bluuebunny/crossref_metadata_2025 huggingface dataset:
Relative outflow enhancements during major geomagnetic storms – Cluster observations
Authors: Schillings Audrey , Nilsson Hans , Slapak Rikard , Yamauchi Masatoshi , Westerberg Lars-Göran
Published: December 2017

Abstract. The rate of ion outflow from the polar ionosphere is known to vary by orders of magnitude, depending on the geomagnetic activity. However, the upper limit of the outflow rate during the largest geomagnetic storms is not well constrained due to poor spatial coverage during storm events. In this paper, we analyse six major geomagnetic storms between 2001 and 2004 using Cluster data. The six major storms fulfil the criteria of Dst  < −100 nT or Kp  > 7+. Since the shape of the magnetospheric regions (plasma mantle, lobe and inner magnetosphere) are distorted during large magnetic storms, we use both plasma beta (β) and ion characteristics to define a spatial box where the upward O+ flux scaled to an ionospheric reference altitude for the extreme event is observed. The relative enhancement of the scaled outflow in the spatial boxes as compared to the data from the full year when the storm occurred is estimated. Only O+ data were used because H+ may have a solar wind origin. The storm time data for most cases showed up as a clearly distinguishable separate peak in the distribution toward the largest fluxes observed. The relative enhancement in the outflow region during storm time is 1 to 2 orders of magnitude higher compared to less disturbed time. The largest relative scaled outflow enhancement is 83 (7 November 2004) and the highest scaled O+ outflow observed is 2  ×  1014 m−2 s−1 (29 October 2003).
Impact of numerical choices on water conservation in the E3SM Atmosphere Model Version 1 (EAM V1)
Authors: Zhang Kai , Rasch Philip J. , Taylor Mark A. , Wan Hui , Leung Lai-Yung Ruby , Ma Po-Lun , Golaz Jean-Christophe , Wolfe Jon , Lin Wuyin , Singh Balwinder , Burrows Susannah , Yoon Jin-Ho , Wang Hailong , Qian Yun , Tang Qi , Caldwell Peter , Xie Shaocheng
Published: December 2017

Abstract. The conservation of total water is an important numerical feature for global Earth system models. Even small conservation problems in the water budget can lead to systematic errors in century-long simulations for sea level rise projection. This study quantifies and reduces various sources of water conservation error in the atmosphere component of the Energy Exascale Earth System Model. Several sources of water conservation error have been identified during the development of the version 1 (V1) model. The largest errors result from the numerical coupling between the resolved dynamics and the parameterized sub-grid physics. A hybrid coupling using different methods for fluid dynamics and tracer transport provides a reduction of water conservation error by a factor of 50 at 1° horizontal resolution as well as consistent improvements at other resolutions. The second largest error source is the use of an overly simplified relationship between the surface moisture flux and latent heat flux at the interface between the host model and the turbulence parameterization. This error can be prevented by applying the same (correct) relationship throughout the entire model. Two additional types of conservation error that result from correcting the surface moisture flux and clipping negative water concentrations can be avoided by using mass-conserving fixers. With all four error sources addressed, the water conservation error in the V1 model is negligible and insensitive to the horizontal resolution. The associated changes in the long-term statistics of the main atmospheric features are small. A sensitivity analysis is carried out to show that the magnitudes of the conservation errors decrease strongly with temporal resolution but increase with horizontal resolution. The increased vertical resolution in the new model results in a very thin model layer at the Earth’s surface, which amplifies the conservation error associated with the surface moisture flux correction. We note that for some of the identified error sources, the proposed fixers are remedies rather than solutions to the problems at their roots. Future improvements in time integration would be beneficial for this model.
Non-destructive estimates of soil carbonic anhydrase activity and associated soil water oxygen isotope composition
Authors: Jones Sam P. , Ogée Jérôme , Sauze Joana , Wohl Steven , Saavedra Noelia , Fernández-Prado Noelia , Maire Juliette , Launois Thomas , Bosc Alexandre , Wingate Lisa
Published: December 2017

Abstract. The contribution of photosynthesis and soil respiration to net land–atmosphere carbon dioxide (CO2) exchange can be estimated based on the differential influence of leaves and soils on budgets of the oxygen isotope composition (δ18O) of atmospheric CO2. To do so, the activity of carbonic anhydrases (CAs), a group of enzymes that catalyse the hydration of CO2 in soils and plants, needs to be understood. Measurements of soil CA activity typically involve the inversion of models describing the δ18O of CO2 fluxes to solve for the apparent, potentially catalysed, rate of CO2 hydration. This requires information about the δ18O of CO2 in isotopic equilibrium with soil water, typically obtained from destructive, depth-resolved sampling and extraction of soil water. In doing so, an assumption is made about the soil water pool that CO2 interacts with, which may bias estimates of CA activity if incorrect. Furthermore, this can represent a significant challenge in data collection given the potential for spatial and temporal variability in the δ18O of soil water and limited a priori information with respect to the appropriate sampling resolution and depth. We investigated whether we could circumvent this requirement by inferring the rate of CO2 hydration and the δ18O of soil water from the relationship between the δ18O of CO2 fluxes and the δ18O of CO2 at the soil surface measured at different ambient CO2 conditions. This approach was tested through laboratory incubations of air-dried soils that were re-wetted with three waters of different δ18O. Gas exchange measurements were made on these soils to estimate the rate of hydration and the δ18O of soil water, followed by soil water extraction to allow for comparison. Estimated rates of CO2 hydration were 6.8–14.6 times greater than the theoretical uncatalysed rate of hydration, indicating that CA were active in these soils. Importantly, these estimates were not significantly different among water treatments, suggesting that this represents a robust approach to assay the activity of CA in soil. As expected, estimates of the δ18O of the soil water that equilibrates with CO2 varied in response to alteration to the δ18O of soil water. However, these estimates were consistently more negative than the composition of the soil water extracted by cryogenic vacuum distillation at the end of the gas measurements with differences of up to −3.94 ‰ VSMOW–SLAP. These offsets suggest that, at least at lower water contents, CO2–H2O isotope equilibration primarily occurs with water pools that are bound to particle surfaces and are depleted in 18O compared to bulk soil water.
Student's Intentions to Use M-Learning: An Empirical Perspective from the Philippines
Authors: Bombaes Ace
Published: December 2017

M-learning is the future modern way of learning; so it is important for the students to keep pace with changing technology and time. M-learning has a key position in the development of new teaching methodologies for higher education students. Learning through M-technology is free of limitation; the student can access the knowledge and information at any time and any place. This research paper measures the intention of students to learn from modern and innovative method that is M-technology. For this research paper data is collected from Filipino tertiary students to perform statistical analysis i.e. structural Equation modeling (SEM) using AMOS-21. Results indicate that student's innovative behavior, lecturer influence, usefulness and ease of use of technology has positive impact on student's intention towards M-learning.
Detecting Risk of Low Health Literacy in Disadvantaged Populations Using Area-based
Measures
Authors: Knighton Andrew J. , Brunisholz Kimberly D. , Savitz Samuel T.
Published: December 2017

Introduction: Socio-economic status (SES) and low health literacy (LHL) are
closely correlated. Both are directly associated with clinical and behavioral risk
factors and healthcare outcomes. Learning healthcare systems are introducing small-area
measures to address the challenges associated with maintaining patient-reported measures
of SES and LHL. This study’s purpose was to measure the association between two
available census block measures associated with SES and LHL. Understanding the
relationship can guide the identification of a multi-purpose area based measure for
delivery system use.Methods: A retrospective observational design was deployed using all
US Census block groups in Utah. The principal dependent variable was a
nationally-standardized health literacy score (HLS). The primary explanatory variable
was a state-standardized area deprivation index (ADI). Statistical methods included
linear regression and tests of association. Receiver operating characteristic (ROC)
analysis was used to develop LHL criteria using ADI. Results: A significant negative
association between the HLS and the ADI score remained after adjusting for area-level
risk factors (β: –0.21 (95% CI: –0.22, –0.19) p < .001). Eighteen block groups
(<1%) were identified as having LHL using HLS. A combination of three or more ADI
components correlated with LHL predicted 78% of HLS LHL block groups and 35 additional
block groups not identified using HLS (c-statistic: 0.64; 95% CI: 0.62,
0.66). Conclusions: HLS and ADI use differing measurement criteria but are closely
correlated. A state-based ADI detected additional neighborhoods with risk of LHL
compared to use of a national HLS. An ADI represents a multi-purpose area measure of
social determinants useful for learning health systems tailoring care.
Data Cleaning in the Evaluation of a Multi-Site Intervention Project
Authors: Welch Gavin , Von Recklinghausen Friedrich , Taenzer Andreas , Savitz Lucy , Weiss Lisa
Published: December 2017

Context: The High Value Healthcare Collaborative (HVHC) sepsis project was a
two-year multi-site project where Member health care delivery systems worked on
improving sepsis care using a dissemination & implementation framework designed by
HVHC. As part of the project evaluation, participating Members provided 5 data
submissions over the project period. Members created data files using a uniform
specification, but the data sources and methods used to create the data sets differed.
Extensive data cleaning was necessary to get a data set usable for the evaluation
analysis. Case Description: HVHC was the coordinating center for the project and
received and cleaned all data submissions. Submissions received 3 sequentially more
detailed levels of checking by HVHC. The most detailed level evaluated validity by
comparing values within-Member over time and between Member. For a subset of episodes
Member-submitted data were compared to matched Medicare claims data.Findings:
Inconsistencies in data submissions, particularly for length-of-stay variables were
common in early submissions and decreased with subsequent submissions. Multiple
resubmissions were sometimes required to get clean data. Data checking also uncovered a
systematic difference in the way Medicare and some members defined intensive care unit
stay.Conclusions: Data checking is a critical for ensuring valid analytic results for
projects using electronic health record data. It is important to budget sufficient
resources for data checking. Interim data submissions and checks help find anomalies
early. Data resubmissions should be checked as fixes can introduce new errors.
Communicating with those responsible for creating the data set provides critical
information.
Overcoming Barriers to Experience Benefits: A Qualitative Analysis of Electronic
Health Records and Health Information Exchange Implementation in Local Health
Departments
Authors: Williams Karmen S. , Shah Gulzar H. , Leider JP , Gupta Akarti
Published: December 2017

Introduction: Electronic Health Records (EHRs) and Health Information Exchanges
(HIEs) are changing surveillance and analytic operations within local health departments
(LHDs) across the United States. The objective of this study was to analyze the status,
benefits, barriers, and ways of overcoming challenges in the implementation of EHRs and
HIEs in LHDs.Methods: This study employed a mixed methods approach, first using the 2013
National Profile of LHDs survey to ascertain the status of EHR and HIE implementation
across the US, as well as to aid in selection of respondents for the second,
interview-based part of project. Next, forty-nine key-informant interviews of local
health department staff were conducted. Data were coded thematically and independently
by two researchers. Coding was compared and re-coded using the consensus
definitions.Results: Twenty-three percent of LHDs nationwide are using EHRs and 14
percent are using HIEs. The most frequently mentioned benefits for implementation were
identified as care coordination, retrieval or managing information, and the ability to
track outcomes of care. A few mentioned barriers included financial resources,
resistance to change, and IT related issues during implementation.Discussion: Despite
financial, technical capacity, and operational constraints, leaders interviewed as part
of this project were optimistic about the future of EHRs in local health departments.
Recent policy changes and accreditation have implications of improving processes to
affect populations served.Conclusions: Overcoming the challenges in implementing EHRs
can result in increased efficiencies in surveillance and higher quality patient care and
tracking. However, significant opportunity cost does exist.
A Data Driven Approach to Achieving High Value Healthcare
Authors: Savitz Lucy A. , Weiss Lisa T.
Published: December 2017

The purpose of this special issue is to disseminate learning from the High Value
Healthcare Collaborative (HVHC). The HVHC is a voluntary, member-led organization based
on trusted, working relationships among delivery system leaders. HVHC’s mission is to be
a provider-based learning health system committed to improving healthcare value through
data, evidence, and collaboration. We begin by describing the organization and structure
of HVHC in order to lay the context for a series of papers that feature work from this
learning health system. HVHC was awarded a grant from the John and Laura Arnold
Foundation to develop a generalizable model for dissemination and implementation.
Implementation of the 3-hour sepsis bundle was used as a prototypic, complex
intervention with an in-depth mixed methods evaluation across 16 member sites. The first
four articles in this issue describe, in detail, various data and methodological
challenges encountered together with strategies for overcoming these (see Knowlton et
al., von Recklinghausen et al., Welch et al., and Taenzer et al.). Next, we illustrate
how the Data Trust can support emerging questions relevant to member organizations. The
paper by Albritton et al., explores the impact of observation stays on readmission
rates. Knighton et al., explore the use of an area-based measure for health literacy to
assess risk in disadvantaged populations. Two final papers illustrate the importance of
fundamental data sources needed to support advanced data science.
Illustrating Informed Presence Bias in Electronic Health Records Data: How Patient
Interactions with a Health System Can Impact Inference
Authors: Phelan Matthew , Bhavsar Nrupen , Goldstein Benjamin A
Published: December 2017

Electronic health record (EHR) data are becoming a primary resource for clinical
research. Compared to traditional research data, such as those from clinical trials and
epidemiologic cohorts, EHR data have a number of appealing characteristics. However,
because they do not have mechanisms set in place to ensure that the appropriate data are
collected, they also pose a number of analytic challenges. In this paper, we illustrate
that how a patient interacts with a health system influences which data are recorded in
the EHR. These interactions are typically informative, potentially resulting in bias. We
term the overall set of induced biases informed presence. To illustrate this, we use
examples from EHR based analyses. Specifically, we show that: 1) Where a patient
receives services within a health facility can induce selection bias; 2) Which health
system a patient chooses for an encounter can result in information bias; and 3)
Referral encounters can create an admixture bias. While often times addressing these
biases can be straightforward, it is important to understand how they are induced in any
EHR based analysis.
The Use of Clinical Registries in the United States: A Landscape Survey
Authors: Blumenthal Seth
Published: December 2017

Introduction: The use of information from clinical registries for improvement and
value-based payment is increasing, yet information about registry use is not widely
available. We conducted a landscape survey to understand registry uses, focus areas and
challenges. The survey addressed the structure and organization of registry programs, as
well as their purpose and scope.Setting: The survey was conducted by the National
Quality Registry Network (NQRN), a community of organizations interested in registries.
NQRN is a program of the PCPI, a national convener of medical specialty and professional
societies and associations, which constitute a majority of registry stewards in the
United States.Methods: We surveyed 152 societies and associations, asking about registry
programs, governance, number of registries, purpose and data uses, data collection,
expenses, funding and interoperability.Results: The response rate was 52 percent. Many
registries were self-funded, with 39 percent spending less than $1 million per year, and
32 percent spending $1-9.9 million. The typical registry had three full-time equivalent
staff. Registries were frequently used for quality improvement, benchmarking and
clinical decision support. 85 percent captured outpatient data. Most registries
collected demographics, treatments, practitioner information and comorbidities; 53
percent captured patient-reported outcomes. 88 percent used manual data entry and 18
percent linked to external secondary data sources. Cost, interoperability and vendor
management were barriers to continued registry development.Conclusions: Registries
captured data across a broad scope, audited data quality using multiple techniques, and
used a mix of automated and manual data capture methods. Registry interoperability was
still a challenge, even among registries using nationally accepted data
standards.
Development of an index based on ultrasonographic measurements for the objective appraisal of body condition in Andalusian horses
Authors: Martin-Gimenez Tamara , Aguirre-Pascasio Carla N. , De Blas Ignacio
Published: December 2017

Body condition scoring (BCS) is an indirect measure of the level of subcutaneous fat; however, by measuring the subcutaneous fat thicknesses (SFT), the precision of the degree of fatness assessment is improved. The aims were: 1) to develop an alternative body fat scoring index (BFSI) based on ultrasonographic measurements; 2) to assess the agreement between BCS and the new index applied to Andalusian horses; 3) to adjust the BCS cut-off values (if necessary) for overweight and obesity in this breed. One hundred and sixty-six Andalusian horses were included in this cross sectional study. On each horse, BCS, body fat percentage (BF%) and ultrasonography of SFT at localized deposits were evaluated. According to BFSI five possible body categories were established. Only one horse (0.6%) was classified as emaciated, 9.0% as thin, 74.7% as normal, 11.4% as overweight and 4.2% as obese. Despite higher BCS and SFT values were observed compared to other breeds, most of the horses evaluated presented a normal body condition under the new BFSI. BCS and BFSI were significantly associated (p<0.001), however, the concordance was low (weighted Cohen’s kappa coefficient, 0.262 ± 0.071; p=0.004). Using BFSI, obese horses had significantly greater BF% than the rest of categories (p<0.001). BCS showed a good diagnostic accuracy for detection overweight (AUC = 0.759 ± 0.055; p<0.001) and obese (AUC = 0.878 ± 0.050; p=0.001) horses; redefining the cut-off values for overweight and obesity condition as 7.5/9 and 8.5/9 respectively in Andalusian horses.
Nanostructures: General information. The use of nanoobjects in medicine and cosmetology
Authors: Dębek Paulina , Feliczak-Guzik Agnieszka , Nowak Izabela
Published: December 2017

The general tendency towards the miniaturization of technological systems and materials has prompted intensive development of nanotechnology. It is a quickly developing area of science devoted to the production and application of nanomaterial structures defined as those whose one size does not exceed 100 nm. Nanostructures have been found to show new physical, chemical and biological properties often better than the corresponding materials made of particles of micrometric or macrometric sizes, so they have become of great interest in many areas of industry as well as other areas [22], such as medicine and cosmetology. According to literature and Scopus database, Fig. 1, the most popular nanostructures used in medicine and cosmetology, besides silver and gold nanoparticles, are those of other transition metals such as platinum, palladium or ruthenium.
This paper is concerned with the wide range of present and potential applications of nanomaterials
in medicine and cosmetology.
The role of pepsin in the laryngopharyngeal reflux
Authors: Kowalik Katarzyna , Krzeski Antoni
Published: December 2017

Laryngopharyngeal reflux (LPR) is a common defect among laryngological and phoniatric patients. Although LPR is
categorized as a superficial gastroesophageal reflux disease (GERD), differential diagnosis should treat these two diseases
separately. LPR symptoms can be assessed in the interview using as a tool the reflux symptom index (RSI). In addition,
changes in the larynx that occur during LPR might be seen during laryngoscopy and classified according to the
reflux finding score (RFS). One of the main mucosal irritants in LPR is pepsin which digests proteins and impairs the
functions of the upper respiratory tract cells by affecting carbonate anhydrase (CAIII) and the Sep 70 protein. Pepsin
initiates inflammatory changes within the larynx, nasopharynx and nasal cavity. The use of pepsin detection in upper
and lower throat secretions is a new direction in LPR diagnostics.
Archeozoologické spracovanie zvieracích pozostatkov zo šibenice pri Slavkove
Authors: Jurkovičová Lenka
Published: December 2017

V doplnění kontextu informací o šibenici ze Slavkova byla provedena archeozoologická analýza, s cílem popsat výskyt živočichů na této lokalitě a rozšířit tak možnosti interpretace archeologické situace. Analyzovaný osteologický materiál byl na základě podrobného zhodnocení tafonomických projevů na kostech rozčleněn do dvou chronologických úseků – první náležející původnímu kontextu provozu šibenice, druhý spíše recentního charakteru. Z prvního období pochází šest druhů domácí i volně žijící fauny, v mladší části souboru bylo identifikováno několik druhů malých či drobných savců, a také pozůstatky ptactva. Lidské zásahy, které byly pozorovány na domestikované fauně ve starším období, svědčí o využití těchto zvířat v rámci potravní strategie lidí na popravišti; stopy natrávení žaludečními šťávami a charakteristické lomy na některých kostech volně žijící fauny v obou etapách odkazují na možné nahromadění vývržků dravým ptactvem.
Wyroki Praskiej Izby Apelacyjnej w sprawach kryminalnych dla sądu w Slavkově u Brna w I połowie XVIII wieku
Authors: Wojtucki Daniel
Published: December 2017

Pražský apelační soud (Appellationsgericht) byl založen nařízením Ferdinanda I. roku 1548. Z počátku se pražští soudci zabývali především rozsudky civilně - správními a teprve od konce 17. století pak i rozsudky kriminálními. Právní naučení se několikrát týkala také Slavkova u Brna. V některých letech, jako např. 1723 a 1732, rozhodovali slavkovské soudní verdikty i opakovaně. Podle rozhodnutí pražských soudců převažoval v první polovině 18. století u odsouzených ze Slavkova trest smrti jako vůbec nejčastější rozsudek. Podle záznamů pražského apelačního soudu byla nejčastěji souzeným trestným činem ve Slavkově vražda (1710, 1711), vražda dítěte nebo plodu (dva případy 1723), krádež (1731, 1732), překupnictví (dva případy 1732), falzifikátorství (1702), kacířství (1706) a prodej kradených věcí (1725). Část odsouzených byla z židovské komunity (1725, 1731, 1732).
Favoriser l’appropriation des propriétés géométriques des quadrilatères à l’école primaire : étude d’une situation d’apprentissage dans le méso-espace
Authors: Gibel Patrick , Blanquart-Henry Sylvie
Published: December 2017

Dans cet article, nous cherchons à déterminer, dans le cadre de l’enseignement des figures planes à l’école primaire, en quoi la confrontation des élèves à des situations d’apprentissage dans l’espace environnant (méso-espace) permet de favoriser la mobilisation et la verbalisation de connaissances spatiales et géométriques. Pour ce faire, nous produisons l’analyse clinique d’une séquence mise en oeuvre dans une classe de fin de primaire dont l’objectif pour les élèves est la reproduction de figures planes dans le méso-espace. Pour identifier précisément les connaissances et les savoirs mobilisés par les élèves en situation d’action et en situation de formulation, nous procédons à une analyse détaillée des différentes formes de raisonnements qui sous-tendent leurs procédures de résolution et de formulation. Pour y parvenir nous utilisons un modèle d’analyse des raisonnements, développé par Bloch et Gibel (2011), qui résulte de l’articulation de deux cadres théoriques : la théorie des situations didactiques et la sémiotique de Peirce. Au-delà de l’utilisation raisonnée des outils mis à disposition des élèves dans l’activité de reproduction des figures, l’analyse didactique donne à voir des éléments particulièrement riches de la dialectique action-formulation. Cette étude permet de rendre compte de la variété, de l’adéquation et de la pertinence des propriétés géométriques mobilisées et formulées par les élèves, favorisant ainsi le passage d’une géométrie instrumentée à une géométrie déductive.
Implication parentale et réussite éducative : différences selon la région de naissance du parent1
Authors: Tardif-Grenier Kristel , Archambault Isabelle
Published: December 2017

L’association entre l’implication parentale dans le suivi scolaire et la réussite éducative de l’élève est bien documentée. La présente étude vise à établir dans quelle mesure l’implication parentale dans le suivi scolaire est associée au rendement et à l’engagement scolaire d’élèves du primaire qui sont issus de l’immigration. Au total, 296 élèves répartis dans cinq écoles montréalaises situées en milieu défavorisé ainsi que leur parent et leur enseignant ont participé à cette étude longitudinale. Étant donné que la population immigrante constitue un groupe hétérogène sur les plans culturel et socioéconomique, nous avons examiné les différences en fonction de la région de naissance du parent, soit le Canada, l’Afrique du Nord et les Antilles. Les résultats quantitatifs issus des analyses de parcours multi-groupes suggèrent que les parents nés dans les Antilles se distinguent des deux autres groupes par le fait que chez ce groupe, les discussions fréquentes avec l’enfant au sujet de l’école et l’encadrement étroit de la période des devoirs sont associés à un rendement scolaire plus faible chez l’enfant.
gapFinisher: a reliable gap filling pipeline for SSPACE-LongRead scaffolder output
Authors: Kammonen Juhana I , Smolander Olli-Pekka , Paulin Lars , Pereira Pedro AB , Laine Pia , Koskinen Patrik , Jernvall Jukka , Auvinen Petri
Published: December 2017

Unknown sequences, or gaps, are largely present in most published genomes across public databases. Gap filling is an important finishing step in de novo genome assembly, especially in large genomes. The gap filling problem is nontrivial and while many computational tools exist partially solving the problem, several have shortcomings as to the reliability and correctness of the output, i.e. the gap filled draft genome. SSPACE-LongRead is a scaffolding software that utilizes long reads from multiple third-generation sequencing platforms in finding links between contigs and combining them. The long reads potentially contain sequence information to fill the gaps, but SSPACE-LongRead currently lacks this functionality. We present an automated pipeline called gapFinisher to process SSPACE-LongRead output to fill gaps after the actual scaffolding. gapFinisher is based on controlled use of a gap filling tool called FGAP and works on all standard Linux/UNIX command lines. We conclude that performing the workflows of SSPACE-LongRead and gapFinisher enables users to fill gaps reliably. There is no need for further scrutiny of the existing sequencing data after performing the analysis.
Does Flexible Flatfoot Require Treatment?: Plantar Pressure Effects of Wearing Over-the-Counter Insoles when Walking on a Level Surface and Up and Down Stairs in Adults with Flexible Flatfoot
Authors: Zhai JunNa , Qiu YuSheng , Wang Jue
Published: December 2017

Background:

Orthotic insole is a popular physiotherapy for flatfoot. However, the effects and whether flexible flatfoot needs orthotic insole treatment are not clear, and how the plantar pressure changes while walking up and down stairs has not been studied. Therefore, this study observed the plantar pressures of different walking conditions to find the answers.

Methods:

Fifteen adults with flexible flatfoot and 15 adults with normal foot were examined while walking on a level surface and while walking up and down 10- and 20-cm stairs before treatment. The maximum force and the arch index were acquired with a force plate system. Participants with flexible flatfoot were instructed to wear the orthotic insoles for 3 months, and plantar pressures were measured again after treatment. The repeated measure was performed to analyze the data.

Results:

The maximum force and the arch index of flatfoot after treatment were significantly decreased under different walking conditions (P < .01). When walking down 10- and 20-cm stairs, the plantar data of normal foot and flatfoot were significantly increased (P < .05).

Conclusions:

Orthotic insoles could effectively improve the plantar pressure of flatfoot under different walking conditions. In addition, the arches of normal foot and flatfoot were obviously influenced when walking down stairs. It is, therefore, necessary to wear orthotic insoles for flexible flatfoot to prevent further deformation.
Multi-scale and multi-site resampling of a study area in spatial genetics: implications for flying insect species
Authors: Haran Julien M. , Rossi Jean-Pierre , Pajares Juan , Bonifacio Luis , Naves Pedro , Roques Alain , Roux Géraldine
Published: December 2017

The use of multiple sampling areas in landscape genetic analysis has been recognized as a useful way of generalizing the patterns of environmental effects on organism gene flow. It reduces the variability in inference which can be substantially affected by the scale of the study area and its geographic location. However, empirical landscape genetic studies rarely consider multiple sampling areas due to the sampling effort required. In this study, we explored the effects of environmental features on the gene flow of a flying long-horned beetle (Monochamus galloprovincialis) using a landscape genetics approach. To account for the unknown scale of gene flow and the multiple local confounding effects of evolutionary history and landscape changes on inference, we developed a way of resampling study areas on multiple scales and in multiple locations (sliding windows) in a single large-scale sampling design. Landscape analyses were conducted in 3*104study areas ranging in scale from 220 to 1,000 km and spread over 132 locations on the Iberian Peninsula. The resampling approach made it possible to identify the features affecting the gene flow of this species but also showed high variability in inference among the scales and the locations tested, independent of the variation in environmental features. This method provides an opportunity to explore the effects of environmental features on organism gene flow on the whole and reach conclusions about general landscape effects on their dispersal, while limiting the sampling effort to a reasonable level.
Information from dynamic length changes improves reliability of static ultrasound fascicle length measurements
Authors: Aeles Jeroen , Lichtwark Glen A. , Lenchant Sietske , Vanlommel Liesbeth , Delabastita Tijs , Vanwanseele Benedicte
Published: December 2017

Purpose

Various strategies for improving reliability of fascicle identification on ultrasound images are used in practice, yet these strategies are untested for effectiveness. Studies suggest that the largest part of differences between fascicle lengths on one image are attributed to the error on the initial image. In this study, we compared reliability results between different strategies.

Methods

Static single-image recordings and image sequence recordings during passive ankle rotations of the medial gastrocnemius were collected. Images were tracked by three different raters. We compared results from uninformed fascicle identification (UFI) and results with information from dynamic length changes, or data-informed tracking (DIT). A second test compared tracking of image sequences of either fascicle shortening (initial-long condition) or fascicle lengthening (initial-short condition).

Results

Intra-class correlations (ICC) were higher for the DIT compared to the UFI, yet yielded similar standard error of measurement (SEM) values. Between the initial-long and initial-short conditions, similar ICC values, coefficients of multiple determination, mean squared errors, offset-corrected mean squared errors and fascicle length change values were found for the DIT, yet with higher SEM values and greater absolute fascicle length differences between raters on the first image in the initial-long condition and on the final image in the initial-short condition.

Conclusions

DIT improves reliability of fascicle length measurements, without lower SEM values. Fascicle length on the initial image has no effect on subsequent tracking results. Fascicles on ultrasound images should be identified by a single rater and care should be taken when comparing absolute fascicle lengths between studies.
Genome-wide characterization and expression profiling ofNACtranscription factor genes under abiotic stresses in radish (Raphanus sativusL.)
Authors: Karanja Bernard Kinuthia , Xu Liang , Wang Yan , Muleke Everlyne M’mbone , Jabir Bashir Mohammed , Xie Yang , Zhu Xianwen , Cheng Wanwan , Liu Liwang
Published: December 2017

NAC (NAM, no apical meristem; ATAF,Arabidopsistranscription activation factor and CUC, cup-shaped cotyledon) proteins are among the largest transcription factor (TF) families playing fundamental biological processes, including cell expansion and differentiation, and hormone signaling in response to biotic and abiotic stresses. In this study, 172 RsNACs comprising 17 membrane-bound members were identified from the whole radish genome. In total, 98RsNACgenes were non-uniformly distributed across the nine radish chromosomes.In silicoanalysis revealed that expression patterns of severalNACgenes were tissue-specific such as a preferential expression in roots and leaves. In addition, 21 representativeNACgenes were selected to investigate their responses to heavy metals (HMs), salt, heat, drought and abscisic acid (ABA) stresses using real-time polymerase chain reaction (RT-qPCR). As a result, differential expressions among these genes were identified whereRsNAC023andRsNAC080genes responded positively to all stresses except ABA, whileRsNAC145responded more actively to salt, heat and drought stresses compared with other genes. The results provides more valuable information and robust candidate genes for future functional analysis for improving abiotic stress tolerances in radish.
Homogenization Methods and Multiscale Modeling
Authors: Zohdi Tarek I.
Published: December 2017

The relatively recent increase in computational power available for mathematical modeling and simulation raises the possibility that modern numerical methods can play a significant role in the analysis of materials possessing heterogeneous microstructure. Ideally, in an attempt to reduce laboratory expense, one would like to make predictions of a new material's behavior by numerical simulations, with the primary goal being to accelerate the trial‐and‐error laboratory development of novel high‐performance materials. This fact, among others, has motivated the work that will be presented in this encyclopedia.
Fluid–Structure Interaction and Flows with Moving Boundaries and Interfaces
Authors: Tezduyar Tayfun E. , Takizawa Kenji , Bazilevs Yuri
Published: December 2017

Flows with moving boundaries and interfaces (MBI) include fluid–structure interaction and a number of other classes of problems, such as fluid–object interaction, fluid–particle interaction, free‐surface and multifluid flows, and flows with solid surfaces in fast, linear, or rotational relative motion. These problems are frequently encountered in engineering analysis and design, pose some of the most formidable computational challenges, and have a common core computational technology need. Bringing solution and analysis to them motivated the development of a good number of core computational methods and special methods targeting specific classes of MBI problems. This chapter is an overview of some of those core and special methods, with a focus on computational examples from the ST‐VMS and ALE‐VMS methods and special methods developed in conjunction with the two.
Predictive Computational Science: Computer Predictions in the Presence of Uncertainty
Authors: Oden John Tinsley , Babuška Ivo , Faghihi Danial
Published: December 2017

Predictive computational science is the scientific discipline concerned with assessing the predictability of mathematical and computational models of physical events in the presence of uncertainties. It embraces the processes of model selection, statistical calibration and validation of models, model verification, and their use in forecasting features of physical events with quantified uncertainty.

In this exposition, the conceptual, mathematical, and statistical foundations of predictive computational science are presented together with demonstrative applications to simple problems in structural mechanics.
Mathematical Foundations of Elastoplastic Deformations in Solids
Authors: Daya Reddy B.
Published: December 2017

This chapter presents a treatment of the mathematical aspects of continuum elastoplasticity. The focus is on rate‐independent material behavior, with the flow relations constructed within the framework of convex analysis. The basis for variational treatments of the problem is the versions of the flow relation that use the dissipation function or, alternatively, the yield surface with a normality law: these are referred to, respectively, as the primal and dual formulations. Both formulations are discussed, with emphasis on the former. Some results on the convergence of fully discrete approximations, using finite elements in space, are presented. The associated predictor–corrector algorithms are described, and their convergence behavior is discussed. A discussion of the large‐deformation theory includes an overview of the derivative‐free energetic formulation, due to Mielke and coworkers, and of which the primal formulation discussed in the small‐strain theory is a special case. Relevant results from functional analysis and function spaces are summarized at appropriate places in the presentation.
Extended Finite Element Methods
Authors: Moës Nicolas , Dolbow J. E. , Sukumar N.
Published: December 2017

This chapter begins with a mechanical description of models involving stationary and moving interfaces. The extended finite element method (X‐FEM) is then detailed for three different scenarios: crack‐like interfaces, material interfaces, and free surfaces. As in the case of related methods (generalized FEM (GFEM), partition of unity FEM (PUFEM)), X‐FEM relies on approximation technology that is based on a partition of unity construction. The method uses evolving enrichment functions to represent evolving geometric features and capture the local character of the solution in their vicinity. The use of the level‐set method to update such features is a natural complement to X‐FEM.
Computational Phase‐Field Modeling
Authors: Gomez Hector , van der Zee Kristoffer G.
Published: December 2017

Phase‐field modeling is emerging as a promising tool for the treatment of problems with interfaces. The classical description of interface problems requires the numerical solution of partial differential equations on moving domains in which the domain motions are also unknowns. The computational treatment of these problems requires moving meshes and is very difficult when these domains undergo topological changes. Phase‐field modeling may be understood as a methodology to reformulate interface problems as equations posed on fixed domains. In some cases, the phase‐field model may be shown to converge to the moving‐boundary problem as a regularization parameter tends to zero, which shows the mathematical soundness of the approach. However, this is only part of the story because phase‐field models do not need to have a moving‐boundary problem associated and can be rigorously derived from classical thermomechanics. In this context, the distinguishing feature is that constitutive models depend on the variational derivative of the free energy. In all, phase‐field models open the opportunity for the efficient treatment of outstanding problems in computational mechanics, such as the interaction of a large number of cracks in three dimensions, cavitation, film and nucleate boiling, tumor growth, or fully three‐dimensional air–water flows with surface tension. In addition, phase‐field models bring a new set of challenges for numerical discretization, which will excite the computational mechanics community.
1D and 2D phase gradient perforated dielectric reflective surfaces atmmWave
Authors: Al-Nuaimi Mustafa K. Taher , Hong Wei , Gao Xiqi
Published: December 2017

This paper presents the design of all dielectric non-absorptive phase gradient reflective surfaces that can be used to manipulate the reflected electromagnetic waves at millimeter-wave regime. Compared with a bare perfect electrical conductor reflector which obeys the classical Snell's law of reflection, the presented design can effectively alter both the shape and level of the backscattered energy and thus radar cross section (RCS) reduction is achieved in the specular direction. One- and two-dimensional phase gradient reflective dielectric surfaces of phase change about 72° across their apertures are designed and their ability to manipulate the reflected waves under normal incidence are investigated both by means of full-wave simulations and experimentally tested for validation. More than 6 dB of specular RCS reduction is achieved from about 66.5–78.2 GHz.
A polygenic score for schizophrenia predicts glycemic control
Authors: Cao Han , Chen Junfang , Meyer-Lindenberg Andreas , Schwarz Emanuel
Published: December 2017

Schizophrenia is substantially comorbid with type 2 diabetes (T2D), but the molecular basis of this effect is incompletely understood. Here, we show that a cortical schizophrenia expression score predicts glycemic control from pancreatic islet cell expression. We used machine learning to identify a cortical expression signature in 212 schizophrenia patients and controls, which explained ~25% of the illness-associated variance. The algorithm was predicted in expression data from 51 subjects (9 with T2D), explained up to 26.3% of the variance in the glycemic control indicator HbA1c and could significantly differentiate T2D patients from controls. The cross-tissue prediction was driven by processes previously linked to diabetes. Genes contributing to this prediction were involved in the electron transport chain as well as kidney development and support oxidative stress as a molecular process underlying the comorbidity between both conditions. Together, the present results suggest a molecular commonality between schizophrenia and glycemic markers of type 2 diabetes.
DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty
Authors: Zhang Xinyu , Hu Ying , Justice Amy C , Li Boyang , Wang Zuoheng , Zhao Hongyu , Krystal John H , Xu Ke
Published: December 2017

Intravenous illicit drug use (IDU) and hepatitis C infection (HCV) commonly co-occur among HIV-infected individuals. These co-occurring conditions may produce interacting epigenetic effects in white blood cells that influence immune function and health outcomes. Here, we report an epigenome-wide association analysis comparing IDU+/ HCV+ and IDU−/HCV− in 386 HIV-infected individuals as a discovery sample and in 412 individuals as a replication sample. We observe 6 significant CpGs in the promoters of 4 genes, NLRC5, TRIM69, CX3CR1, and BCL9, in the discovery sample and in meta-analysis. We identify 19 differentially methylated regions on chromosome 6 harboring MHC gene clusters. Importantly, a panel of IDU+/HCV+-associated CpGs discriminated HIV frailty based upon a validated index with an area under the curve of 79.3% for high frailty and 82.3% for low frailty. These findings suggest that IDU and HCV involve epigenetic programming and that their associated methylation signatures discriminate HIV pathophysiologic frailty.
Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1
Authors: Cifdaloz Metehan , Osterloh Lisa , Graña Osvaldo , Riveiro-Falkenbach Erica , Ximénez-Embún Pilar , Muñoz Javier , Tejedo Cristina , Calvo Tonantzin G. , Karras Panagiotis , Olmeda David , Miñana Belén , Gómez-López Gonzalo , Cañon Estela , Eyras Eduardo , Guo Haihong , Kappes Ferdinand , Ortiz-Romero Pablo L. , Rodríguez-Peralto Jose L. , Megías Diego , Valcárcel Juan , Soengas María S.
Published: December 2017

Melanomas are well-known for their altered mRNA expression profiles. Yet, the specific contribution of mRNA binding proteins (mRBPs) to melanoma development remains unclear. Here we identify a cluster of melanoma-enriched genes under the control of CUGBP Elav-like family member 1 (CELF1). CELF1 was discovered with a distinct prognostic value in melanoma after mining the genomic landscape of the 692 known mRBPs across different cancer types. Genome-wide transcriptomic, proteomic, and RNA-immunoprecipitation studies, together with loss-of-function analyses in cell lines, and histopathological evaluation in clinical biopsies, revealed an intricate repertoire of CELF1-RNA interactors with minimal overlap with other malignancies. This systems approach uncovered the oncogene DEK as an unexpected target and downstream effector of CELF1. Importantly, CELF1 and DEK were found to represent early-induced melanoma genes and adverse indicators of overall patient survival. These results underscore novel roles of CELF1 in melanoma, illustrating tumor type-restricted functions of RBPs in cancer.