bluuebunny/crossref_metadata_2025 huggingface dataset:
Congenital deafness affects deep layers in primary and secondary auditory cortex
Authors: Berger Christoph , Kühne Daniela , Scheper Verena , Kral Andrej
Published: June 2017

Congenital deafness leads to functional deficits in the auditory cortex for which early cochlear implantation can effectively compensate. Most of these deficits have been demonstrated functionally. Furthermore, the majority of previous studies on deafness have involved the primary auditory cortex; knowledge of higher‐order areas is limited to effects of cross‐modal reorganization. In this study, we compared the cortical cytoarchitecture of four cortical areas in adult hearing and congenitally deaf cats (CDCs): the primary auditory field A1, two secondary auditory fields, namely the dorsal zone and second auditory field (A2); and a reference visual association field (area 7) in the same section stained either using Nissl or SMI‐32 antibodies. The general cytoarchitectonic pattern and the area‐specific characteristics in the auditory cortex remained unchanged in animals with congenital deafness. Whereas area 7 did not differ between the groups investigated, all auditory fields were slightly thinner in CDCs, this being caused by reduced thickness of layers IV–VI. The study documents that, while the cytoarchitectonic patterns are in general independent of sensory experience, reduced layer thickness is observed in both primary and higher‐order auditory fields in layer IV and infragranular layers. The study demonstrates differences in effects of congenital deafness between supragranular and other cortical layers, but similar dystrophic effects in all investigated auditory fields.
Searching Online Mendelian Inheritance in Man (OMIM): A Knowledgebase of Human Genes and Genetic Phenotypes
Authors: Amberger Joanna S. , Hamosh Ada
Published: June 2017

Online Mendelian Inheritance in Man (OMIM) at OMIM.org is the primary repository of comprehensive, curated information on genes and genetic phenotypes and the relationships between them. This unit provides an overview of the types of information in OMIM and optimal strategies for searching and retrieving the information. OMIM.org has links to many related and complementary databases, providing easy access to more information on a topic. The relationship between genes and genetic disorders is highlighted in this unit. The basic protocol explains searching OMIM both from a gene perspective and a clinical features perspective. Two alternate protocols provide strategies for viewing gene‐phenotype relationships: a gene map table and Quick View or Side‐by‐Side format for clinical features. OMIM.org is updated nightly, and the MIMmatch service, described in the support protocol, provides a convenient way to follow updates to entries, gene‐phenotype relationships, and collaborate with other researchers. © 2017 by John Wiley & Sons, Inc.
Photoactivated In Vivo Proximity Labeling
Authors: Beck David B. , Bonasio Roberto
Published: June 2017

Identification of molecular interactions is paramount to understanding how cells function. Most available technologies rely on co‐purification of a protein of interest and its binding partners. Therefore, they are limited in their ability to detect low‐affinity interactions and cannot be applied to proteins that localize to difficult‐to‐solubilize cellular compartments. In vivo proximity labeling (IPL) overcomes these obstacles by covalently tagging proteins and RNAs based on their proximity in vivo to a protein of interest. In IPL, a heterobifunctional probe comprising a photoactivatable moiety and biotin is recruited by a monomeric streptavidin tag fused to a protein of interest. Following UV irradiation, candidate interacting proteins and RNAs are covalently biotinylated with tight spatial and temporal control and subsequently recovered using biotin as an affinity handle. Here, we describe experimental protocols to discover novel protein‐protein and protein‐RNA interactions using IPL. © 2017 by John Wiley & Sons, Inc.
Designing Drug‐Response Experiments and Quantifying their Results
Authors: Hafner Marc , Niepel Mario , Subramanian Kartik , Sorger Peter K.
Published: June 2017

We developed a Python package to help in performing drug‐response experiments at medium and high throughput and evaluating sensitivity metrics from the resulting data. In this article, we describe the steps involved in (1) generating files necessary for treating cells with the HP D300 drug dispenser, by pin transfer or by manual pipetting; (2) merging the data generated by high‐throughput slide scanners, such as the Perkin Elmer Operetta, with treatment annotations; and (3) analyzing the results to obtain data normalized to untreated controls and sensitivity metrics such as IC50 or GR50. These modules are available on GitHub and provide an automated pipeline for the design and analysis of high‐throughput drug response experiments, that helps to prevent errors that can arise from manually processing large data files. © 2017 by John Wiley & Sons, Inc.
Corporate Social Responsibility in Supply Chains of Small and Medium‐Sized Enterprises
Authors: Lee Hee‐Yong , Kwak Dong‐Wook , Park Jeong‐Yang
Published: June 2017

Research has shown that implementation of corporate social responsibility (CSR) practice represents a considerable challenge for small and medium‐sized enterprises (SMEs). This research conceptualises the dimensions and contingencies of CSR in SME supply chains. Drawing on institutional theory and stakeholder theory, we investigated the degree of importance and implementation of CSR practices in SMEs. A large‐scale questionnaire survey with SMEs in manufacturing sectors and panel discussions were conducted in South Korea. The findings indicate that SMEs tend to focus on explicit CSR practices that can be easily identified by their customers. Consistent with this, stakeholder and institutional pressures were valid in the performance of CSR practices, but largely biased to customers, government, and regulatory pressures. Based on institutional theory and stakeholder theory as overarching theoretical lenses, this research contributes to a fuller understanding of the dimensions of CSR practices in the supply chains from an SME perspective. Copyright © 2017 John Wiley & Sons, Ltd and ERP Environment
Molecular Self‐Assembly Fabrication and Carrier Dynamics of Stable and Efficient CH3NH3Pb(1−x)SnxI3 Perovskite Solar Cells
Authors: Fan Jiandong , Liu Chong , Li Hongliang , Zhang Cuiling , Li Wenzhe , Mai Yaohua
Published: June 2017

The Sn‐based perovskite solar cells (PSCs) provide the possibility of swapping the Pb element toward developing toxic‐free PSCs. Here, we innovatively employed a molecular self‐assembly approach to obtain a series CH3NH3Pb(1−x)SnxI3 (0≤x≤1) perovskite thin films with full coverage. The optimized planar CH3NH3Pb0.75Sn0.25I3 PSC with inverted structure was consequently realized with a maximum power conversion efficiency (PCE) over 14 %, which displayed a stabilized power output (SPO) over 12 % within 200 s at 0.6 V forward bias. Afterward, we investigated the factors that limited the efficiency improvement of hybrid Sn–Pb PSCs, and analyzed the possible reason of the hysteresis effect occurred even in the inverted structure cell. Particularly, the oxidation of hybrid Sn–Pb perovskite thin film was demonstrated to be the main reason that limited its further efficiency improvement. The imbalance of charge transport was intensified, which was associated with the increased hole defect‐state density and decreased electron defect‐state density after Sn was introduced. This study helps tackle the intractable issue regarding the toxic Pb in perovskite devices and is a step forward toward realizing lead‐free PSCs with high stability and efficiency.
Shear resistance verification of late 19th century masonry according to EC 6 – State of the art
Authors: Dunjic Viktor , Kolbitsch Andreas
Published: June 2017

A large part of buildings in Central European cities like Vienna was built in the Gründerzeit period between about 1840 and 1918 [1]. These buildings were constructed according to traditional rules. Current urban development requires historic buildings to be structurally adapted, which requires retroactive analysis of the masonry walls; in Austria according to ÖNORM EN 1998‐3 [2] and ÖNORM EN 1996‐3 (EC 6) [3]. Here, special focus is on the load transfer of horizontal earthquake loads, i. e. the shear strength of masonry walls.

This paper describes the verification of historic masonry in detail and discusses individual components. Initial shear strength, load‐influenced friction and the length of the compressed part of the wall are first determined using results from experimental testing and relevant literature and then compared to the approaches in EC 6. Based on this analysis, recommendations are provided to make theoretical approaches more realistic.
Energy‐efficient masonry buildings
Authors: Schoch Torsten
Published: June 2017

In line with the general trend to improved energy‐related properties of buildings in massive construction, many massive buildings have been designed and built in recent years, which have proactively observed and also helped to determine the specification of future building standards in Europe. According to [1], the first low‐energy house was built in Kassel in 1986 with an area‐related energy demand for hot water and heating of only 60 kWh/(m2a). The use of massive building materials with low thermal conductivity played a similarly important role in this case to the increasing use of thermal insulation materials and new building services technology using renewable energy sources. Keeping the constructional details simple to build by tradesmen in order to avoid thermal bridging and useless building mistakes was and is still an important practical requirement. With the help of examples, the article demonstrates that monolithic construction is suitable for compliance with current energy‐related requirements and how this is carried out.
Maximizing functional axon repair in the injured central nervous system: Lessons from neuronal development
Authors: Kaplan Andrew , Bueno Mardja , Hua Luyang , Fournier Alyson E.
Published: June 2017

The failure of damaged axons to regrow underlies disability in central nervous system injury and disease. Therapies that stimulate axon repair will be critical to restore function. Extensive axon regeneration can be induced by manipulation of oncogenes and tumor suppressors; however, it has been difficult to translate this into functional recovery in models of spinal cord injury. The current challenge is to maximize the functional integration of regenerating axons to recover motor and sensory behaviors. Insights into axonal growth and wiring during nervous system development are helping guide new approaches to boost regeneration and functional connectivity after injury in the mature nervous system. Here we discuss our current understanding of axonal behavior after injury and prospects for the development of drugs to optimize axon regeneration and functional recovery after CNS injury. Developmental Dynamics 247:18–23, 2018. © 2017 Wiley Periodicals, Inc.
Pairing field methods to improve inference in wildlife surveys while accommodating detection covariance
Authors: Clare John , McKinney Shawn T. , DePue John E. , Loftin Cynthia S.
Published: June 2017

It is common to use multiple field sampling methods when implementing wildlife surveys to compare method efficacy or cost efficiency, integrate distinct pieces of information provided by separate methods, or evaluate method‐specific biases and misclassification error. Existing models that combine information from multiple field methods or sampling devices permit rigorous comparison of method‐specific detection parameters, enable estimation of additional parameters such as false‐positive detection probability, and improve occurrence or abundance estimates, but with the assumption that the separate sampling methods produce detections independently of one another. This assumption is tenuous if methods are paired or deployed in close proximity simultaneously, a common practice that reduces the additional effort required to implement multiple methods and reduces the risk that differences between method‐specific detection parameters are confounded by other environmental factors. We develop occupancy and spatial capture–recapture models that permit covariance between the detections produced by different methods, use simulation to compare estimator performance of the new models to models assuming independence, and provide an empirical application based on American marten (Martes americana) surveys using paired remote cameras, hair catches, and snow tracking. Simulation results indicate existing models that assume that methods independently detect organisms produce biased parameter estimates and substantially understate estimate uncertainty when this assumption is violated, while our reformulated models are robust to either methodological independence or covariance. Empirical results suggested that remote cameras and snow tracking had comparable probability of detecting present martens, but that snow tracking also produced false‐positive marten detections that could potentially substantially bias distribution estimates if not corrected for. Remote cameras detected marten individuals more readily than passive hair catches. Inability to photographically distinguish individual sex did not appear to induce negative bias in camera density estimates; instead, hair catches appeared to produce detection competition between individuals that may have been a source of negative bias. Our model reformulations broaden the range of circumstances in which analyses incorporating multiple sources of information can be robustly used, and our empirical results demonstrate that using multiple field‐methods can enhance inferences regarding ecological parameters of interest and improve understanding of how reliably survey methods sample these parameters.
Alternative foraging strategies enable a mountain ungulate to persist after migration loss
Authors: Courtemanch Alyson B. , Kauffman Matthew J. , Kilpatrick Steve , Dewey Sarah R.
Published: June 2017

The persistence of many migratory ungulate populations worldwide is threatened due to anthropogenic impacts to seasonal ranges and migration routes. While many studies have linked migratory ungulate declines to migration disruption or loss, very few have explored the underlying factors that determine whether a population perishes or persists. In some cases, populations undergo severe declines and extirpation after migration loss; however, others appear able to persist as residents. We predict that to persist, populations must replace the traditional benefits of migration by altering the foraging strategies they employ as residents within one seasonal range. We propose the alternative foraging strategies (AFS) hypothesis as a framework for identifying various behavioral strategies that populations may use to cope with migration loss. We tested the hypothesis using the formerly migratory Teton bighorn sheep population in northwest Wyoming, which ceased migrating over 60 yr ago, but has persisted as a resident population. We used global positioning system data to evaluate winter and summer habitat selection and seasonal elevational movements for 28 adult female bighorn sheep (Ovis canadensis) from 2008 to 2010. Resource selection functions revealed that bighorn sheep employ winter foraging strategies to survive as residents by seeking out rugged, high‐elevation, windswept ridgelines. Seasonal movement analyses indicated that bighorn sheep undergo a newly documented “abbreviated migration” strategy that is closely synchronized with vegetation green‐up patterns within their one range. Bighorn sheep descend 500 m in elevation and travel up to 10 km in spring, gaining access to newly emergent forage approximately 30 d before it appears on their high‐elevation winter and summer ranges. Our findings indicate that the Teton bighorn sheep population has persisted due to its habitat selection, AFS, and unique movement patterns, which allow migration loss to be mediated to some extent. The identification of AFS and the habitats that support them can help reveal the underlying benefits of migration and conserve populations in the face of future migration loss.
Defining ecosystem thresholds for human activities and environmental pressures in the California Current
Authors: Samhouri Jameal F. , Andrews Kelly S. , Fay Gavin , Harvey Chris J. , Hazen Elliott L. , Hennessey Shannon M. , Holsman Kirstin , Hunsicker Mary E. , Large Scott I. , Marshall Kristin N. , Stier Adrian C. , Tam Jamie C. , Zador Stephani G.
Published: June 2017

The oceans are changing more rapidly than ever before. Unprecedented climatic variability is interacting with unmistakable long‐term trends, all against a backdrop of intensifying human activities. What remains unclear, however, is how to evaluate whether conditions have changed sufficiently to provoke major responses of species, habitats, and communities. We developed a framework based on multimodel inference to define ecosystem‐based thresholds for human and environmental pressures in the California Current marine ecosystem. To demonstrate how to apply the framework, we explored two decades of data using gradient forest and generalized additive model analyses, screening for nonlinearities and potential threshold responses of ecosystem states (n = 9) across environmental (n = 6) and human (n = 10) pressures. These analyses identified the existence of threshold responses of five ecosystem states to four environmental and two human pressures. Both methods agreed on threshold relationships in two cases: (1) the winter copepod anomaly and habitat modification, and (2) sea lion pup production and the summer mode of the Pacific Decadal Oscillation (PDO). Considered collectively, however, these alternative analytical approaches imply that as many as five of the nine ecosystem states may exhibit threshold changes in response to negative PDO values in the summer (copepods, scavengers, groundfish, and marine mammals). This result is consistent with the idea that the influence of the PDO extends across multiple trophic levels, but extends current knowledge by defining the nonlinear nature of these responses. This research provides a new way to interpret changes in the intensities of human and environmental pressures as they relate to the ecological integrity of the California Current ecosystem. These insights can be used to make more informed assessments of when and under what conditions intervention, preparation, and mitigation may enhance progress toward ecosystem‐based management goals.
ABNO‐Catalyzed Aerobic Oxidative Synthesis of 2‐Substituted 4H‐3,1‐Benzoxazines and Quinazolines
Authors: Ma Jiaqi , Wan Yan , Hong Chao , Li Meichao , Hu Xinquan , Mo Weimin , Hu Baoxiang , Sun Nan , Jin Liqun , Shen Zhenlu
Published: June 2017

A new transition‐metal‐free 9‐azabicyclo[3.3.1]nonan‐N‐oxyl (ABNO) catalyzed aerobic oxidative synthesis of 2‐substituted 4H‐3,1‐benzoxazines and quinazolines has been developed through cascade reaction of aldehydes with 2‐aminobenzyl alcohols and 2‐aminobenzylamines, respectively. Under the optimal reaction conditions, the two kinds of heterocycles were obtained in 72–97 % isolated yield.
Focus on the 5 Ts for effective word‐of‐mouth marketing
Authors: Hope Joan
Published: June 2017

NEW ORLEANS —When people are excited about your college, they want to talk about it. And word‐of‐mouth marketing is the most effective kind, said Michele Kersten‐Hart, manager of multimedia and web services at Oakland Community College and president of the National Council for Marketing and Public Relations.
Seven strategies to apply design thinking in higher education
Authors: Costa Karen
Published: June 2017

You may have heard of the term design thinking and wondered how it differs from regular thinking. Design thinking is intentional, creative, and supercharged. It's a style of thinking for the 21st century. Applying the principles of design thinking in higher education can help you to solve intransigent problems, generate new models and partnerships, and add an element of playfulness to your work.
Wall modeling via function enrichment within a high‐order DG method for RANS simulations of incompressible flow
Authors: Krank Benjamin , Kronbichler Martin , Wall Wolfgang A.
Published: June 2017

We present a novel approach to wall modeling for the Reynolds‐averaged Navier‐Stokes equations within the discontinuous Galerkin method. Wall functions are not used to prescribe boundary conditions as usual, but they are built into the function space of the numerical method as a local enrichment, in addition to the standard polynomial component. The Galerkin method then automatically finds the optimal solution among all shape functions available. This idea is fully consistent and gives the wall model vast flexibility in separated boundary layers or high adverse pressure gradients. The wall model is implemented in a high‐order discontinuous Galerkin solver for incompressible flow complemented by the Spalart‐Allmaras closure model. As benchmark examples, we present turbulent channel flow starting from Reτ=180 and up to Reτ=100000 as well as flow past periodic hills at Reynolds numbers based on the hill height of ReH=10595 and ReH=19000.
Therapeutic D2/3 receptor occupancies and response with low amisulpride blood concentrations in very late‐onset schizophrenia‐like psychosis (VLOSLP)
Authors: Reeves Suzanne , Eggleston Kate , Cort Elizabeth , McLachlan Emma , Brownings Stuart , Nair Akshay , Greaves Suki , Smith Alan , Dunn Joel , Marsden Paul , Kessler Robert , Taylor David , Bertrand Julie , Howard Robert
Published: June 2017

Objective

Antipsychotic drug sensitivity in very late‐onset schizophrenia‐like psychosis (VLOSLP) is well documented, but poorly understood. This study aimed to investigate blood drug concentration, D2/3 receptor occupancy and outcome in VLOSLP during open amisulpride prescribing, and compare this with Alzheimer's disease (AD).

Methods

Blood drug concentration, prolactin, symptoms and extrapyramidal side‐effects (EPS) were serially assessed during dose titration. [18F]fallypride imaging was used to quantify D2/3 receptor occupancy. Average steady‐state amisulpride concentration (Caverage, ng/ml) was estimated by incorporating pharmacokinetic (PK) data into an existing population PK model (25 AD participants, 20 healthy older people).

Results

Eight patients (target 20) were recruited (six women; 76 + − 6 years; six treatment compliant; five serially sampled; three with paired imaging data). Mean + − SD symptom reduction was 74 ± 12% (50–100 mg/day; 92.5 + −39.4 ng/ml). Mild EPS emerged at 96 ng/ml (in AD, severe EPS, 50 mg/day, 60 ng/ml). In three participants, imaged during optimal treatment (50 mg/day; 41–70 ng/ml), caudate occupancy was 44–59% (58–74% in AD across a comparable Caverage).

Conclusions

Despite the small sample size, our findings are highly relevant as they suggest that, as in AD, 50 mg/day amisulpride is associated with >40% occupancy and clinically relevant responses in VLOSLP. It was not possible to fully characterise concentration–occupancy relationships in VLOSLP, and it is thus unclear whether the greater susceptibility of those with AD to emergent EPS was accounted for by increased central drug access. Further investigation of age‐ and diagnosis‐specific threshold sensitivities is warranted, to guide amisulpride prescribing in older people, and therapeutic drug monitoring studies offer a potentially informative future approach. Copyright © 2017 John Wiley & Sons, Ltd.
Development of thumb endurance curves associated with various exertion levels
Authors: Choi Kyeong‐Hee , Lee Sung‐Yong , Lee Jun‐Hyub , Kong Yong‐Ku
Published: June 2017

Tasks involving the thumbs of workers are frequently carried out at industrial sites or in laboratories. This study measured thumb endurance time according to relative force levels in males and females. The experiment in this study involved 30 healthy participants (15 males and 15 females). Maximum thumb pressing force (MTPF) was measured and thumb endurance curves were developed using the measured thumb endurance time of participants’ dominant hand according to various force levels (10, 20, 40, 60, 80, and 100% MTPF). On the basis of the results, females demonstrated greater endurance time than males at 20% MTPF, and statistically significant differences according to gender are not shown at MTPF levels of 40% or higher. A rapid increase in endurance time was observed at low force levels. The findings of this study are expected to facilitate the establishment of appropriate working levels for the thumbs of workers in order to optimize work design. In this study, the effects of gender and target force level on thumb endurance time performance were evaluated. The findings of this study could provide valuable information for developing ergonomic guidelines of thumb pressing force tasks for the workers.
The effect of collagen coating on titanium with nanotopography on in vitro osteogenesis
Authors: Costa Daniel G. , Ferraz Emanuela P. , Abuna Rodrigo P. F. , de Oliveira Paulo T. , Morra Marco , Beloti Marcio M. , Rosa Adalberto L.
Published: June 2017

Several studies have shown the positive effects of Ti either with nanotopography or coated with collagen on osteoblast differentiation. Thus, we hypothesized that the association of nanotopography with collagen may increase the in vitro osteogenesis on Ti surface. Ti discs with nanotopography with or without collagen coating were characterized by scanning electron microscopy and atomic force microscopy. Rat calvaria‐derived osteoblastic cells were cultured on both Ti surfaces for up to 14 days and the following parameters were evaluated: cell proliferation, alkaline phosphatase (ALP) activity, extracellular matrix mineralization, protein expression of bone sialoprotein (BSP) and osteopontin (OPN), and gene expression of collagen type 1a (Coll1a), runt‐related transcription factor 2 (Runx2), osterix (OSX), osteocalcin (OC), Ki67, Survivin, and Bcl2‐associated X protein (BAX). Surface characterization evidenced that collagen coating did not alter the nanotopography. Collagen coating increased cell proliferation, ALP activity, extracellular matrix mineralization, and Coll1a, OSX, OC, and BAX gene expression. Also, OPN and BSP proteins were strongly detected in cultures grown on both Ti surfaces. In conclusion, our results showed that the combination of nanotopography with collagen coating stimulates the early, intermediate, and final events of the in vitro osteogenesis and may be considered a potential approach to promote osseointegration of Ti implants. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2783–2788, 2017.
Hemostatic efficiency of modern topical sealants: Comparative evaluation after liver resection and splenic laceration in a swine model
Authors: Fonouni Hamidreza , Kashfi Arash , Majlesara Ali , Stahlheber Oliver , Konstantinidis Lukas , Gharabaghi Negin , Kraus Thomas W. , Mehrabi Arianeb , Oweira Hani
Published: June 2017

Parenchymal transection during hepatobiliary surgery can disrupt small vasculature or bile ducts, which could be managed difficultly. Sealants are helpful tools to achieve better hemostasis. The aim of this study is to analyze the hemostatic efficiency of four modern sealants in a porcine model. In this study, 40 landrace pigs were assigned equally to the control (without sealant) and four sealant groups. Standardized liver resection and splenic lesions were performed and left without using sealant (control) or treated with one of the following sealants: TachoSil®, Tissucol Duo®, Coseal®, and FloSeal®. We measured relative and absolute bleeding times (seconds) as well as total blood loss (g) in a maximum observation time of 300 s. Sealants could show a significantly improved hemostasis comparing to the control group. However, hemostasis was heterogeneous among the sealant groups (liver resection: 60%–100%, spleen injury: 70%–100%). The mean blood loss decreased significantly using sealants comparing to control group (liver resection: 6–120 fold, spleen injury: 2.5–36 fold). The hemostatic time in groups that achieved complete hemostasis was different in each sealant group (liver resection: 30–166 s, spleen injury: 60–180 s). We conclude that the hemostatic efficacy of modern sealants is impressive but heterogeneous in liver resection or splenic lesion. To maximize the effectiveness of these tools, the indication of each sealant should be carefully considered in individual settings by the surgeons. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 1307–1316, 2018.
Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins
Authors: Le Nguyen‐Quoc‐Khanh , Ho Quang‐Thai , Ou Yu‐Yen
Published: June 2017

In several years, deep learning is a modern machine learning technique using in a variety of fields with state‐of‐the‐art performance. Therefore, utilization of deep learning to enhance performance is also an important solution for current bioinformatics field. In this study, we try to use deep learning via convolutional neural networks and position specific scoring matrices to identify electron transport proteins, which is an important molecular function in transmembrane proteins. Our deep learning method can approach a precise model for identifying of electron transport proteins with achieved sensitivity of 80.3%, specificity of 94.4%, and accuracy of 92.3%, with MCC of 0.71 for independent dataset. The proposed technique can serve as a powerful tool for identifying electron transport proteins and can help biologists understand the function of the electron transport proteins. Moreover, this study provides a basis for further research that can enrich a field of applying deep learning in bioinformatics. © 2017 Wiley Periodicals, Inc.
Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems
Authors: Suzuki Kimichi , Morokuma Keiji , Maeda Satoshi
Published: June 2017

We propose a multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems. MSM is a simple extension of the geometrical microiteration technique. In conventional microiteration, the structure of the non‐reaction‐center (surrounding) part is optimized by fixing atoms in the reaction‐center part before displacements of the reaction‐center atoms. In this method, the surrounding part is described as the weighted sum of multiple surrounding structures that are independently optimized. Then, geometric displacements of the reaction‐center atoms are performed in the mean field generated by the weighted sum of the surrounding parts. MSM was combined with the QM/MM‐ONIOM method and applied to chemical reactions in aqueous solution or enzyme. In all three cases, MSM gave lower reaction energy profiles than the QM/MM‐ONIOM‐microiteration method over the entire reaction paths with comparable computational costs. © 2017 Wiley Periodicals, Inc.
Ethnography, Applied Theatre and Stiwanism: Creative Methods in Search of Praxis Amongst Men and Women in Jinja, Uganda
Authors: McQuaid Katie , Plastow Jane
Published: June 2017

This article critically reflects on a long‐term intergenerational project combining ethnographic and social science research methods and Freirean‐inspired applied theatre in a long‐term participatory process working alongside men and women in search of a ‘plenitude of praxis’: strengthening and promoting an urban community's capacity to unite across social barriers in recognising systemic injustices and inequalities and challenging these through community‐led interventions in pursuit of common social justice outcomes. It reflects on the successes, complexities and failures of an approach rooted in African feminism, and in particular stiwanism, in a context of entrenched urban poverty in Jinja Municipality, Uganda. Copyright © 2017 John Wiley & Sons, Ltd.
Influence of Thermo‐Oxidative Ageing of HNBR in Oil Field Applications
Authors: Balasooriya Winoj , Schrittesser Bernd , Karunakaran Santhosh , Schlögl Sandra , Pinter Gerald , Schwarz Thomas , Kadar Zalan
Published: June 2017

The oxidative ageing behavior of carbon black‐ (85 phr) filled hydrogenated nitrile‐butadiene rubber (HNBR) was characterized in this study. HNBR is widely used in many oil and gas field applications for seals, hoses, down‐hole packers etc., due to its intrinsic combination of good heat and excellent oil and chemical resistance, coupled with outstanding physical properties. Hence, to support the material development, it is of prime theoretical and practical importance to characterize the ageing behavior of HNBR. In this work, mechanical properties and dynamic mechanical properties of aged and un‐aged material were examined using tensile, tear and dynamic mechanical analysis tests. Possible micro structural changes and functional groups involved in aging were detected using DQ NMR, Raman spectroscopy and FT‐IR spectroscopy in ATR mode. The results indicated that the ageing process caused the material to deteriorate; tensile strength − strain at break, the strain at tear strength and the damping properties were decreased. Additionally, the stiffness and the glass transition temperature of the material were also raised. According to the literature, residual double bonds in HNBR are involved in forming hydro peroxide and propagating the autocatalytic oxidation process in the presence of oxygen at higher temperature. This process leads to the oxidative degradation resulting in cross‐linking and in chain scissions as the predominant reactions contributing to properties. Furthermore, at ∼100 °C, oxidation through the nitrile group was observed converting the cyano functional group into the imino group; but at higher temperatures, it was negligible. The results suggest that the cross‐linking and the chain scission mechanisms are significant after 72 hours and 168 hours of exposure, respectively, at 150 °C. However, when aged at 170 °C, both cross‐linking and chain scission were even effective after 24 hours of exposure time.
Mixed Mode Fracture Mechanics Behaviour of PMMA
Authors: Lach Ralf , Grellmann Wolfgang
Published: June 2017

The mixed mode brittle fracture (mode I/mode II) of poly(methyl methacrylate) (PMMA) was investigated using single‐edge notched tensile (SENT) specimens by applying a mixed mode special loading device which allows varying the loading angle from 0° (pure mode I) to 90° (pure mode II). The experimental results dealing with mixed mode fracture toughness and initial angle of crack propagation are in good agreement with predictions based on a modified criterion of maximum tangential stress (MTS criterion) where non‐singular stresses (T stresses) are considered. These additional T stresses are the reason why distinct fracture by normal stress with crazing is always macroscopically observed in PMMA under the selected loading conditions including pure external mode II loading. Therefore, the length of the craze zone, i.e. the process zone, has been determined to be about 0.5 mm independent of the loading angle. It has to be pointed out that the fracture surface morphology should be kept in mind more often in future for assessing the mixed mode fracture mechanics parameters.
Circulating microRNA as candidates for early embryonic viability in cattle
Authors: Pohler Ky G. , Green Jonathan A. , Moley Laura A. , Gunewardena Sumedha , Hung Wei‐Ting , Payton Rebecca R. , Hong Xiaoman , Christenson Lane K. , Geary Tom W. , Smith Michael F.
Published: June 2017

Blood‐borne extracellular vesicles (i.e., exosomes and microvesicles) carrying microRNAs (miRNAs) could make excellent biomarkers of disease and different physiologic states, including pregnancy status. We tested the hypothesis that circulating extracellular vesicle‐derived miRNAs might differentiate the pregnancy status of cows that had maintained pregnancy to Day 30 from non‐pregnant cows or from those that exhibited embryonic mortality between Days 17 and 30 of gestation. Cows were randomly assigned for artificial insemination with fertile semen (n = 36) or dead semen (n = 8; control group) on Day 0 (day of estrus). Blood was collected from all animals on Day 0 and on Days 17 and 24 after artificial insemination. Cows receiving live sperm were retrospectively classified as pregnant on Day 30 (n = 17) or exhibiting embryonic mortality between Days 17 and 30 (n = 19). Extracellular vesicles from Day 17 and 24 samples were isolated from serum using ultra‐centrifugation, and their presence was confirmed by nanoparticle tracking and Western blot analyses (for CD81) prior to RNA extraction. MicroRNA sequencing was performed on pregnant, embryonic‐mortality, and control cows (n = 4 per day), for a total of 24 independent reactions. In total, 214 miRNAs were identified in serum, 40 of which were novel. Based on differential abundance parameters, we identified 32 differentially abundant loci, representing 27 differentially abundant mature miRNA. At Days 17 and 24, specific miRNAs (e.g., miR‐25, ‐16b, and ‐3596) were identified that differentiated the pregnancy status. In summary, we identified several circulating extracellular vesicles derived miRNAs that differ in abundance between embryonic mortality and pregnant cows.
Simultaneous mapping of metabolites and individual macromolecular components via ultra‐short acquisition delay 1H MRSI in the brain at 7T
Authors: Považan Michal , Strasser Bernhard , Hangel Gilbert , Heckova Eva , Gruber Stephan , Trattnig Siegfried , Bogner Wolfgang
Published: June 2017

Purpose

Short‐echo‐time proton MR spectra at 7T feature nine to 10 distinct macromolecule (MM) resonances that overlap with the signals of metabolites. Typically, a metabolite‐nulled in vivo MM spectrum is included in the quantification`s prior knowledge to provide unbiased metabolite quantification. However, this MM model may fail if MMs are pathologically altered. In addition, information about the individual MM peaks is lost. In this study, we aimed to create an improved MM model by parameterization of the in vivo MM spectrum into individual components, and to use this new model to quantify free induction decay MR spectroscopic imaging (FID‐MRSI) data.

Methods

The measured in vivo MM spectrum was parameterized using advanced method for accurate, robust, and efficient spectral fitting (AMARES) and Hankel‐Lanczos singular value decomposition algorithms from which six different MM models were derived. Soft constraints were applied to avoid over‐parameterization. All MM models were combined with simulated metabolite spectra to form complete basis sets. FID‐MRSI data from 14 healthy volunteers were quantified via LCModel, and the results were compared between all basis sets.

Results

The MM model using nine individual AMARES‐parameterized MM components with additional soft constraints achieved the most reliable results. Nine MMs and seven metabolites were mapped simultaneously over the whole slice.

Conclusion

The proposed MM model may facilitate studies that involve patients with pathologically altered MMs. Magn Reson Med 79:1231–1240, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Non‐Gaussian diffusion imaging with a fractional order calculus model to predict response of gastrointestinal stromal tumor to second‐line sunitinib therapy
Authors: Tang Lei , Sui Yi , Zhong Zheng , Damen Frederick C. , Li Jian , Shen Lin , Sun Yingshi , Zhou Xiaohong Joe
Published: June 2017

Purpose

To demonstrate the clinical value of a non‐Gaussian diffusion model using fractional order calculus (FROC) for early prediction of the response of gastrointestinal stromal tumor to second‐line sunitinib targeted therapy.

Methods

Fifteen patients underwent sunitinib treatment after imatinib resistance. Diffusion‐weighted imaging with multiple b‐values was performed before treatment (baseline) and 2 weeks (for early prediction of response) after initiating sunitinib treatment. Conventional MRI images at 12 weeks were used to determine the good and poor responders according to the modified Choi criteria for MRI. Diffusion coefficient D, fractional order parameter β (which correlates to intravoxel tissue heterogeneity), and a microstructural quantity µ were calculated using the FROC model. The FROC parameters and the longest diameter of the lesion, as well as their changes after 2 weeks of treatment, were compared between the good and poor responders. Additionally, the pretreatment FROC parameters were individually combined with the change in D (ΔD) using a logistic regression model to evaluate response to sunitinib treatment with a receiver operating characteristic analysis.

Results

Forty‐two good‐responding and 32 poor‐responding lesions were identified. Significant differences were detected in pretreatment β (0.67 versus 0.74, P = 0.011) and ΔD (45.7% versus 12.4%, P = 0.001) between the two groups. The receiver operating characteristic analysis showed that ΔD had a significantly higher predictive power than the tumor size change (area under the curve: 0.725 versus 0.580; 0.95 confidence interval). When ΔD was combined with pretreatment β, the area under the curve improved to 0.843 with a predictive accuracy of 75.7% (56 of 74).

Conclusions

The non‐Gaussian FROC diffusion model showed clinical value in early prediction of gastrointestinal stromal tumor response to second‐line sunitinib targeted therapy. The pretreatment FROC parameter β can increase the predictive accuracy when combined with the change in diffusion coefficient during treatment. Magn Reson Med 79:1399–1406, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Off‐resonance based assessment of metallic wear debris near total hip arthroplasty
Authors: Koch Kevin M. , Koff Matthew F. , Bauer Thomas W. , Shah Parina H. , Nencka Andrew S. , Sivaram Kaushik S. , Potter Hollis G.
Published: June 2017

Purpose

The presence of metallic debris near total hip arthroplasty can have a significant impact on longitudinal patient management. Methods for magnetic resonance imaging‐based quantification of metallic debris near painful total hip replacements are described and applied to cohorts of symptomatic and control subject cases.

Methods

A combination of metal artifact reduction, off‐resonance mapping, off‐resonance background removal, and spatial clustering methods are utilized to quantify off‐resonance signatures in cases of suspected metallosis. These methods are applied to a cohort of symptomatic hip arthroplasties composed of cobalt‐chromium alloys. Magnetostatic simulations and theoretical principles are used to illuminate the potential sources of the measured off‐resonance effects. Reported metrics from histological tissue assays extracted during surgical revision procedures are also correlated with the proposed magnetic resonance imaging‐based quantification results.

Results

The presented methods identified quantifiable metallosis signatures in more than 70% of the symptomatic and none of the control cases. Preliminary correlations of the MR data with direct histological evaluation of retrieved tissue samples indicate that the observed off‐resonance effect may be related to tissue necrosis.

Conclusions

Magnetostatic simulations, theoretical principles, and preliminary histological trends suggest that disassociated cobalt is the source of the observed off‐resonance signature. Magn Reson Med 79:1628–1637, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Modelling large plastic deformations of cohesive soils using sequential limit analysis
Authors: Kong D. , Martin C. M. , Byrne B. W.
Published: June 2017

This paper introduces sequential limit analysis (SLA) as a method for modelling large plastic deformations of purely cohesive materials such as undrained clay. The method involves solving a series of consecutive small‐deformation plastic collapse problems using finite element limit analysis, thus ensuring high levels of accuracy, efficiency, and robustness. The techniques needed to develop an SLA implementation for two‐dimensional (plane strain) problems are described in detail, including model geometry updating routines, treatment of rigid bodies, interfaces and boundaries, and periodic remeshing and interpolation of field variables. A simple total stress‐based constitutive model is used to account for strain softening and strain rate effects. Extensive verifications and validations are performed using analytical solutions and physical model test results, comparing both collapse loads and failure mechanisms, to demonstrate the effectiveness of the SLA approach. Additional solution quality checks on the bracketing discrepancy between lower‐bound and upper‐bound limit analysis solutions, and on the incompressibility of the rigid‐plastic material, are also presented.
Diffusion MRI microstructure models with in vivo human brain Connectome data: results from a multi‐group comparison
Authors: Ferizi Uran , Scherrer Benoit , Schneider Torben , Alipoor Mohammad , Eufracio Odin , Fick Rutger H.J. , Deriche Rachid , Nilsson Markus , Loya‐Olivas Ana K. , Rivera Mariano , Poot Dirk H.J. , Ramirez‐Manzanares Alonso , Marroquin Jose L. , Rokem Ariel , Pötter Christian , Dougherty Robert F. , Sakaie Ken , Wheeler‐Kingshott Claudia , Warfield Simon K. , Witzel Thomas , Wald Lawrence L. , Raya José G. , Alexander Daniel C.
Published: June 2017

A large number of mathematical models have been proposed to describe the measured signal in diffusion‐weighted (DW) magnetic resonance imaging (MRI). However, model comparison to date focuses only on specific subclasses, e.g. compartment models or signal models, and little or no information is available in the literature on how performance varies among the different types of models. To address this deficiency, we organized the ‘White Matter Modeling Challenge’ during the International Symposium on Biomedical Imaging (ISBI) 2015 conference. This competition aimed to compare a range of different kinds of models in their ability to explain a large range of measurable in vivo DW human brain data. Specifically, we assessed the ability of models to predict the DW signal accurately for new diffusion gradients andbvalues. We did not evaluate the accuracy of estimated model parameters, as a ground truth is hard to obtain. We used the Connectome scanner at the Massachusetts General Hospital, using gradient strengths of up to 300 mT/m and a broad set of diffusion times. We focused on assessing the DW signal prediction in two regions: the genu in the corpus callosum, where the fibres are relatively straight and parallel, and the fornix, where the configuration of fibres is more complex. The challenge participants had access to three‐quarters of the dataset and their models were ranked on their ability to predict the remaining unseen quarter of the data. The challenge provided a unique opportunity for a quantitative comparison of diverse methods from multiple groups worldwide. The comparison of the challenge entries reveals interesting trends that could potentially influence the next generation of diffusion‐based quantitative MRI techniques. The first is that signal models do not necessarily outperform tissue models; in fact, of those tested, tissue models rank highest on average. The second is that assuming a non‐Gaussian (rather than purely Gaussian) noise model provides little improvement in prediction of unseen data, although it is possible that this may still have a beneficial effect on estimated parameter values. The third is that preprocessing the training data, here by omitting signal outliers, and using signal‐predicting strategies, such as bootstrapping or cross‐validation, could benefit the model fitting. The analysis in this study provides a benchmark for other models and the data remain available to build up a more complete comparison in the future.