution microscopy images. The IF is robust in the sense that it is independent of cluster density, and it only depends on the extent of the pair-wise interaction between different types of molecular clusters in the image. The IF for a single or a collection of images is estimated by first using stochastic modelling where the locations of clusters in the images are repeatedly randomized to estimate the distribution of the overlaps between the clusters in the absence of interaction (IF = 0). Second, an analytical form of the relationship between IF and the overlap (which has the random overlap as its only parameter) is used to estimate the IF for the experimentally observed overlap. The advantage of IF compared to conventional methods to quantify interaction in microscopy images is that it is insensitive to changing cluster density and is an absolute measure of interaction, making the interpretation of experiments easier. We validate the IF method by using both simulated and experimental data and provide an ImageJ plugin for determining the IF of an image.
Hamp1 but not Hamp2 regulates ferroportin in fish with two functionally distinct hepcidin types
Authors: Neves João V. , Ramos Miguel F. , Moreira Ana C. , Silva Tânia , Gomes Maria S. , Rodrigues Pedro N. S. 
Published: October 2017

AbstractHepcidin is a small cysteine rich peptide that regulates the sole known cellular iron exporter, ferroportin, effectively controlling iron metabolism. Contrary to humans, where a single hepcidin exists, many fish have two functionally distinct hepcidin types, despite having a single ferroportin gene. This raises the question of whether ferroportin is similarly regulated by the iron regulator Hamp1 and the antimicrobial Hamp2. In sea bass (Dicentrarchus labrax), iron overload prompted a downregulation of ferroportin, associated with an upregulation of hamp1, whereas an opposite response was observed during anemia, with no changes in hamp2 in either situation. During infection, ferroportin expression decreased, indicating iron withholding to avoid microbial proliferation. In vivo administration of Hamp1 but not Hamp2 synthetic peptides caused significant reduction in ferroportin expression, indicating that in teleost fish with two hepcidin types, ferroportin activity is mediated through the iron-regulator Hamp1, and not through the dedicated antimicrobial Hamp2. Additionally, in vitro treatment of mouse macrophages with fish Hamp1 but not Hamp2 caused a decrease in ferroportin levels. These results raise questions on the evolution of hepcidin and ferroportin functional partnership and open new possibilities for the pharmaceutical use of selected fish Hamp2 hepcidins during infections, with no impact on iron homeostasis.
Genome-wide profiling of nardilysin target genes reveals its role in epigenetic regulation and cell cycle progression
Authors: Morita Yusuke , Ohno Mikiko , Nishi Kiyoto , Hiraoka Yoshinori , Saijo Sayaka , Matsuda Shintaro , Kita Toru , Kimura Takeshi , Nishi Eiichiro 
Published: October 2017

AbstractPost-translational histone modifications, such as acetylation and methylation, are prerequisites for transcriptional regulation. The metalloendopeptidase nardilysin (Nrdc) is a H3K4me2-binding protein that controls thermoregulation and β-cell functions through its transcriptional coregulator function. We herein combined high-throughput ChIP-seq and RNA-seq to achieve the first genome-wide identification of Nrdc target genes. A ChIP-seq analysis of immortalized mouse embryo fibroblasts (iMEF) identified 4053 Nrdc-binding sites, most of which were located in proximal promoter sites (2587 Nrdc-binding genes). Global H3K4me2 levels at Nrdc-binding promoters slightly increased, while H3K9ac levels decreased in the absence of Nrdc. Among Nrdc-binding genes, a comparative RNA-seq analysis identified 448 candidates for Nrdc target genes, among which cell cycle-related genes were significantly enriched. We confirmed decreased mRNA and H3K9ac levels at the promoters of individual genes in Nrdc-deficient iMEF, which were restored by the ectopic introduction of Nrdc. Reduced mRNA levels, but not H3K9ac levels were fully restored by the reintroduction of the peptidase-dead mutant of Nrdc. Furthermore, Nrdc promoted cell cycle progression at multiple stages, which enhanced cell proliferation in vivo. Collectively, our integrative studies emphasize the importance of Nrdc for maintaining a proper epigenetic status and cell growth.
Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities
Authors: Sato Hirotoshi , Sogo Yuki , Doi Hideyuki , Yamanaka Hiroki 
Published: October 2017

AbstractEnvironmental DNA (eDNA) metabarcoding has been used increasingly to assess biodiversity of aquatic vertebrates. However, there still remains to be developed a sampling design of eDNA metabarcoding that can ensure high detection rates of species with minimum total survey effort, especially for large-scale surveys of aquatic organisms. We here tested whether pooling of eDNA samples can be used to evaluate biodiversity of freshwater fishes in four satellite lakes of Lake Biwa, Japan. Fish communities detected by eDNA metabarcoding of the mitochondrial 12S region were compared between the individual and pooled samples. In the individual samples, 31, 22, 33, and 31 fish lineages (proxies for species) were observed at the respective sites, within which moderate spatial autocorrelation existed. In the pooled samples, 30, 20, 29, and 27, lineages were detected, respectively, even after 15 PCR replicates. Lineages accounting for < 0.05% of the total read count of each site’s individual samples were mostly undetectable in the pooled samples. Moreover, fish communities detected were similar among PCR replicates in the pooled samples. Because of the decreased detection rates, the pooling strategy is unsuitable for estimating fish species richness. However, this procedure is useful potentially for among-site comparison of representative fish communities.
Sequencing of glycosaminoglycans with potential to interrogate sequence-specific interactions
Authors: van Kuppevelt Toin H. , Oosterhof Arie , Versteeg Elly M. M. , Podhumljak Emina , van de Westerlo Els M. A. , Daamen Willeke F. 
Published: October 2017

AbstractTechnologies to sequence nucleic acids/proteins are widely available, but straightforward methodologies to sequence complex polysaccharides are lacking. We here put forward a strategy to sequence glycosaminoglycans, long linear polysaccharides involved in many biochemical processes. The method is based on the covalent immobilization and (immuno)chemical characterization of only those size-separated saccharides that harbor the original reducing end of the full-length chain. Using this methodology, the saccharide sequence of the chondroitin sulfate chain of the proteoglycan bikunin was determined. The method can be performed in any standard biochemical lab and opens studies to the interaction of complex saccharide sequences with other biomolecules.
Promoting Hearing Health Collaboration Through an Interprofessional Education Experience
Authors: James Jerald , Chappell Rachel , Mercante Donald E. , Gunaldo Tina Patel 
Published: October 2017

Purpose
To enhance audiology and physician assistant (PA) student appreciation for collaboration/team-based care through an interprofessional educational activity focused on hearing assessments.

Method
A total of 18 students from Louisiana State University Health–New Orleans's audiology and PA programs participated in an optional interprofessional education learning opportunity, which included a demonstration of hearing assessments. To assess student perspectives regarding interprofessional learning, the students completed pre- and post-surveys.

Results
Eighteen students completed a survey, including 5 questions using a Likert scale and 1 open-ended question. Both audiology and PA students demonstrated significant statistical improvement in 2 interprofessional competencies: roles/responsibilities and interprofessional communication. Students also reported increased awareness and knowledge in the skills of the opposite professions as related to hearing assessments.

Conclusion
Integrating interprofessional education experiences within an audiology program promotes collaborative practice patterns and supports new educational accreditation standards.

Supplemental Material

https://doi.org/10.23641/asha.5491669
Verbal Working Memory in Children With Cochlear Implants
Authors: Nittrouer Susan , Caldwell-Tarr Amanda , Low Keri E. , Lowenstein Joanna H. 
Published: October 2017

Purpose
Verbal working memory in children with cochlear implants and children with normal hearing was examined.

Participants
Ninety-three fourth graders (47 with normal hearing, 46 with cochlear implants) participated, all of whom were in a longitudinal study and had working memory assessed 2 years earlier.

Method
A dual-component model of working memory was adopted, and a serial recall task measured storage and processing. Potential predictor variables were phonological awareness, vocabulary knowledge, nonverbal IQ, and several treatment variables. Potential dependent functions were literacy, expressive language, and speech-in-noise recognition.

Results
Children with cochlear implants showed deficits in storage and processing, similar in size to those at second grade. Predictors of verbal working memory differed across groups: Phonological awareness explained the most variance in children with normal hearing; vocabulary explained the most variance in children with cochlear implants. Treatment variables explained little of the variance. Where potentially dependent functions were concerned, verbal working memory accounted for little variance once the variance explained by other predictors was removed.

Conclusions
The verbal working memory deficits of children with cochlear implants arise due to signal degradation, which limits their abilities to acquire phonological awareness. That hinders their abilities to store items using a phonological code.
Acoustics of Clear and Noise-Adapted Speech in Children, Young, and Older Adults
Authors: Smiljanic Rajka , Gilbert Rachael C. 
Published: October 2017

PurposeThis study investigated acoustic–phonetic modifications produced in noise-adapted speech (NAS) and clear speech (CS) by children, young adults, and older adults.MethodTen children (11–13 years of age), 10 young adults (18–29 years of age), and 10 older adults (60–84 years of age) read sentences in conversational and clear speaking style in quiet and in noise. A number of acoustic measurements were obtained.ResultsNAS and CS were characterized by a decrease in speaking rate and an increase in 1–3 kHz energy, sound pressure level (SPL), vowel space area (VSA), and harmonics-to-noise ratio. NAS increased fundamental frequency (F0) mean and decreased jitter and shimmer. CS increased frequency and duration of pauses. Older adults produced the slowest speaking rate, longest pauses, and smallest increase in F0 mean, 1–3 kHz energy, and SPL when speaking clearly. They produced the smallest increases in VSA in NAS and CS. Children slowed down less, increased the VSA least, increased harmonics-to-noise ratio, and decreased jitter and shimmer most in CS. Children increased mean F0 and F1 most in noise.ConclusionsFindings have implications for a model of speech production in healthy speakers as well as the potential to aid in clinical decision making for individuals with speech disorders, particularly dysarthria.
Wide stopband out‐of‐phase filtering power divider using double‐sided parallel‐strip line
Authors: Lu Yun‐Long , Wang Yi , Hua Changzhou , Liu Taijun 
Published: October 2017

This Letter presents a novel out‐of‐phase filtering power divider (FPD) with a very wide stopband by using double‐sided parallel‐strip line (DSPSL) and through ground via (TGV). The DSPSL structure facilitates the out‐of‐phase outputs of the FPD. The TGV and two complex‐impedance terminations connected to the common input port are employed to achieve the isolation. By choosing proper feeding coupling region and the loading resistors at the centre of the resonators, the second, third and fourth harmonics are suppressed. For verification, a prototype FPD operating at 1.85 GHz (f0) with 5.2% bandwidth is designed, fabricated and measured. The experimental results show that the isolation between the output ports is better than 24 dB across the passband, and the 28 dB rejection band is extended to 4.6f0.