bluuebunny/crossref_metadata_2025 huggingface dataset:
Carbohydrate supplementation attenuates decrement in performance in overtrained rats
Authors: Coutinho de Oliveira Caio Victor , Barbosa Carlos Vinícius , Massa Nayara Moreira , Pereira Reabias de Andrade , Félix Gustavo da Silva , Aquino Jailane de Souza , Oliveira Edilamar Menezes de , Silva Alexandre Sérgio
Published: October 2015

Carbohydrate ingestion at the end of a single exercise is recognized as delaying fatigue and accelerating recovery, but whether chronic ingestion can prevent overtraining during periods of intense training has not yet been elucidated. This study aimed to determine whether carbohydrate supplementation minimizes overtraining in Wistar rats. The animals underwent 11 weeks of training (running) on a treadmill, and the last 3 weeks were designed to induce overtraining. One group was supplemented with carbohydrates (EX-CHO) (n = 13), 1 group had no supplementation (EX) (n = 10), and a third group remained inactive (C) (n = 9). Performance tests were given before training (Pr1) and at the 8th (Pr2) and 11th (Pr3) training week. Food intake, body weight, testosterone, cortisol, malondialdehyde, creatine kinase, and activities of the PI3-K, Akt-1, mTOR, and GSK-3 enzymes were measured. In the EX group, there was a significant 32.6% performance decrease at Pr3 when compared with Pr2. In addition, at protocol completion, the EX-CHO group had a greater gastrocnemius weight than did the C group (p = 0.02), which the EX group did not. Training caused anorexia, decreased testosterone (p = 0.001), and increased malondialdehyde (p = 0.009) in both exercise groups compared with the C group, with no influence of carbohydrate supplementation on these variables (p > 0.05). Compared with in the C group, the activity of Akt-1 was higher in the EX-CHO group but not in the EX group (p = 0.013). Carbohydrate supplementation promoted an attenuation in the performance decrement and maintained gastrocnemius muscle mass in animals that had undergone overtraining protocols, which was accompanied by increased activity of the Akt-1 molecular indicator.
Dinosaur trackways from the Upper Cretaceous Oldman and Dinosaur Park formations (Belly River Group) of southern Alberta, Canada, reveal novel ichnofossil preservation style
Authors: Therrien François , Zelenitsky Darla K. , Quinney Annie , Tanaka Kohei
Published: October 2015

Dinosaur tracksites recently discovered in exposures of the Belly River Group in the Milk River Natural Area (MRNA) and Dinosaur Provincial Park (DPP) of southern Alberta represent a novel type of ichnofossils. The tracks, all referable to hadrosaurs, occur as sideritic or calcareous concretions protruding above fine-grained deposits and are here termed concretionary tracks. Detailed sedimentological, petrographic, and geochemical analyses reveal that, although the MRNA and DPP tracks are of different mineralogical compositions (calcium carbonate versus siderite, respectively), they display similar internal structures (microscopic convoluted laminations) and occur in depositional settings indicative of wet paleoenvironments, where the ground was soft and water saturated. These characteristics suggest that concretionary tracks are footprint casts that formed as groundwater rich in dissolved carbonates flooded depressions left in the soft substrate. As the ponded water evaporated, minerals began to precipitate and mix with clastic material transported into the depressions, settling as finely laminated mud within the tracks and filling them either completely or partially. The geochemical composition of the precipitate would depend on the prevalent groundwater conditions (e.g., pH, dissolved carbonate and sulphate concrentrations). Cementation of the tracks occurred relatively soon after burial (<100 years), possibly in response to microbial activity and saturation by mineral-rich groundwater, and modern erosion exposed the concretionary tracks by removing the softer host unit. Recognition of this novel type of ichnofossils suggests dinosaur tracks may be more common than previously thought. Unfortunately, concretionary tracks tend to break apart rapidly when the encasing and underlying substrate erodes away, altering their diagnostic shape and rendering them indistinguishable from nonichnogenic concretions. As such, concretionary tracks may be transient ichnofossils in the badlands, explaining why they are rarely recognized.
An economic analysis of private incentives to adopt DNA barcoding technology for fish species authentication in Canada
Authors: Ugochukwu Albert I. , Hobbs Jill E. , Phillips Peter W.B. , Gray Richard
Published: October 2015

The increasing spate of species substitution and mislabelling in fish markets has become a concern to the public and a challenge to both the food industry and regulators. Species substitution and mislabelling within fish supply chains occurs because of price incentives to misrepresent products for economic gain. Emerging authenticity technologies, such as the DNA barcoding technology that has been used to identify plants and animal (particularly fish) species through DNA sequencing, offer a potential technological solution to this information problem. However, the adoption of these authenticity technologies depends also on economic factors. The present study uses economic welfare analysis to examine the effects of species substitution and mislabelling in fish markets, and examines the feasibility of the technology for a typical retail store in Canada. It is assumed that increased accuracy of the technology in detecting fraud and enforcement of legal penalties and other associated costs would be likely to discourage cheating. Empirical results suggest that DNA barcoding technology would be feasible presently for a typical retail store only if authentication is done in a third party laboratory, as it may not be feasible on an individual retail store level once fixed and other associated costs of the technology are considered.
Neuronal Entropy-Rate Feature of Entopeduncular Nucleus in Rat Model of Parkinson’s Disease
Authors: Darbin Olivier , Jin Xingxing , Von Wrangel Christof , Schwabe Kerstin , Nambu Atsushi , Naritoku Dean K. , Krauss Joachim K. , Alam Mesbah
Published: October 2015

The function of the nigro-striatal pathway on neuronal entropy in the basal ganglia (BG) output nucleus, i.e. the entopeduncular nucleus (EPN) was investigated in the unilaterally 6-hyroxydopamine (6-OHDA)-lesioned rat model of Parkinson’s disease (PD). In both control subjects and subjects with 6-OHDA lesion of dopamine (DA) the nigro-striatal pathway, a histological hallmark for parkinsonism, neuronal entropy in EPN was maximal in neurons with firing rates ranging between 15 and 25[Formula: see text]Hz. In 6-OHDA lesioned rats, neuronal entropy in the EPN was specifically higher in neurons with firing rates above 25[Formula: see text]Hz. Our data establishes that the nigro-striatal pathway controls neuronal entropy in motor circuitry and that the parkinsonian condition is associated with abnormal relationship between firing rate and neuronal entropy in BG output nuclei. The neuronal firing rates and entropy relationship provide putative relevant electrophysiological information to investigate the sensory-motor processing in normal condition and conditions such as movement disorders.
Complete intersections primitive structures on space curves
Authors: Ellia Philippe
Published: October 2015

A multiple structure [Formula: see text] on a smooth curve [Formula: see text] is said to be primitive if [Formula: see text] is locally contained in a smooth surface. We give some numerical conditions for a curve [Formula: see text] to be a primitive set theoretical complete intersection (i.e. to have a primitive structure which is a complete intersection).
Calculations of first passage time of delayed tree-like networks
Authors: Wang Shuai , Sun Weigang , Zheng Song
Published: October 2015

In this paper, we study random walks in a family of delayed tree-like networks controlled by two network parameters, where an immobile trap is located at the initial node. The novel feature of this family of networks is that the existing nodes have a time delay to give birth to new nodes. By the self-similar network structure, we obtain exact solutions of three types of first passage time (FPT) measuring the efficiency of random walks, which includes the mean receiving time (MRT), mean sending time (MST) and mean first passage time (MFPT). The obtained results show that the MRT, MST and MFPT increase with the network parameters. We further show that the values of MRT, MST and MFPT are much shorter than the nondelayed counterpart, implying that the efficiency of random walks in delayed trees is much higher.
A theoretical model to study melting of metals under pressure
Authors: Kholiya Kuldeep , Chandra Jeewan
Published: October 2015

On the basis of the thermal equation-of-state a simple theoretical model is developed to study the pressure dependence of melting temperature. The model is then applied to compute the high pressure melting curve of 10 metals (Cu, Mg, Pb, Al, In, Cd, Zn, Au, Ag and Mn). It is found that the melting temperature is not linear with pressure and the slope [Formula: see text] of the melting curve decreases continuously with the increase in pressure. The results obtained with the present model are also compared with the previous theoretical and experimental data. A good agreement between theoretical and experimental result supports the validity of the present model.
HCNN: A Neural Network Model for Combining Local and Global Features Towards Human-Like Classification
Authors: Zhang Tielin , Zeng Yi , Xu Bo
Published: October 2015

Brain-inspired algorithms such as convolutional neural network (CNN) have helped machine vision systems to achieve state-of-the-art performance for various tasks (e.g. image classification). However, CNNs mainly rely on local features (e.g. hierarchical features of points and angles from images), while important global structured features such as contour features are lost. Global understanding of natural objects is considered to be essential characteristics that the human visual system follows, and for developing human-like visual systems, the lost of consideration from this perspective may lead to inevitable failure on certain tasks. Experimental results have proved that well-trained CNN classifier cannot correctly distinguish fooling images (in which some local features from the natural images are chaotically distributed) from natural images. For example, a picture that is composed of yellow–black bars will be recognized as school bus with very high confidence by CNN. On the contrary, human visual system focuses on both the texture and contour features to form representation of images and would not mis-take them. In order to solve the upper problem, we propose a neural network model, named as histogram of oriented gradient (HOG) improved CNN (HCNN), that combines local and global features towards human-like classification based on CNN and HOG. The experimental results on MNIST datasets and part of ImageNet datasets show that HCNN outperforms traditional CNN for object classification with fooling images, which indicates the feasibility, accuracy and potential effectiveness of HCNN for solving image classification problem.
Grothendieck groups of the Khovanov–Kuperberg algebras
Authors: Robert Louis-Hadrien
Published: October 2015

The aim of this paper is to take benefit of the foam nature of the Khovanov–Kuperberg algebras to compute the Grothendieck groups of their categories of finite-dimensional projective modules. The computation relies on the Hattori–Stallings trace and some geometrical properties of foams in the solid torus.
The strong AJ conjecture for cables of torus knots
Authors: Tran Anh T.
Published: October 2015

The AJ conjecture, formulated by Garoufalidis, relates the A-polynomial and the colored Jones polynomial of a knot in the 3-sphere. It has been confirmed for all torus knots, some classes of two-bridge knots and pretzel knots, and most cable knots over torus knots. The strong AJ conjecture, formulated by Sikora, relates the A-ideal and the colored Jones polynomial of a knot. It was confirmed for all torus knots. In this paper we confirm the strong AJ conjecture for most cable knots over torus knots.
Perspective of detecting very high energy gamma-ray emission from active galactic nuclei with Large High Altitude Air Shower Observatory (LHAASO)
Authors: Zhao Yi , Yuan Qiang , Bi Xiao-Jun , Zhu Feng-Rong , Jia Huan-Yu
Published: October 2015

The detectability of active galactic nuclei (AGN), a major class of [Formula: see text]-ray emitters in the sky, by the newly planned Chinese project, Large High Altitude Air Shower Observatory (LHAASO), is investigated. The expectation is primarily based on the AGN catalog of Fermi Large Area Telescope (Fermi-LAT), with an extrapolation to the very high energy (VHE) range taking into account the absorption effect by the extragalactic background light (EBL). It is found that LHAASO may have the potential to detect more than several tens of the Fermi detected AGN, basically BL Lacertaes, with one-year sky survey. The capability of measuring the energy spectrum and light curve are also discussed.
INFLUENCE OF NANOWIRE DIAMETER ON STRUCTURAL AND OPTICAL PROPERTIES OF Cu NANOWIRE SYNTHESIZED IN ANODIC ALUMINIUM OXIDE FILM
Authors: CETINEL A. , ÖZCELIK Z.
Published: October 2015

Copper (Cu) nanowire arrays embedded in anodic aluminium oxide films (AAO) on aluminium substrate have been synthesized by alternating current electrochemical deposition. Two-step anodization process has been performed to get the through-hole AAO with ordered nanochannels in 0.3[Formula: see text]M oxalic acids at DC voltages 30, 40, 50 and 60[Formula: see text]V, respectively. Structural characterization of the Cu nanowires has been analyzed by scanning electron microscopy (SEM) and X-ray diffraction (or) X-ray diffractometer (XRD). Our SEM analysis has revealed that the diameters of vertically oriented Cu nanowires are 15, 25, 45 and 60[Formula: see text]nm and the length of Cu nanowires having high packing density is about 15[Formula: see text][Formula: see text]m. XRD measurement has indicated that polycrystalline Cu nanowires prefer growth orientation along the (111) direction. Optical measurements show that reflection of the Cu nanowires/AAO on aluminium reduces with decreasing diameter of the Cu nanowires. This effect can be associated with increased light scattering from metal nanoparticles near their localized plasmon resonance frequency depending on the size and shape of the nanoparticles.
Parametric Analysis of Ride Comfort for Tilting Railway Vehicles Running on Irregular Curved Tracks
Authors: Cheng Yung-Chang , Hsu Chin-Te
Published: October 2015

The ride comfort of a tilting railway vehicle moving on curved tracks with rail irregularities is studied. Using the nonlinear creep model and Kalker's linear theory, the governing differential equations of motion for a tilting railway vehicle running on irregular tracks are first derived. The tilting railway vehicle is modeled by a 27 degree-of-freedom (DOF) car system, considering the lateral displacement, vertical displacement, roll angle and yaw angle of both the wheelsets and bogie frames, as well as the lateral displacement, roll angle and yaw angle of the car body. Based on the international standard ISO 2631-1, the effect of vehicle speed on the ride comfort index of the tilting vehicle is investigated for various tilting angles, using both linear and nonlinear creep models, and various radii of curved tracks, as well as for various suspension parameters. Finally, the ride comfort indices computed with rail irregularities are found to be higher than those with no rail irregularities, indicating that the effect of rail irregularities on the ride comfort of a tilting vehicle cannot be disregarded in practice.
A Multi-Body Dynamic Model for Analysis of Localized Track Responses in Vicinity of Rail Discontinuities
Authors: Askarinejad H. , Dhanasekar M.
Published: October 2015

Rail discontinuities are one of the main sources of wheel impact causing high levels of noise, vibration and stresses in railway track. Even though various multi-body train–track interaction models have been developed in the past decade, accurate modeling and analysis of the track dynamic behavior in the vicinity of rail discontinuities is rare in the literature. In this paper, formulation of a new explicit multi-body dynamic (MBD) model incorporating detailed wagon, wheel–rail subsystems and track containing a rail discontinuity (rail joint) is reported. The predictions of the localized track responses are validated using the data from two gapped rail joints in the field test. The validated model accurately determines the impact forces and dynamic responses. The simulation results provide valuable insight on the behavior of track in vicinity of a rail discontinuity, the sensitivity of the design parameters to the impact forces and the track dynamic responses currently unavailable in the literature.
Investigation of the Traffic Noise Attenuation Provided by Roadside Green Belts
Authors: Karbalaei Samaneh Sadat , Karimi Elham , Naji Hamid Reza , Ghasempoori Seyed Mahmood , Hosseini Seyed Mohsen , Abdollahi Mina
Published: October 2015

Greenbelts are remarkably effective tools for minimizing traffic induced noise pollution. This study revealed the potential role of greenbelts along the roadside for the noise attenuation using various tree species of three different widths (25, 50 and 100[Formula: see text]m). Statistical analysis showed significant differences between stations. The reduction of noise level was also statistically analyzed. The results indicated that the greenbelts significantly contributed to the attenuation of noise pollution with positive correlation. The maximum noise level reduction compared to the open area was for trees and shrubs of 100[Formula: see text]m in width, and a mixture of conifers and broadleaves of 100[Formula: see text]m in width and 50[Formula: see text]m width by 44[Formula: see text]dB (A), 42.84[Formula: see text]dB (A) and 40.34[Formula: see text]dB (A), respectively. The results can be used as guidance for construction of tree belts for noise attenuation in environmental planning and management.
Malcev–Poisson–Jordan algebras
Authors: Ait Ben Haddou Malika , Benayadi Saïd , Boulmane Said
Published: October 2015

Malcev–Poisson–Jordan algebra (MPJ-algebra) is defined to be a vector space endowed with a Malcev bracket and a Jordan structure which are satisfying the Leibniz rule. We describe such algebras in terms of a single bilinear operation, this class strictly contains alternative algebras. For a given Malcev algebra [Formula: see text], it is interesting to classify the Jordan structure ∘ on the underlying vector space of [Formula: see text] such that [Formula: see text] is an MPJ-algebra (∘ is called an MPJ-structure on Malcev algebra [Formula: see text]. In this paper we explicitly give all MPJ-structures on some interesting classes of Malcev algebras. Further, we introduce the concept of pseudo-Euclidean MPJ-algebras (PEMPJ-algebras) and we show how one can construct new interesting quadratic Lie algebras and pseudo-Euclidean Malcev (non-Lie) algebras from PEMPJ-algebras. Finally, we give inductive descriptions of nilpotent PEMPJ-algebras.
Comprehensive modeling of the antioxidant mechanism of ebselen
Authors: Jiang Jun-Hao , Zhou Hui , Li Hui-Jie , Wang Yu-Chun , Tian Mei , Huang Ya-Lin , Deng Ping
Published: October 2015

Three possible catalytic cycles for ebselen have been comprehensively modeled by theoretical calculations using density functional theory (DFT) at a mixed basis set level; the 6-31G(d) basis set for hydrocarbon fragments and the 6-31[Formula: see text]G(d,p) basis set for other atoms. The 2[Formula: see text] cycle is the main pathway in the glutathione peroxidase (GPx) cycle (cycle A), and IM3[Formula: see text]TS3 is the rate controlling process. The 1[Formula: see text]1 cycle is the main pathway for the oxidation cycle (cycle B), and the rate controlling step is the [Formula: see text] step. Ebselen reacts with the selenol 3 to form the diselenide 9, and this is the rate controlling step for cycle C. The extremely high energy barrier for the IM9[Formula: see text]TS9 process indicates that cycle C is unlikely to occur in vivo. Although cycle B is favored based on the energy analysis, with a maximum energy barrier of only 26.68[Formula: see text]kcal/mol at the mixed basis set level, it is generally unlikely to have very high concentrations of peroxides present in vivo. The results indicate that in order to improve the antioxidant activity of ebselen, it would be necessary to suitably modify the molecular structure of ebselen to reduce the energy barrier of the IM3[Formula: see text]TS3 process.
In silico modeling of aspalathin and nothofagin against SGLT2
Authors: Liu Wei , Wang Huanjie , Meng Fancui
Published: October 2015

Aspalathin and nothofagin are the major dihydrochalcones found in rooibos (Aspalathus linearis), which display anti-diabetic activities, but the mechanism is still unclear. In this paper, hSGLT2 (human sodium dependent glucose co-transporter 2), a target for diabetes mellitus, was built using homology modeling method. Molecular docking and dynamics simulations were carried out on aspalathin, nothofagin and SGLT2 complexes with dapagliflozin as positive control. The results show that both the binding energies and binding modes of aspalathin and nothofagin are similar to dapagliflozin, indicating that either component of rooibos may exhibit anti-diabetic effects through inhibiting SGLT2 receptor. However, the predicted permeability value of aspalathin and nothofagin is low, which may cause poor absorption, resulting in weak SGLT2 inhibition. Calculation results elucidate the possible inhibiting mechanism of aspalathin and nothofagin against SGLT2, and therefore enhance our understanding of anti-diabetic activities of rooibos.
Predicting bedforms and primary current stratification in cohesive mixtures of mud and sand
Authors: Baas Jaco H. , Best James L. , Peakall Jeff
Published: October 2015

The use of sedimentary structures as indicators of flow and sediment morphodynamics in ancient sediments lies at the very heart of sedimentology, and allows reconstruction of formative flow conditions generated in a wide range of grain sizes and sedimentary environments. However, the vast majority of past research has documented and detailed the range of bedforms generated in essentially cohesionless sediments that lack the presence of mud within the flow and within the sediment bed itself. Yet most sedimentary environments possess fine-grained sediments and recent work has shown how the presence of this fine sediment may substantially modify the fluid dynamics of such flows. It is increasingly evident that understanding the influence of mud, and the presence of cohesive forces, is essential to permit a fuller interpretation of many modern and ancient sedimentary successions.

In this paper, the present state of knowledge on the stability of current- and wave-generated bedforms and their primary current stratification is reviewed, and a new extended bedform phase diagram is presented that summarizes the bedforms generated in mixtures of sand and mud under rapidly decelerated flows. This diagram provides a phase space using the variables of yield strength and grain mobility as the abscissa and ordinate axes, respectively, and defines the stability fields of a range of bedforms generated under flows that have modified fluid dynamics owing to the presence of suspended sediment within the flow. Our results also present unique data on a range of bedforms generated in such flows, whose recognition is essential to help interpret such deposits in the ancient sedimentary record, including the following: (1) heterolithic stratification, comprising alternating laminae or layers of sand and mud; (2) the preservation of low-amplitude bed-waves, large current ripples and bed scours with intrascour composite bedforms; (3) low-angle cross-lamination and long lenses and streaks of sand and mud formed by bed-waves; (4) complex stacking of reverse bedforms, mud layers and low-angle cross-lamination on the upstream face of bed scours; (5) planar bedding comprising stacked mud–sand couplets. Furthermore, the results shown herein demonstrate that flow variability is not required to produce deposits consisting of interbedded sand and muds, and that the nature of flaser, wavy and lenticular bedding (
sensu
Reineck & Wunderlich 1968) may also need reconsideration in the deposits of such sediment-laden flows.
Decoupling seasonal fluctuations in fluvial discharge from the tidal signature in ancient deltaic deposits: an example from the Neuquén Basin, Argentina
Authors: Gugliotta Marcello , Kurcinka Colleen E. , Dalrymple Robert W. , Flint Stephen S. , Hodgson David M.
Published: October 2015

Fluvial discharge fluctuations are a fundamental characteristic of almost all modern rivers and can produce distinctive deposits that are rarely described from ancient fluvial or mixed-energy successions. Large-scale outcrops from the Middle Jurassic Lajas Formation (Argentina) expose a well-constrained stratigraphic succession of marginal-marine deposits with a strong fluvial influence and well-known tidal indicators. The studied deposits show decimetre-scale interbedding of coarser- and finer-grained facies with mixed fluvial and tidal affinities. The alternation of these two types of beds forms non-cyclic successions that are interpreted to be the result of seasonal variation in river discharge, rather than regular and predictable changes in current velocity caused by tides. Seasonal bedding is present in bar deposits that form within or at the mouth of minor and major channels. Seasonal bedding is not preserved in channel thalweg deposits, where river flood processes were too powerful, or in floodplain, muddy interdistributary-bay, prodelta and transgressive deposits, where the river signal was weak and sporadic. The identification of sedimentary facies characteristic of seasonal river discharge variations is important for accurate interpretation of ancient deltaic process regime.
Tethyan versus Iberian extension during the Cretaceous period in the eastern Iberian Peninsula: insights from magnetic fabrics
Authors: García-Lasanta C. , Román-Berdiel T. , Oliva-Urcia B. , Casas A. M. , Gil-Peña I. , Speranza F. , Mochales T.
Published: October 2015

This work investigates how anisotropy of magnetic susceptibility (AMS) recorded the strain related to the Early Cretaceous extensional processes in synrift sediments of the Maestrat basin (eastern Spain). Forty-two sites, distributed throughout the Lower Cretaceous sequence with dominant gentle dips, were sampled. Minerals contributing to the AMS are mainly phyllosilicates. The parallelism between magnetic and sedimentary foliation seems to indicate that a primary (synsedimentary and early diagenetic) magnetic fabric was preserved at 84% of sites. Consequently, preferred orientations of magnetic lineations are interpreted to record the effect of extensional processes coeval with sedimentation and diagenesis during this period. At these 35 sites, two main magnetic lineation orientations are found, delimiting two large domains: a NE–SW orientation prevailing in the NW sector of the basin (parallel to the extension direction of the Iberian basin), and NW–SE to NNW–SSE orientations to the SE (parallel to the extension direction controlling the western Tethys margin). Directional variability demonstrates that the Maestrat basin is located at the boundary between two domains (Iberian and Tethyan) undergoing different plate-scale extensional processes. The subsequent Cenozoic tectonic inversion affected the synsedimentary magnetic fabrics at only a few sites at the borders of the basin, where compressive features are more developed.
Translating the Genome in Time and Space: Specialized Ribosomes, RNA Regulons, and RNA-Binding Proteins
Authors: Shi Zhen , Barna Maria
Published: October 2015

A central question in cell and developmental biology is how the information encoded in the genome is differentially interpreted to generate a diverse array of cell types. A growing body of research on posttranscriptional gene regulation is revealing that both global protein synthesis rates and the translation of specific mRNAs are highly specialized in different cell types. How this exquisite translational regulation is achieved is the focus of this review. Two levels of regulation are discussed: the translation machinery and cis-acting elements within mRNAs. Recent evidence shows that the ribosome itself directs how the genome is translated in time and space and reveals surprising functional specificity in individual components of the core translation machinery. We are also just beginning to appreciate the rich regulatory information embedded in the untranslated regions of mRNAs, which direct the selective translation of transcripts. These hidden RNA regulons may interface with a myriad of RNA-binding proteins and specialized translation machinery to provide an additional layer of regulation to how transcripts are spatiotemporally expressed. Understanding this largely unexplored world of translational codes hardwired in the core translation machinery is an exciting new research frontier fundamental to our understanding of gene regulation, organismal development, and evolution.
Adaptation and Adaptedness of Organisms to Urban Environments
Authors: McDonnell Mark J. , Hahs Amy K.
Published: October 2015

Around the world the development and growth of cities and towns are having a significant impact on local and global biodiversity. There is growing interest in the adaptation of nonhuman organisms to urban environments, and we distinguish between the concepts of adaptation and adaptedness. Most of these studies have focused on animals, especially birds. Commonly recorded responses to urban environments include regulatory and acclimatory responses involving changes in behavior, communication, and physiology. Developmental responses tend to be morphological in nature but can also involve cultural learning. There is growing evidence of microevolutionary changes associated with adaptive responses to urban environments. This review also highlights the urgent need to refine the terminology currently used to describe the adaptation of organisms to urban environments in order to improve scientific understanding and more effectively identify and communicate the actions required to create biodiversity- and adaptation-friendly cities and towns for the future.
The History of Patenting Genetic Material
Authors: Sherkow Jacob S. , Greely Henry T.
Published: October 2015

The US Supreme Court's recent decision in Association for Molecular Pathology v. Myriad Genetics, Inc. declared, for the first time, that isolated human genes cannot be patented. Many have wondered how genes were ever the subjects of patents. The answer lies in a nuanced understanding of both legal and scientific history. Since the early twentieth century, “products of nature” were not eligible to be patented unless they were “isolated and purified” from their surrounding environment. As molecular biology advanced, and the capability to isolate genes both physically and by sequence came to fruition, researchers (and patent offices) began to apply patent-law logic to genes themselves. These patents, along with other biological patents, generated substantial social and political criticism. Myriad Genetics, a company with patents on BRCA1 and BRCA2, two genes critical to assessing early-onset breast and ovarian cancer risk, and with a particularly controversial business approach, became the antagonist in an ultimately successful campaign to overturn gene patents in court. Despite Myriad's defeat, some questions concerning the rights to monopolize genetic information remain. The history leading to that defeat may be relevant to these future issues.
General Stress Signaling in the Alphaproteobacteria
Authors: Fiebig Aretha , Herrou Julien , Willett Jonathan , Crosson Sean
Published: October 2015

The Alphaproteobacteria uniquely integrate features of two-component signal transduction and alternative σ factor regulation to control transcription of genes that ensure growth and survival across a range of stress conditions. Research over the past decade has led to the discovery of the key molecular players of this general stress response (GSR) system, including the sigma factor σEcfG, its anti-σ factor NepR, and the anti-anti-σ factor PhyR. The central molecular event of GSR activation entails aspartyl phosphorylation of PhyR, which promotes its binding to NepR and thereby releases σEcfG to associate with RNAP and direct transcription. Recent studies are providing a new understanding of complex, multilayered sensory networks that activate and repress this central protein partner switch. This review synthesizes our structural and functional understanding of the core GSR regulatory proteins and highlights emerging data that are defining the systems that regulate GSR transcription in a variety of species.
Causal Inference in Developmental Origins of Health and Disease (DOHaD) Research
Authors: Gage Suzanne H. , Munafò Marcus R. , Davey Smith George
Published: October 2015

Studies of the developmental origins of health and disease (DOHaD) often rely on prospective observational data, from which associations between developmental exposures and outcomes in later life can be identified. Typically, conventional statistical methods are used in an attempt to mitigate problems inherent in observational data, such as confounding and reverse causality, but these have serious limitations. In this review, we discuss a variety of methods that are increasingly being used in observational epidemiological studies to help strengthen causal inference. These methods include negative controls, cross-contextual designs, instrumental variables (including Mendelian randomization), family-based studies, and natural experiments. Applications within the DOHaD framework, and in relation to behavioral, psychiatric, and psychological domains, are considered, and the considerable potential for expanding the use of these methods is outlined.
Dynamic contrast-enhanced quantitative susceptibility mapping with ultrashort echo time MRI for evaluating renal function
Authors: Xie Luke , Layton Anita T. , Wang Nian , Larson Peder E. Z. , Zhang Jeff L. , Lee Vivian S. , Liu Chunlei , Johnson G. Allan
Published: October 2015

Dynamic contrast-enhanced (DCE) MRI can provide key insight into renal function. DCE MRI is typically achieved through an injection of a gadolinium (Gd)-based contrast agent, which has desirable T1 quenching and tracer kinetics. However, significant T2* blooming effects and signal voids can arise when Gd becomes very concentrated, especially in the renal medulla and pelvis. One MRI sequence designed to alleviate T2* effects is the ultrashort echo time (UTE) sequence. In the present study, we observed T2* blooming in the inner medulla of the mouse kidney, despite using UTE at an echo time of 20 microseconds and a low dose of 0.03 mmol/kg Gd. We applied quantitative susceptibility mapping (QSM) and resolved the signal void into a positive susceptibility signal. The susceptibility values [in parts per million (ppm)] were converted into molar concentrations of Gd using a calibration curve. We determined the concentrating mechanism (referred to as the concentrating index) as a ratio of maximum Gd concentration in the inner medulla to the renal artery. The concentrating index was assessed longitudinally over a 17-wk course (3, 5, 7, 9, 13, 17 wk of age). We conclude that the UTE-based DCE method is limited in resolving extreme T2* content caused by the kidney's strong concentrating mechanism. QSM was able to resolve and confirm the source of the blooming effect to be the large positive susceptibility of concentrated Gd. UTE with QSM can complement traditional magnitude UTE and offer a powerful tool to study renal pathophysiology.
Efficient reinforcement learning of a reservoir network model of parametric working memory achieved with a cluster population winner-take-all readout mechanism
Authors: Cheng Zhenbo , Deng Zhidong , Hu Xiaolin , Zhang Bo , Yang Tianming
Published: October 2015

The brain often has to make decisions based on information stored in working memory, but the neural circuitry underlying working memory is not fully understood. Many theoretical efforts have been focused on modeling the persistent delay period activity in the prefrontal areas that is believed to represent working memory. Recent experiments reveal that the delay period activity in the prefrontal cortex is neither static nor homogeneous as previously assumed. Models based on reservoir networks have been proposed to model such a dynamical activity pattern. The connections between neurons within a reservoir are random and do not require explicit tuning. Information storage does not depend on the stable states of the network. However, it is not clear how the encoded information can be retrieved for decision making with a biologically realistic algorithm. We therefore built a reservoir-based neural network to model the neuronal responses of the prefrontal cortex in a somatosensory delayed discrimination task. We first illustrate that the neurons in the reservoir exhibit a heterogeneous and dynamical delay period activity observed in previous experiments. Then we show that a cluster population circuit decodes the information from the reservoir with a winner-take-all mechanism and contributes to the decision making. Finally, we show that the model achieves a good performance rapidly by shaping only the readout with reinforcement learning. Our model reproduces important features of previous behavior and neurophysiology data. We illustrate for the first time how task-specific information stored in a reservoir network can be retrieved with a biologically plausible reinforcement learning training scheme.
Goal-dependent modulation of the long-latency stretch response at the shoulder, elbow, and wrist
Authors: Weiler Jeffrey , Gribble Paul L. , Pruszynski J. Andrew
Published: October 2015

Many studies have demonstrated that muscle activity 50–100 ms after a mechanical perturbation (i.e., the long-latency stretch response) can be modulated in a manner that reflects voluntary motor control. These previous studies typically assessed modulation of the long-latency stretch response from individual muscles rather than how this response is concurrently modulated across multiple muscles. Here we investigated such concurrent modulation by having participants execute goal-directed reaches to visual targets after mechanical perturbations of the shoulder, elbow, or wrist while measuring activity from six muscles that articulate these joints. We found that shoulder, elbow, and wrist muscles displayed goal-dependent modulation of the long-latency stretch response, that the relative magnitude of participants' goal-dependent activity was similar across muscles, that the temporal onset of goal-dependent muscle activity was not reliably different across the three joints, and that shoulder muscles displayed goal-dependent activity appropriate for counteracting intersegmental dynamics. We also observed that the long-latency stretch response of wrist muscles displayed goal-dependent modulation after elbow perturbations and that the long-latency stretch response of elbow muscles displayed goal-dependent modulation after wrist perturbations. This pattern likely arises because motion at either joint could bring the hand to the visual target and suggests that the nervous system rapidly exploits such simple kinematic redundancy when processing sensory feedback to support goal-directed actions.
Changes in the transcriptome of bovine ovarian cortex during follicle activation in vitro
Authors: Yang M. Y. , Fortune J. E.
Published: October 2015

The signals that regulate activation, a key transition in ovarian follicular development, are still not well understood, especially in nonrodent species. To gain insight into the regulation of this transition in cattle, we combined a microarray approach with an in vitro system in which ovarian cortical pieces cultured in control medium are enriched for primordial follicles, whereas pieces cultured with insulin are enriched for primary follicles. Total RNA was extracted from cultured cortical pieces, and then transcripts were identified and analyzed using the Affymetrix Bovine Genome GeneChip array. Around 65% of the transcripts in the bovine GeneChip were detected in cultured cortical pieces. Comparison between pieces cultured with or without insulin generated 158 differentially expressed transcripts. Compared with controls, 90 transcripts were upregulated and 68 were downregulated by insulin. These transcripts are involved in many biological processes and functions, but most are associated with cellular growth or cell cycle/cell death. The transcript encoding ubiquitin-conjugating enzyme E2C (UBE2C) was significantly upregulated during follicle activation, and Ingenuity Pathways Analysis revealed that UBE2C can interact with the tumor suppressor phosphatase and tensin homolog (PTEN). Both PTEN mRNA and protein were lower in cortical pieces cultured with insulin than in controls. In addition, FOXO3a, a downstream effector of PTEN signaling, underwent nuclear-cytoplasmic shuttling during primordial to primary follicle development in bovine fetal ovaries, further suggesting the involvement of the PTEN pathway in follicle activation in cattle. Genes and pathways identified in this study provide interesting candidates for further investigation of mechanisms underlying follicle activation.
Nonpoint Symmetry and Reduction of Nonlinear Evolution and Wave Type Equations
Authors: Tsyfra Ivan , Czyżycki Tomasz
Published: October 2015

We study the symmetry reduction of nonlinear partial differential equations with two independent variables. We propose new ansätze reducing nonlinear evolution equations to system of ordinary differential equations. The ansätze are constructed by using operators of nonpoint classical and conditional symmetry. Then we find solution to nonlinear heat equation which cannot be obtained in the framework of the classical Lie approach. By using operators of Lie-Bäcklund symmetries we construct the solutions of nonlinear hyperbolic equations depending on arbitrary smooth function of one variable too.
The Quantified Level of Circulating Prostate Stem Cell Antigen mRNA relative to GAPDH Level Is a Clinically Significant Indictor for Predicting Biochemical Recurrence in Prostate Cancer Patients after Radical Prostatectomy
Authors: Kim Sung Han , Park Weon Seo , Lee Sang Jin , Choi Moon Kyung , Yeon Seung Min , Joo Jeong Nam , Ko Ara , Lee Eun Sik , Joung Jae Young , Seo Ho Kyung , Chung Jinsoo , Lee Kang Hyun
Published: October 2015

The study quantified the relative absolute PSCA level in relation to the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) level in the peripheral blood of 478 hormone-naive prostate cancer (PC) patients who underwent radical prostatectomy from 2005 to 2012 and evaluated its prognostic significance as a risk factor for predicting biochemical recurrence (BCR), compared to known parameters. Nested real-time polymerase chain reaction (RT-PCR) and gel electrophoresis detected PSCA levels and measured the PSCA/GAPDH ratio. Clinicopathological data from the institutional database were examined to determine the adequate cut-off level to predict postoperative BCR. A total of 110 patients had a positive PSCA result (23.0%) via RT-PCR (mean blood ratio 1.1 ± 0.4). The BCR was significantly higher in the PSCA-positive detection group (p=0.009). A multivariate model was created to show that a PSCA/GAPDH ratio between 1.0 and 1.5 (HR 12.722), clinical T2c stage (HR 0.104), preoperative PSA (HR 1.225), extraprostatic capsule extension (HR 0.006), lymph node dissection (HR 16.437), and positive resection margin (HR 27.453) were significant predictive factors for BCR (p<0.05). The study showed successful quantification of PSCA with its significance for BCR-related risk factor; however, further studies are needed to confirm its clinical predictive value.
On the Initial-Boundary-Value Problem for the Time-Fractional Diffusion Equation on the Real Positive Semiaxis
Authors: Goos D. , Reyero G. , Roscani S. , Santillan Marcus E.
Published: October 2015

We consider the time-fractional derivative in the Caputo sense of orderα∈(0, 1). Taking into account the asymptotic behavior and the existence of bounds for the Mainardi and the Wright function inR+, two different initial-boundary-value problems for the time-fractional diffusion equation on the real positive semiaxis are solved. Moreover, the limit whenα↗1of the respective solutions is analyzed, recovering the solutions of the classical boundary-value problems whenα= 1, and the fractional diffusion equation becomes the heat equation.
Recent Approaches for Broadening the Spectral Bandwidth in Resonant Cavity Optoelectronic Devices
Authors: Ju Gun Wu , Na Byung Hoon , Park Yong-Hwa , Song Young Min , Lee Yong Tak
Published: October 2015

Resonant cavity optoelectronic devices, such as vertical cavity surface emitting lasers (VCSELs), resonant cavity enhanced photodetectors (RCEPDs), and electroabsorption modulators (EAMs), show improved performance over their predecessors by placing the active device structure inside a resonant cavity. The effect of the optical cavity, which allows wavelength selectivity and enhancement of the optical field due to resonance, allows the devices to be made thinner and therefore faster, while simultaneously increasing the quantum efficiency at the resonant wavelengths. However, the narrow spectral bandwidth significantly reduces operating tolerances, which leads to severe problems in applications such as optical communication, imaging, and biosensing. Recently, in order to overcome such drawbacks and/or to accomplish multiple functionalities, several approaches for broadening the spectral bandwidth in resonant cavity optoelectronic devices have been extensively studied. This paper reviews the recent progress in techniques for wide spectral bandwidth that include a coupled microcavity, asymmetric tandem quantum wells, and high index contrast distributed Bragg-reflectors. This review will describe design guidelines for specific devices together with experimental considerations in practical applications.
Mutual Information-Assisted Wavelet Function Selection for Enhanced Rolling Bearing Fault Diagnosis
Authors: Yan Ruqiang , Shan Mengxiao , Cui Jianwei , Wu Yahui
Published: October 2015

This paper presents an enhanced rolling bearing fault diagnosis approach, based on optimized wavelet packet transform (WPT) assisted with quantitative wavelet function selection. Mutual information is utilized as a quantitative measure to select the most suitable wavelet function for the WPT-based vibration analysis. Energy features from coefficients of an optimal set of orthogonal wavelet subspaces which resulted from the WPT-based vibration analysis are input to different classifiers. The fault states of the rolling bearings can then be identified. Experiment studies conducted on a rolling bearing test system have verified the effectiveness of the proposed approach for rolling bearing fault diagnosis.