bluuebunny/crossref_metadata_2025 huggingface dataset:
Cascade convolutional neural networks for automatic detection of thyroid nodules in ultrasound images
Authors: Ma Jinlian , Wu Fa , Jiang Tian'an , Zhu Jiang , Kong Dexing
Published: February 2017

Purpose

It is very important for calculation of clinical indices and diagnosis to detect thyroid nodules from ultrasound images. However, this task is a challenge mainly due to heterogeneous thyroid nodules with distinct components are similar to background in ultrasound images. In this study, we employ cascade deep convolutional neural networks (CNNs) to develop and evaluate a fully automatic detection of thyroid nodules from 2D ultrasound images.

Methods

Our cascade CNNs are a type of hybrid model, consisting of two different CNNs and a new splitting method. Specifically, it employs a deep CNN to learn the segmentation probability maps from the ground true data. Then, all the segmentation probability maps are split into different connected regions by the splitting method. Finally, another deep CNN is used to automatically detect the thyroid nodules from ultrasound thyroid images.

Results

Experiment results illustrate the cascade CNNs are very effective in detection of thyroid nodules. Specially, the value of area under the curve of receiver operating characteristic is 98.51%. The Free‐response receiver operating characteristic (FROC) and jackknife alternative FROC (JAFROC) analyses show a significant improvement in the performance of our cascade CNNs compared to that of other methods. The multi‐view strategy can improve the performance of cascade CNNs. Moreover, our special splitting method can effectively separate different connected regions so that the second CNN can correctively gain the positive and negative samples according to the automatic labels.

Conclusions

The experiment results demonstrate the potential clinical applications of this proposed method. This technique can offer physicians an objective second opinion, and reduce their heavy workload so as to avoid misdiagnosis causes because of excessive fatigue. In addition, it is easy and reproducible for a person without medical expertise to diagnose thyroid nodules.
Interchangeable neck shape–specific coils for a clinically realizable anterior neck phased array system
Authors: Beck Michael J. , Parker Dennis L. , Bolster Bradley D. , Kim Seong‐Eun , McNally J. Scott , Treiman Gerald S. , Hadley J. Rock
Published: February 2017

Purpose

To demonstrate the interchangeable neck shape–specific (NSS) coil concept that supplements standard commercial spine and head/neck coils to provide simultaneous high‐resolution (hi‐res) head/neck imaging with high signal‐to‐noise ratio (SNR).

Methods

Two NSS coils were constructed on formers designed to fit two different neck shapes. A 7‐channel (7ch) ladder array was constructed on a medium neck former, and a 9‐channel (9ch) ladder array was constructed on large neck former. Both coils were interchangeable with the same preamp housing.

Results

The 7ch and 9ch coils demonstrate SNR gains of approximately 4 times and 3 times over the Siemens 20‐channel head/neck coil in the carotid arteries of our volunteers, respectively. Coupling between the Siemens 32‐channel spine coil, Siemens 20‐channel head/neck coil, and the NSS coils was negligible, allowing for simultaneous hi‐res head/neck imaging with high SNR.

Conclusions

This study demonstrates that supplementing existing commercial spine and head/neck coils with an NSS coil allows uniform simultaneous hi‐res imaging with high SNR in the anterior neck, while maintaining SNR of the commercial coil in the head and posterior neck. Magn Reson Med 78:2460–2468, 2017. © 2017 International Society for Magnetic Resonance in Medicine.
Detection of fasciculations in amyotrophic lateral sclerosis: The optimal ultrasound scan time
Authors: Noto Yu‐ichi , Shibuya Kazumoto , Shahrizaila Nortina , Huynh William , Matamala José M. , Dharmadasa Thanuja , Kiernan Matthew C.
Published: February 2017

Introduction

This study seeks to elucidate the optimal scan time to detect fasciculations by using ultrasound in the diagnosis of amyotrophic lateral sclerosis (ALS).

Methods

The intervals between fasciculations were recorded from tongue, abdominal, and limb muscles in ALS patients, incorporating assessment of the cumulative probability of 2 fasciculations occurring.

Results

From prospective studies of 228 muscles from 19 ALS patients, fasciculations were detectable in 68% of patients. The longest interfasciculation interval recorded was 81.4 s in the hand muscle. The cumulative probability of 2 fasciculations occurring was calculated as ≥0.9 in all muscles during a period of 60 s.

Discussion

A definition of 2 or more fasciculations occurring during a scan time of 60 s reliably allowed detection of fasciculations in ALS. Muscle Nerve, 2017
Dynamic response of a pile considering the interaction of pile variable cross section with the surrounding layered soil
Authors: Gao Liu , Wang Kuihua , Xiao Si , Wu Wenbing
Published: February 2017

Assuming that the pile variable cross section interacts with the surrounding soil in the same way as the pile toe does with the bearing stratus, the interaction of pile variable cross section with the surrounding soil is represented by a Voigt model, which consists of a spring and a damper connected in parallel, and the spring constant and damper coefficient are derived. Thus, a more rigid pile–soil interaction model is proposed. The surrounding soil layers are modeled as axisymmetric continuum in which its vertical displacements are taken into account and the pile is assumed to be a Rayleigh–Love rod with material damping. Allowing for soil properties and pile defects, the pile–soil system is divided into several layers. By means of Laplace transform, the governing equations of soil layers are solved in frequency domain, and a new relationship linking the impedance functions at the variable‐section interface between the adjacent pile segments is derived using a Heaviside step function, which is called amended impedance function transfer method. On this basis, the impedance function at pile top is derived by amended impedance function transfer method proposed in this paper. Then, the velocity response at pile top can be obtained by means of inverse Fourier transform and convolution theorem. The effects of pile–soil system parameters are studied, and some conclusions are proposed. Then, an engineering example is given to confirm the rationality of the solution proposed in this paper. Copyright © 2017 John Wiley & Sons, Ltd.
Beta‐3 adrenergic receptor is expressed in acetylcholine‐containing nerve fibers of the human urinary bladder: An immunohistochemical study
Authors: Coelho Ana , Antunes‐Lopes Tiago , Gillespie James , Cruz Francisco
Published: February 2017

AIMS

To identify in the human bladder the structures which express the Beta‐3 adrenoceptor (β3AR).

METHODS

Human bladders from cadaveric organ donors (equally balanced in sex and age) were collected. Bladders were immediately fixed in paraformaldehyde and further processed for cryostat sectioning. Single and double immunohistochemistry was performed using antibodies against β3AR C‐terminal, β3AR N‐terminal, a pan‐neuronal marker (β3‐Tubulin) and markers of cholinergic (Vesicular Acetylcholine Transporter), adrenergic (Tyrosine Hidroxylase), and peptidergic (Calcitonin Gene‐Related Peptide) nerve fibers.

RESULTS

Nerve fibers expressing immunoreactivity for β3AR were abundantly found in the mucosa and muscular layers of the human bladder. No β3AR‐IR was detected on urothelial or smooth muscle cells. The presence of β3AR‐IR in nerve fibers was confirmed by co‐expression with β3‐Tubulin. Nerve fibers expressing β3AR‐IR were cholinergic, VAChT+, and abundantly observed in the suburothelium. The cholinergic fibers were in close proximity and intermingled with adrenergic TH+ and peptidergic CGRP+ fibers.

CONCLUSIONS

We demonstrated that β3AR is abundantly located in acetylcholine‐containing nerve fibers. These findings have important consequences to understand the mechanism of action of β3AR agonists currently used for the treatment of OAB.
Gabapentenoids in pain management in urological chronic pelvic pain syndrome: Gabapentin or pregabalin?
Authors: Agarwal Mayank Mohan , Elsi Sy Mudelin
Published: February 2017

AIMS

To compare efficacy of gabapentin and pregabalin in patients with urological chronic pelvic‐pain syndrome (UCPPS).

METHODS

Design—retrospective, setting—urology outpatient services of a secondary‐care private hospital, inclusion criteria—men 18‐50 years, presenting with pelvic pain (lower abdomen, groin, scrotum, perineum, low‐back, hip) with or without lower urinary tract symptoms for at least 3 months duration. Hospital database was searched using keywords for neuropathic pain (ICD9—729.2, 719.45) and prostatitis (ICD9—601.1, 601.9). Clinical data were retrieved from patient‐records, laboratory and radiology data, and analyzed using SPSS‐19 statistical software.

RESULTS

Between Mar 2013 and Oct 2015, data of consecutive 119 patients fulfilling the above criteria was analyzed. Median age of patients was 35 years (IQR 29‐43) and median duration of symptoms 12 months (IQR 6‐24 months). Before treatment median VAS (0‐10) pain score was 5 (IQR 4‐6). Gabapentin was significantly more effective in controlling pain compared to pregabalin. Three fourth of patients on gabapentin alone (47/62) reported at least 50% improvement in pain compared to only 40% on pregabalin alone (12/30) (P = 0.0012; χ2 = 9.765. NNT 2.9, 95%CI 1.8‐6.5). Twenty patients who were initially put on pregabalin had to switch to gabapentin for lack of efficacy. Forty four percent of patients on pregabalin required amitriptyline (24/54) compared to only 13.6% of those on gabapentin (10/72) required the same (P value of difference 0.0001; χ2 = 14.622. NNT 4, CI 95% 2.2‐6.6).

CONCLUSIONS

Gabapentin may be more effective than pregabalin in UCPPS.
A local artificial‐boundary condition for simulating transient wave radiation in fluid‐saturated porous media of infinite domains
Authors: Xu Chengshun , Song Jia , Du Xiuli , Zhao Mi
Published: February 2017

The dynamic problem of wave propagation in infinite fluid‐saturated porous media is usually solved using the finite element method. Therefore, proper artificial‐boundary conditions are required to be imposed on the truncated boundaries of the dynamic finite‐element model to consider the radiation damping effect of the truncated media. A local artificial‐boundary condition is proposed for the dynamic problems in fluid‐saturated porous media in the u−p formulation. It avoids making the unrealistic assumption of zero permeability that is widely used in the existing artificial‐boundary conditions. Moreover, the proposed method can be implemented easily into finite element or finite difference codes as stress and flow velocity boundary conditions. Numerical results obtained from the finite element model using the proposed artificial boundary indicate that the proposed method is stable for long time and is more accurate than several existing methods. Copyright © 2017 John Wiley & Sons, Ltd.
A combined low‐pressure hydrogen peroxide evaporation plus hydrogen plasma treatment method for sterilization – Part 1: Characterization of the condensation process and proof‐of‐concept
Authors: Stapelmann Katharina , Fiebrandt Marcel , Raguse Marina , Lackmann Jan‐Wilm , Postema Michiel , Moeller Ralf , Awakowicz Peter
Published: February 2017

A combined hydrogen peroxide evaporation and hydrogen low‐pressure plasma treatment process for sterilization is introduced and investigated. The combination of hydrogen peroxide evaporation followed by hydrogen plasma treatment offers an advantage regarding sterilization in complex metal geometries or in sealed sterile bags, where plasma treatment alone faces challenges. Within this contribution, the droplet size and film homogeneity after condensation is investigated by optical diagnostics. Sterilization tests with common challenge organisms show the sterilization capabilities of the combined process in a process challenge device, mimicking the worst‐case‐scenario for plasma treatment in a small metal box. Furthermore, sterilization in sealed sterile bags clearly demonstrates the advantage of the combined process, showing full spore inactivation solely for the combined process.
Cumulative effects of neonatal hyperoxia on murine alveolar structure and function
Authors: Cox Angela M. , Gao Yong , Perl Anne‐Karina T. , Tepper Robert S. , Ahlfeld Shawn K.
Published: February 2017

Background

Bronchopulmonary dysplasia (BPD) results from alveolar simplification and abnormal development of alveolar and capillary structure. Survivors of BPD display persistent deficits in airflow and membrane and vascular components of alveolar gas diffusion. Despite being the defining feature of BPD, various neonatal hyperoxia models of BPD have not routinely assessed pulmonary gas diffusion.

Methods

To simulate the most commonly‐utilized neonatal hyperoxia models, we exposed neonatal mice to room air or ≥90% hyperoxia during key stages of distal lung development: through the first 4 (saccular), 7 (early alveolar), or 14 (bulk alveolar) postnatal days, followed by a period of recovery in room air until 8 weeks of age when alveolar septation is essentially complete. We systematically assessed and correlated the effects of neonatal hyperoxia on the degree of alveolar–capillary structural and functional impairment. We hypothesized that the degree of alveolar–capillary simplification would correlate strongly with worsening diffusion impairment.

Results

Neonatal hyperoxia exposure, of any duration, resulted in alveolar simplification and impaired pulmonary gas diffusion. Mean Linear Intercept increased in proportion to the length of hyperoxia exposure while alveolar and total lung volume increased markedly only with prolonged exposure. Surprisingly, despite having a similar effect on alveolar surface area, only prolonged hyperoxia for 14 days resulted in reduced pulmonary microvascular volume. Estimates of alveolar and capillary structure, in general, correlated poorly with assessment of gas diffusion.

Conclusion

Our results help define the physiological and structural consequences of commonly‐employed neonatal hyperoxia models of BPD and inform their clinical utility. Pediatr Pulmonol. 2017;52:616–624. © 2016 Wiley Periodicals, Inc.
High‐pressure phase transitions and properties of MTO4 compounds with the monazite‐type structure
Authors: Errandonea Daniel
Published: February 2017

This article extensively reviews recent developments on high‐pressure studies carried out on MTO4 monazite‐type oxides. The group of compounds considered includes phosphates, vanadates, selenates, and chromates, among others. The occurrence of pressure‐induced phase transitions will be discussed. The compressibility and pressure stability range of the different compounds will be also examined; as well as the influence of compression in the vibrational, optical, and transport properties. A part of the report will be devoted to discuss the determination of the crystal structure of the high‐pressure post‐monazite phases and to look into the influence of compression in the electronic and vibrational properties. Similarities and differences of the high‐pressure behavior of different members of the monazite family will be commented. The reviewed results are of importance for basic research and Earth sciences, and for the development of technological applications. Finally, future challenges associated to the reviewed subject will be presented.
Localized Synthesis of Iron Oxide Nanowires and Fabrication of High Performance Nanosensors Based on a Single Fe2O3 Nanowire
Authors: Lupan Oleg , Postica Vasile , Wolff Niklas , Polonskyi Oleksandr , Duppel Viola , Kaidas Victor , Lazari Eugen , Ababii Nicolai , Faupel Franz , Kienle Lorenz , Adelung Rainer
Published: February 2017

A composed morphology of iron oxide microstructures covered with very thin nanowires (NWs) with diameter of 15–50 nm has been presented. By oxidizing metallic Fe microparticles at 255 °C for 12 and 24 h, dense iron oxide NW networks bridging prepatterned Au/Cr pads are obtained. X‐ray photoelectron spectroscopy studies reveal formation of α‐Fe2O3 and Fe3O4 on the surface and it is confirmed by detailed high‐resolution transmission electron microscopy and selected area electron diffraction (SAED) investigations that NWs are single phase α‐Fe2O3 and some domains of single phase Fe3O4. Localized synthesis of such nano‐ and microparticles directly on sensor platform/structure at 255 °C for 24 h and reoxidation at 650 °C for 0.2–2 h, yield in highly performance and reliable detection of acetone vapor with fast response and recovery times. First nanosensors on a single α‐Fe2O3 nanowire are fabricated and studied showing excellent performances and an increase in acetone response by decrease of their diameter was developed. The facile technological approach enables this nanomaterial as candidate for a range of applications in the field of nanoelectronics such as nanosensors and biomedicine devices, especially for breath analysis in the treatment of diabetes patients.
Activating nuclear xenobiotic receptors and triggering ER stress and hepatic cytochromes P450 systems in quails (Coturnix C. coturnix) during atrazine exposure
Authors: Du Zheng‐Hai , Qin Lei , Lin Jia , Sun Yan‐Chun , Xia Jun , Zhang Cong , Li Xue‐Nan , Li Jin‐Long
Published: February 2017

Atrazine (ATR) is one of the most widely detected contaminant in the ecosystem. Nuclear xenobiotic receptors are activated by herbicides and induce the transcription of CYP450 isoforms involved in xenobiotic metabolism and transport. However, little is known about hepatic nuclear xenobiotic receptors in birds are responsible for ATR‐induced hepatotoxicity via regulating the cytochrome P450 enzyme systems (CYP450s). The objective of this study was to investigate the mechanism of ATR hepatotoxicity in quails. For this purpose, male quails were dosed by oral gavage from sexual immaturity to maturity with 0, 50, 250, and 500 mg/kg/day ATR for 45 days. The results showed that ATR exposure caused the hepatotoxicity damage and endoplasmic reticulum (ER) degeneration. It suggested that ER is a target organelle of ATR toxicity in hepatocytes. ATR exposure disrupted the hepatic CYP450s homeostasis. This study also demonstrated that ATR triggered the CYP450 isoforms transcription via activating the hepatic CAR/PXR pathway. The present study provides new insights regarding the mechanism of the ATR‐induced hepatotoxicity through activating nuclear xenobiotic receptors and triggering ER stress and hepatic CYP450s in quails.
What [shall][should] we do? Why a binding climate treaty is in your interest
Authors: Hall Nicholas
Published: February 2017

This paper investigates whether and under what conditions a binding climate treaty can affect our individual moral obligations. Walter Sinnott‐Armstrong has argued that our sole moral obligation regarding climate change is to develop something like a binding treaty. On such an understanding, a binding agreement of the right type would absolve individuals of any further moral responsibilities to reduce carbon emissions. However, while something like this may be true in ideal circumstances of strict compliance, this paper argues that this is not the case in nonideal circumstances of partial compliance. The paper will proceed, first, by outlining the distinction between constitutive and nonconstitutive rules, or practice and summary rules, in Rawlsian terminology. I will then suggest that climate treaties, under the right circumstances, could fulfill the role of a practice with constitutive rules. If this is right, then the binding or nonbinding nature of a treaty (as well as the content of the treaty itself) could make it such that, under ideal circumstances, individuals have no obligation to reduce their carbon output beyond the requirements of the treaty. However, in the nonideal conditions of the actual world, the absence of full compliance to such institutions results in individual actions being subject to strict moral obligations. Consequently, it is in an individual's interest to enact such a binding treaty, at least insofar as they are at least somewhat concerned with fulfilling their moral obligations and would like to reduce the burdens of doing so.WIREs Clim Change2017, 8:e459. doi: 10.1002/wcc.459

This article is categorized under:

Climate, Nature, and Ethics > Climate Change and Human Rights
Climate change, migration, and the crisis of humanism
Authors: Baldwin Andrew
Published: February 2017

Climate change is more and more said to be a problem of migration. The common refrain is that climate change will bear in some way on patterns of human mobility, resulting in either insecurity, humanitarian crises, or all manner of inventive adaptive responses. The inherent challenge in such claims is, however, that of causality: the degree to which climate change influences migration alongside the myriad social, political, and economic reasons people migrate. This challenge is far from being settled. Importantly, the unsettled question of causality exposes how the crisis of humanism is central to the construction of the climate migrant or climate refugee. Coming to terms with this crisis means having to confront how issues of power and knowledge shape how we understand the relationship between climate change and migration. But even more importantly it means having to ask probing questions about what it means to be human today. The study develops these arguments through an engagement with the concept of the monster and with Timothy Morton's concept of the hyperobject. WIREs Clim Change 2017, 8:e460. doi: 10.1002/wcc.460

This article is categorized under:

Trans‐Disciplinary Perspectives > Humanities and the Creative Arts
State‐to‐state quantum reactive scattering in four‐atom systems
Authors: Zhao Bin , Guo Hua
Published: February 2017

The recent advances in quantum mechanical studies of four‐atom reactions at the state‐to‐state level are reviewed. With six internal degrees of freedom, such reactions offer richer chemistry than the much studied atom–diatom reactions, but also pose challenges to the quantum mechanical treatment of the state‐to‐state scattering process. Several approaches that are capable of providing a complete solution to the problem have recently been suggested and a brief description and comparison of these approaches are given here. In addition, recent quantum mechanical state‐to‐state results for tetratomic reactions are discussed and a simple transition‐state‐based model is shown to provide useful insights into the correlation between reactant and product quantum states during a reaction. WIREs Comput Mol Sci 2017, 7:e1301. doi: 10.1002/wcms.1301

This article is categorized under:

Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics
Nonparametric functional concurrent regression models
Authors: Maity Arnab
Published: February 2017

Function‐on‐function regression refers to the situation where both independent and dependent variables in a regression model are of functional nature. Functional concurrent regression is a specific type of function‐on‐function regression that relates the response function at a specific point to the covariate value at that point and the point itself. Standard functional concurrent models are linear (a linear combination of the covariates is used), and often criticized due to their linearity assumption and lack of flexibility. This gives rise to nonparametric functional concurrent regression that models the response function at a specific point using a multivariate nonparametric function of both the point and the covariate value at that point. Such models allow for much more flexibility and predictive accuracy, especially when the underlying relationship is nonlinear. In the past decade, several methods have been proposed to perform estimation, prediction and inference in the nonparametric concurrent models using various methods such as spline smoothing, Gaussian process regression and local polynomial kernel regression. Such models have been shown to be useful tools in functional regression as well as stepping stone for further development. WIREs Comput Stat 2017, 9:e1394. doi: 10.1002/wics.1394

This article is categorized under:

Statistical and Graphical Methods of Data Analysis > Nonparametric Methods
An introduction toMajorization‐Minimizationalgorithms for machine learning and statistical estimation
Authors: Nguyen Hien D.
Published: February 2017

MM(majorization–minimization) algorithms are an increasingly popular tool for solving optimization problems in machine learning and statistical estimation. This article introduces theMMalgorithm framework in general and via three commonly considered example applications: Gaussian mixture regressions, multinomial logistic regressions, and support vector machines. Specific algorithms for these three examples are derived and Mathematical Programming Series A numerical demonstrations are presented. Theoretical and practical aspects ofMMalgorithm design are discussed.WIREs Data Mining Knowl Discov2017, 7:e1198. doi: 10.1002/widm.1198

This article is categorized under:

Algorithmic Development > Statistics

Technologies > Machine Learning
Randomness in neural networks: an overview
Authors: Scardapane Simone , Wang Dianhui
Published: February 2017

Neural networks, as powerful tools for data mining and knowledge engineering, can learn from data to build feature‐based classifiers and nonlinear predictive models. Training neural networks involves the optimization of nonconvex objective functions, and usually, the learning process is costly and infeasible for applications associated with data streams. A possible, albeit counterintuitive, alternative is to randomly assign a subset of the networks’ weights so that the resulting optimization task can be formulated as a linear least‐squares problem. This methodology can be applied to both feedforward and recurrent networks, and similar techniques can be used to approximate kernel functions. Many experimental results indicate that such randomized models can reach sound performance compared to fully adaptable ones, with a number of favorable benefits, including (1) simplicity of implementation, (2) faster learning with less intervention from human beings, and (3) possibility of leveraging overall linear regression and classification algorithms (e.g.,ℓ1norm minimization for obtaining sparse formulations). This class of neural networks attractive and valuable to the data mining community, particularly for handling large scale data mining in real‐time. However, the literature in the field is extremely vast and fragmented, with many results being reintroduced multiple times under different names. This overview aims to provide a self‐contained, uniform introduction to the different ways in which randomization can be applied to the design of neural networks and kernel functions. A clear exposition of the basic framework underlying all these approaches helps to clarify innovative lines of research, open problems, and most importantly, foster the exchanges of well‐known results throughout different communities.WIREs Data Mining Knowl Discov2017, 7:e1200. doi: 10.1002/widm.1200

This article is categorized under:

Technologies > Machine Learning
Deconstruction of complex protein signaling switches: a roadmap toward engineering higher‐order gene regulators
Authors: Davey James A. , Wilson Corey J.
Published: February 2017

The control of gene expression is an important tool for metabolic engineering, the design of synthetic gene networks, gene‐function analysis, and protein manufacturing. The most successful approaches to date are based on modulating messenger RNA (mRNA) synthesis via their inducible coupling to transcriptional effectors, which requires biosensing functionality. A hallmark of biological sensing is the conversion of an exogenous signal, usually a small molecule or environmental cue such as a protein–ligand interaction, into a useful output or response. One of the most utilized regulatory proteins is the lactose repressor (LacI). In this review we will (1) explore the mechanochemical structure–function relationship of LacI; (2) discuss how the physical attributes of LacI can be leveraged to identify and understand other regulatory proteins; (3) investigate the designability (tunability) of LacI; (4) discuss the potential of the modular design of novel regulatory proteins, fashioned after the topology and mechanochemical properties of LacI. WIREs Nanomed Nanobiotechnol 2017, 9:e1461. doi: 10.1002/wnan.1461

This article is categorized under:

Diagnostic Tools > Biosensing

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology

Biology-Inspired Nanomaterials > Protein and Virus-Based Structures
Understanding the mTOR signaling pathway via mathematical modeling
Authors: Sulaimanov Nurgazy , Klose Martin , Busch Hauke , Boerries Melanie
Published: February 2017

The mechanistic target of rapamycin (mTOR) is a central regulatory pathway that integrates a variety of environmental cues to control cellular growth and homeostasis by intricate molecular feedbacks. In spite of extensive knowledge about its components, the molecular understanding of how these function together in space and time remains poor and there is a need for Systems Biology approaches to perform systematic analyses. In this work, we review the recent progress how the combined efforts of mathematical models and quantitative experiments shed new light on our understanding of the mTOR signaling pathway. In particular, we discuss the modeling concepts applied in mTOR signaling, the role of multiple feedbacks and the crosstalk mechanisms of mTOR with other signaling pathways. We also discuss the contribution of principles from information and network theory that have been successfully applied in dissecting design principles of the mTOR signaling network. We finally propose to classify the mTOR models in terms of the time scale and network complexity, and outline the importance of the classification toward the development of highly comprehensive and predictive models. WIREs Syst Biol Med 2017, 9:e1379. doi: 10.1002/wsbm.1379

This article is categorized under:

Biological Mechanisms > Cell Signaling

Models of Systems Properties and Processes > Mechanistic Models
Xylitol production by genetically modified industrial strain of Saccharomyces cerevisiae using glycerol as co-substrate
Authors: Kogje Anushree B , Ghosalkar Anand
Published: February 2017

Xylitol is commercially used in chewing gum and dental care products as a low calorie sweetener having medicinal properties. Industrial yeast strain of S. cerevisiae was genetically modified to overexpress an endogenous aldose reductase gene GRE3 and a xylose transporter gene SUT1 for the production of xylitol. The recombinant strain (XP-RTK) carried the expression cassettes of both the genes and the G418 resistance marker cassette KanMX integrated into the genome of S. cerevisiae. Short segments from the 5′ and 3′ delta regions of the Ty1 retrotransposons were used as homology regions for integration of the cassettes. Xylitol production by the industrial recombinant strain was evaluated using hemicellulosic hydrolysate of the corn cob with glucose as the cosubstrate. The recombinant strain XP-RTK showed significantly higher xylitol productivity (212 mg L−1 h−1) over the control strain XP (81 mg L−1 h−1). Glucose was successfully replaced by glycerol as a co-substrate for xylitol production by S. cerevisiae. Strain XP-RTK showed the highest xylitol productivity of 318.6 mg L−1 h−1 and titre of 47 g L−1 of xylitol at 12 g L−1 initial DCW using glycerol as cosubstrate. The amount of glycerol consumed per amount of xylitol produced (0.47 mol mol−1) was significantly lower than glucose (23.7 mol mol−1). Fermentation strategies such as cell recycle and use of the industrial nitrogen sources were demonstrated using hemicellulosic hydrolysate for xylitol production.
Seasonal leaf phenology data for 12 tree species in a cool‐temperate deciduous broadleaved forest in Japan from 2005 to 2014
Authors: Nagai Shin , Nasahara Kenlo Nishida
Published: February 2017

This paper reports seasonal data regarding leaf number, leaf length and width, leaf area, leaf angle, and SPAD (leaf chlorophyll content index) for 11 genera (12 species) in a cool‐temperate deciduous broadleaved forest in Japan. Knowing the leaf phenology of tree species is important for accurately evaluating the temporal variability of ecosystem functions (e.g., photosynthesis and evapotranspiration) under rapid climate change. However, there is a lack of freely available long‐term observation data regarding leaf phenological characteristics for many tree species. We collected leaf phenological data from tagged shoots every 1–4 weeks from April or May to October or November each year from 2005 to 2014 in Takayama, Japan (36°08′46″N, 137°25′23″E, 1420 m a.s.l.). We targeted typical dominant, codominant, and understory tree species at the site. To evaluate differences among individuals and between sunlit and shaded leaves, we measured one to four shoots of some species and individuals. Our data provide input, calibration, and validation parameters for a terrestrial ecosystem and for radiative‐transfer models and remote‐sensing observations.
The peer's point of view: Observing a peer performing an action enhances third‐person perspective in adolescents
Authors: Conson Massimiliano , Salzano Sara , Frolli Alessandro , Mazzarella Elisabetta
Published: February 2017

Adolescents are particularly prone to peer influence. Since group membership modulates the person's tendency to take someone else's viewpoint, here we decided to investigate whether adolescents are influenced by the presence of a peer when taking another person's perspective. A group of adolescents from upper secondary schools in Naples (Italy) had to observe scenes of an actor (an adolescent or an adult) gazing, grasping, gazing/grasping an object or staying still. When required to judge the spatial location of the object, the adolescent participants adopted the actor's viewpoint (third‐person perspective) more frequently when the actor was an adolescent rather than when he was an adult and when the adolescent actor grasped the object. Thus, adolescents seem particularly prone to mentally simulate someone else's actions when the other person is a peer. These findings suggest that modulating motor simulation processes via social environmental factors could influence adolescents' perspective taking.
A Response to Pathways to Sustainability
Authors: Huckle John
Published: February 2017

There has been very limited progress along the pathways to sustainability sketched in my 1991 article. Some would argue we have taken several steps backwards. Environmental education is now more prepared to acknowledge the role of neoliberal global capitalism in promoting unsustainable development, and to associate sustainability with social movements and parties of the green left who urge new forms of economy and global democracy. Corporations and governments have been successful in linking education for sustainable development to ecological modernisation or light green versions of the status-quo, but in England, even the limited advance of a policy on sustainable schools under New Labour has been swept away by the present coalition government.
Socio-Ecological Formations of Nature's Others: A Response
Authors: Payne Phillip G
Published: February 2017

The process of researching ‘Children's conceptions of nature’ was spontaneous — a story in itself! Having taught in Victorian primary schools in the 1970s, after 15 years in teacher education in the university sector, I felt it was important to ‘return’ to the classroom — to walk the talk! Each Friday afternoon for an hour or so, I met with Year 6 children to ‘chat’. In the mid-1990s, ‘philosophy for children’ was emerging. My doctoral, completed in the early 1990s, focused on philosophies of education and environmental ethics. We chatted a lot in class — about anything. One puzzled kid asked, ‘Where does space start and finish?’ Another, ‘Are not running spikes a way to enhance sport performance?’
Gender and Other Forms of Difference/Diversity
Authors: Whitehouse Hilary
Published: February 2017

Diversity is integral to socio-ecological sustainability at all scales and dimensions of education practice. The Australian Journal of Environmental Education (AJEE) has published research and reports of practice from a variety of novel and established perspectives and methodologies, recognising both small and large research studies and, in the process, becoming an energetic record of what we have been thinking about gender and culture and difference over the past 30 years. The editors of the AJEE have promoted diversity, given the purpose of environmental education is to change how we think about our social arrangements and to reconsider how it is possible to act within our world. As with any long-existing journal, the articles reflect historical scholarly trends and societal change, and the publications track what has been counted as legitimate in terms of being and knowing within the academy. Many kinds of useful knowledge were delegitimised and ignored until quite recently, so one of the tasks of researchers and educators and their AJEE editors has been to redress these silences and absences. If progress has been imperfect, this is a reflection of the difficulties of the task and not a reflection of the quality of the journal.
Co-operative Wineries in Italy and Spain in the Second Half of the Twentieth Century: Success or Failure of the Co-operative Business Model?
Authors: MEDINA-ALBALADEJO FRANCISCO J. , MENZANI TITO
Published: February 2017

The evolution of the co-operative wine sector in traditional wine-producing countries in southern Europe, such as France, Italy, Spain, and Portugal, presents similar historical features in the first half of the twentieth century. However, the analysis of their current state shows that Spanish co-operatives are smaller in size than their French and Italian counterparts. Additionally, the analysis shows that Italian (and French) co-operatives have adopted a more modern business model. The main target of this work is to establish the reasons behind the differences between the Spanish and the more successful Italian co-operative wine sectors. This is carried out through comparative analysis and the examination of the development of both sectors. For this, the framework of the co-operative business life cycle is used.
A PREQUEL TOLAW AND REVOLUTION: A LONG LOST MANUSCRIPT OF HAROLD J. BERMAN COMES TO LIGHT
Authors: Witte John , Manzer Christopher J.
Published: February 2017

The late Harold Berman was a pioneering scholar of Soviet law, legal history, jurisprudence, and law and religion; he is best known today for his monumentalLaw and Revolutionseries on the Western legal tradition. Berman wrote a short book,Law and Language, in the early 1960s, but it was not published until 2013. In this early text, he adumbrated many of the main themes of his later work, includingLaw and Revolution.He also anticipated a good deal of the interdisciplinary and comparative methodology that we take for granted today, even though it was rare in the intense legal positivist era during which he was writing. This essay contextualizes Berman'sLaw and Languagewithin the development of his own legal thought and in the evolution of interdisciplinary legal studies. It focuses particularly on the themes of law and religion, law and history, and law and communication that dominated Berman's writing until his death in 2007.
Retrospective Voting in Big-City US Mayoral Elections
Authors: Hopkins Daniel J. , Pettingill Lindsay M.
Published: February 2017

Retrospective voting is a central explanation for voters’ support of incumbents. Yet, despite the variety of conditions facing American cities, past research has devoted little attention to retrospective voting for mayors. This paper first develops hypotheses about how local retrospective voting might differ from its national analog, due to both differing information sources and the presence of national benchmarks. It then analyzes retrospective voting using the largest data set on big-city mayoral elections between 1990 and 2011 to date. Neither crime rates nor property values consistently influence incumbent mayors’ vote shares, nor do changes in local conditions. However, low city-level unemployment relative to national unemployment correlates with higher incumbent support. The urban voter is a particular type of retrospective voter, one who compares local economic performance to conditions elsewhere. Moreover, these effects appear to be present only in cities that dominate their media markets, suggesting media outlets’ role in facilitating retrospective voting.
Effect of heat waves on embryo mortality in the pine processionary moth
Authors: Rocha S. , Kerdelhué C. , Ben Jamaa M.L. , Dhahri S. , Burban C. , Branco M.
Published: February 2017

Extreme climate events such as heat waves are predicted to become more frequent with climate change, representing a challenge for many organisms. The pine processionary moth Thaumetopoea pityocampa is a Mediterranean pine defoliator, which typically lays eggs during the summer. We evaluated the effects of heat waves on egg mortality of three populations with different phenologies: a Portuguese population with a classical life cycle (eggs laid in summer), an allochronic Portuguese population reproducing in spring, and a Tunisian population from the extreme southern limit of T. pityocampa distribution range, in which eggs are laid in fall. We tested the influence of three consecutive hot days on egg survival and development time, using either constant (CT) or daily cycling temperatures (DT) with equivalent mean temperatures. Maximum temperatures (Tmax) used in the experiment ranged from 36 to 48°C for DT and from 30 to 42°C for CT. Heat waves had a severe negative effect on egg survival when Tmax reached 42°C for all populations. No embryo survived above this threshold. At high mean temperatures (40°C), significant differences were observed between populations and between DT and CT regimes. Heat waves further increased embryo development time. The knowledge we gained about the upper lethal temperature to embryos of this species will permit better prediction of the potential expansion of this insect under different climate warming scenarios.
FACTORS ASSOCIATED WITH WOMEN’S HEALTH CARE DECISION-MAKING AUTONOMY: EMPIRICAL EVIDENCE FROM NIGERIA
Authors: Osamor Pauline , Grady Christine
Published: February 2017

Women’s decision-making autonomy has been poorly studied in most developing countries. The few existing studies suggest that it is closely linked to women’s socio-demographic characteristics and the social settings in which they live. This study examined Nigerian women’s perceived decision-making autonomy about their own health care using nationally representative data from the 2013 Nigerian Demographic and Health Survey. The study sample consisted of 27,135 women aged 15–49 years who lived with their husbands/partners. Responses to questions about who usually makes decisions about the respondent’s health care were analysed. Factors associated with women’s health care decision-making were investigated using logistic regression models. Only 6.2% of the women reported making their own decisions about health care. For most women (61.1%), this decision was made by their husband/partner alone and 32.7% reported joint decision-making with their husband/partner. Factors independently associated with decision-making by the woman included: geographical region, rural/urban residence, age, education, religion, wealth index, occupation, home ownership and husband’s occupation. A strong association between women making their own health care decision was seen with region of residence (χ2=3221.48,p<0.0001), even after controlling for other factors. Notably, women from the South West region were 8.3 times more likely to make their own health care decisions than women from the North West region. Factors that were significantly associated with joint health care decision-making were also significantly associated with decision-making by the woman alone. The study found that individual-level factors were significantly associated with Nigerian women’s decision-making autonomy, as well as other factors, in particular geographic region. The findings provide an important perspective on women’s health care decision-making autonomy in a developing country.
Impaired awareness of motor intention in functional neurological disorder: implications for voluntary and functional movement
Authors: Baek K. , Doñamayor N. , Morris L. S. , Strelchuk D. , Mitchell S. , Mikheenko Y. , Yeoh S. Y. , Phillips W. , Zandi M. , Jenaway A. , Walsh C. , Voon V.
Published: February 2017

Background

Functional neurological disorders (FNDs), also known as conversion disorder, are unexplained neurological symptoms unrelated to a neurological cause. The disorder is common, yet poorly understood. The symptoms are experienced as involuntary but have similarities to voluntary processes. Here we studied intention awareness in FND.

Method

A total of 26 FND patients and 25 healthy volunteers participated in this functional magnetic resonance study using Libet's clock.

Results

FND is characterized by delayed awareness of the intention to move relative to the movement itself. The reporting of intention was more precise, suggesting that these findings are reliable and unrelated to non-specific attentional deficits. That these findings were more prominent with aberrant positive functional movement symptoms rather than negative symptoms may be relevant to impairments in timing for an inhibitory veto process. Attention towards intention relative to movement was associated with lower right inferior parietal cortex activity in FND, a region early in the processing of intention. During rest, aberrant functional connectivity was observed with the right inferior parietal cortex and other motor intention regions.

Conclusions

The results converge with observations of low inferior parietal activity comparing involuntary with voluntary movement in FND, emphasizing core deficiencies in intention. Heightened precision of this impaired intention is consistent with Bayesian theories of impaired top-down priors that might influence the sense of involuntariness. A primary impairment in voluntary motor intention at an early processing stage might explain clinical observations of slowed effortful voluntary movement, heightened self-directed attention and underlie functional movements. These findings further suggest novel therapeutic targets.
Selective functional disconnection of the orbitofrontal subregions in schizophrenia
Authors: Xu Y. , Qin W. , Zhuo C. , Xu L. , Zhu J. , Liu X. , Yu C.
Published: February 2017

Background

As a disconnection syndrome, schizophrenia has shown impaired resting-state functional connectivity (rsFC) in the orbitofrontal cortex (OFC); however, the OFC is a rather heterogeneous region and the rsFC changes in the OFC subregions remain unknown.

Method

A total of 98 schizophrenia patients and 102 healthy controls underwent resting-state functional MRI using a sensitivity-encoded spiral-in imaging sequence (SENSE-SPIRAL) to reduce susceptibility-induced signal loss and distortion. The OFC subregions were defined according to a previous parcellation study that divided the OFC into the anterior (OFCa), medial (OFCm), posterior (OFCp), intermediate (OFCi), and lateral (OFCl) subregions. The rsFC was compared using two-way repeated-measures ANOVA.

Results

Whether or not global signal regression, compared with healthy controls, schizophrenia patients consistently exhibited decreased rsFC between the left OFCi and the left middle temporal gyrus and the right middle frontal gyrus (MFG), between the right OFCi and the right MFG and the left inferior frontal gyrus, between the right OFCm and the middle cingulate cortex and the left Rolandic operculum. These rsFC changes still remained significant even after cortical atrophy correction.

Conclusions

These findings suggest a selective functional disconnection of the OFC subregions in schizophrenia, and provide more precise information about the functional disconnections of the OFC in this disorder.