bluuebunny/crossref_metadata_2025 huggingface dataset:
Wave focusing using symmetry matching in axisymmetric acoustic gradient index lenses
Authors: Romero-García V. , Cebrecos A. , Picó R. , Sánchez-Morcillo V. J. , Garcia-Raffi L. M. , Sánchez-Pérez J. V.
Published: January 2014

The symmetry matching between the source and the lens results in fundamental interest for lensing applications. In this work, we have modeled an axisymmetric gradient index (GRIN) lens made of rigid toroidal scatterers embedded in air considering this symmetry matching with radially symmetric sources. The sound amplification obtained in the focal spot of the reported lens (8.24 dB experimentally) shows the efficiency of the axisymmetric lenses with respect to the previous Cartesian acoustic GRIN lenses. The axisymmetric design opens new possibilities in lensing applications in different branches of science and technology.
Irradiation-induced magnetic ordering in SiC: Experimental results and a density functional study
Authors: He Xiujie , Tan Jie , Zhang Baoliang , Zhao Mingwen , Xia Huihao , Liu Xiangdong , He Zhoutong , Yang Xinmei , Zhou Xingtai
Published: January 2014

Magnetism of 6H-SiC single crystals implanted with 3 MeV protons is studied both experimentally and theoretically. We found that proton irradiation can induce stable ferromagnetism in 6H-SiC with a Curie temperature above 300 K. There is a dose window available for tuning the magnetization of the samples. The maximum saturation magnetizations (0.17 emu/g) are three orders of magnitude larger than that reported in neutron-irradiated SiC crystals (1 × 10−4 emu/g). First-principles calculations indicate that the ferromagnetism is related to the divacancy-related defects (VSiVC + nH, (n = 1–3)) generated under proton irradiation. This offers a promising route for the development of metal-free SiC magnets.
Effects of antidot shape on the spin wave spectra of two-dimensional Ni80Fe20 antidot lattices
Authors: Mandal Ruma , Laha Pinaki , Das Kaustuv , Saha Susmita , Barman Saswati , Raychaudhuri A. K. , Barman Anjan
Published: January 2014

We show that the optically induced spin wave spectra of nanoscale Ni80Fe20 (permalloy) antidot lattices can be tuned by changing the antidot shape. The spin wave spectra also show an anisotropy with the variation of the in-plane bias field orientation. Analyses show this is due to various quantized and extended modes, whose nature changes with the antidot shape and bias field orientation as a result of the variation of the internal magnetic field profile. The observed variation and anisotropy in the spin waves with the internal and external parameters are important for their applications in magnonic devices.
Magnetic manipulation by resistance switching in CeO2/PrBa2Cu3O7−δ/Pt heterostructure: The role of oxygen vacancies
Authors: Yun C. , Chen X. G. , Fu J. B. , Sun J. R. , Zhang Y. X. , Wang Y. F. , Zhang Y. , Liu S. Q. , Xiong G. C. , Lian G. J. , Yang Y. C. , Yang J. B.
Published: January 2014

Pronounced bipolar resistance switching with a good retention property has been observed in CeO2/PrBa2Cu3O7−δ/Pt heterostructure. The low resistance state and high resistance state exhibited distinguished ferromagnetic signals, as compared to the nearly non-magnetic initial state. It is found that the migration of the oxygen vacancies under electric field is mainly responsible for the electric and the magnetic changes. The modified interfacial electronic structure by the oxygen vacancy migration and the trapping/detrapping of the carriers leads to the resistance switching. The exchange interaction of the hydrogen-like orbitals formed around the singly occupied oxygen vacancies in CeO2 is accounting for the emerged and modulated ferromagnetic signals. Temperature dependence of resistance in the low resistance state follows a variable range hopping law, further confirming that the amount of oxygen vacancies in the CeO2 layer directly affects the hydrogen-like orbital radius, which determines the strength of the ferromagnetic coupling.
The instability of silicene on Ag(111)
Authors: Acun A. , Poelsema B. , Zandvliet H. J. W. , van Gastel R.
Published: January 2014

We have used low energy electron microscopy to directly visualize the formation and stability of silicene layers on a Ag(111) substrate. Theoretical calculations call into question the stability of this graphene-like analog of silicon. We find that silicene layers are intrinsically unstable against the formation of an “sp3-like” hybridized, bulk-like silicon structure. The irreversible formation of this bulk-like structure is triggered by thermal Si adatoms that are created by the silicene layer itself. To add injury to insult, this same instability prevents the formation of a fully closed silicene layer or a thicker bilayer, rendering the future large-scale fabrication of silicene layers on Ag substrates unlikely.
On the specific absorption rate of hyperthermia fluids
Authors: Périgo E. A. , Sampaio F. A. , de Campos M. F.
Published: January 2014

The specific absorption rate (SAR) concept of hyperthermia ferrofluids is discussed. It is first suggested that SAR can be characterized at the steady state condition, taking into account the heating flow mechanism from the ferrofluid to the external environment. The temperature dependence of SAR is then addressed, indicating that the influence arises from both magnetic susceptibility and relaxation time of the system. At last, a single equation able to express the temperature versus time profile of a ferrofluid, when SAR is virtually temperature independent, is proposed up to the equilibrium condition.
Order parameter and scaling behavior in BaZrxTi1−xO3 (0.3 < x < 0.6) relaxor ferroelectrics
Authors: Usman Muhammad , Mumtaz Arif , Raoof Sobia , Hasanain S. K.
Published: January 2014

We report the relaxor behavior of the zirconium doped barium titanate BaZrxTi1−xO3 solid solutions and discuss the temperature, frequency, and concentration dependence in terms of correlations among the polar nanoregions. The relaxor behavior is analyzed within the mean field theory by estimating the Edward-Anderson order parameter qEA. Additionally, we find that qEA calculated for the different concentrations obeys a scaling behavior qEA=1−(T/Tm)n, where Tm are the respective dielectric maxima temperatures and n = 2.0 ± 0.1. The frequency dependence of the qEA also shows results consistent with the above mentioned picture.
GaN nanowire/thin film vertical structure p–n junction light-emitting diodes
Authors: Hong Young Joon , Lee Chul-Ho , Beom Park Jun , Jin An Sung , Yi Gyu-Chul
Published: January 2014

Here, we report vertical-type GaN nanowire-based light-emitting diodes (LEDs) fabricated by the metal-catalyzed vapor–liquid–solid (VLS) method. The nickel-catalyzed VLS process yielded both n-GaN nanowires and GaN nanoislands on substrates. The nanoislands markedly deteriorated the diode and electroluminescent characteristics in n-nanowire/p-film LED structures because of parasitic resistance and deep level emission caused by nanoislands. By burying the nanoislands with an insulating layer and adopting coaxial p–n junction nanowire structures, nanowire-based LEDs were shown to exhibit superior device performance, including highly rectifying and monochromatic electroluminescent characteristics. Thus, the undesirable effects associated with nanoislands were considerably suppressed. This work provides a rationale for designing high-performance vertical nanowire-based LEDs.
An atmospheric air gas-liquid diffuse discharge excited by bipolar nanosecond pulse in quartz container used for water sterilization
Authors: Wang Sen , Yang De-Zheng , Wang Wen-Chun , Zhang Shuai , Liu Zhi-Jie , Tang Kai , Song Ying
Published: January 2014

In this Letter, we report that the air gas-liquid diffuse discharge plasma excited by bipolar nanosecond pulse in quartz container with different bottom structures at atmospheric pressure. Optical diagnostic measurements show that bountiful chemically and biologically active species, which are beneficial for effective sterilization in some areas, are produced. Such diffuse plasmas are then used to treat drinking water containing the common microorganisms (Candida albicans and Escherichia coli). It is found that these plasmas can sterilize the microorganisms efficiently.
Pressure-induced densification in GeO2 glass: A transmission x-ray microscopy study
Authors: Lin Yu , Zeng Qiaoshi , Yang Wenge , Mao Wendy L.
Published: January 2014

Nanoscale transmission x-ray microscopy measurements have been performed to determine the effect of pressure (P) on the volume (V) change in GeO2 glass up to 38.5 GPa. The P-V data show a continuous increase upon compression, indicating that the density-driven structural transformation is a gradual process. Over the pressure range studied, a transition is observed at approximately 10–13 GPa, where the material displays distinct compression behaviors. The pressure-induced densification that involves the coordination number change has been discussed. Using this newly developed high-pressure imaging technique with tens of nanometer resolution, we have provided a direct and unequivocal way for measuring density of amorphous materials to much higher pressures with accuracy rivaling x-ray diffraction of crystalline solids.
Communication: Non-monotonic supersaturation dependence of the nucleus size of crystals with anisotropically interacting molecules
Authors: Bingham R. J. , Rizzi L. G. , Cabriolu R. , Auer S.
Published: January 2014

We study the nucleation of model two-dimensional crystals formed from anisotropically interacting molecules using kinetic Monte Carlo simulations and the forward flux sampling algorithm. The growth probability P(n) of a cluster of n molecules is measured while the supersaturation s and interaction anisotropy of the molecules are varied, in order to gain insight into the nucleation mechanism. It is found that with increasing degree of interaction anisotropy the nucleus size (defined as the cluster size at which P(n) = 0.5) can increase with increasing s, with sharp jumps at certain s values. Analysis of the cluster shape reveals that nucleation in the system studied is of a non-standard form, in that it embodies elements of both the classical nucleation theory and the density functional theory frameworks.
Wind power prediction system for wind farm based on auto regressive statistical model and physical model
Authors: Wu Bingheng , Song Mengxuan , Chen Kai , He Zhongyang , Zhang Xing
Published: January 2014

Extracting energy from renewable sources such as wind energy is widely investigated in the past decades to mitigate the global energy crisis and environmental pollution. For a wind farm that converts wind energy into electricity power, a real-time prediction system of the output power is significant. In this paper, a prediction system is developed with a method of combining statistical model and physical model. In this system, the inlet condition of the wind farm is forecasted by the auto regressive model. The flow field is computed by the Reynolds average Navier-stokes simulation in the computational fluid dynamics model. The wake flow is calculated by the particle model, which can be used over complex terrain. Taking also the terrain condition, the property of turbines and wake flow model into account, the output power of the wind farm can be further predicted. The proposed prediction system is tested by the data from Wattle Point Wind Farm in Australia. Through the data post-processing, the error of the mean daily output power is less than 5%. The proposed system is effective for power output prediction of wind farm.
Note: Refractive index as an indicator for non-homogeneous solid identification
Authors: Wang Jin , Ye Qing , Deng Zhichao , Zhou Wenyuan , Zhang Chunping , Tian Jianguo
Published: January 2014

Non-homogenous material such as solid composite materials examination using refractive index-sensing remains a challenge for researchers. A derivative total reflection method for simultaneous measurement of the refractive indices of various components of a non-homogeneous solid was developed. Only a measurement of the reflectance from the surface of composite sample is necessary. In our experiments, simulation samples, porcine tissue, and Rosso Levanto marble samples were measured to verify proposed method.
Earth-size exoplanets in habitable orbits are common
Authors: Schwarzschild Bertram M.
Published: January 2014

NASA’s Kepler orbiter has clarified the demographics of planets orbiting Sun-like stars.
Bohr’s molecular model, a century later
Authors: Svidzinsky Anatoly , Scully Marlan , Herschbach Dudley
Published: January 2014

The Bohr model, newly reconciled with quantum mechanics in the limit of infinite dimensions and modestly extended, yields surprisingly accurate predictions for hydrogen and other small molecules.
Breeding progress in the pasta-making quality of durum wheat cultivars released in Italy and Spain during the 20th Century
Authors: Subira Joan , Peña Roberto Javier , Álvaro Fanny , Ammar Karim , Ramdani Abdelhamid , Royo Conxita
Published: January 2014

Genetic improvement of quality traits of durum wheat achieved in Italy and Spain during the 20th Century was investigated using an historical series of 12 cultivars from each country. The European Union durum wheat quality index increased by 6.25% (0.13% year–1 in Italian and 0.06% year–1 in Spanish cultivars). Protein content decreased by ~10% (–0.14% year–1 in Italian and –0.19% year–1 in Spanish cultivars) but protein per ha increased at a rate of 0.35% year–1 (0.41% year–1 in Spanish and 0.26% year–1 in Italian cultivars). Yellow colour index increased by 9.9% (0.15% year–1 in Italian and 0.10% year–1 in Spanish cultivars). Test weight and vitreousness did not suffer significant changes over time. Gluten strength increased by 32.1% or 0.54% year–1 in Italian, and 27.9% or 0.33% year–1 in Spanish cultivars. Much larger genetic control on gluten strength was found in Italian than in Spanish cultivars. Changes in sedimentation index (41.1% or 0.64% year–1 in Italy, and 41.6% or 0.49% year–1 in Spain) were the consequence of the progressive incorporation into recent cultivars of favourable low molecular weight glutenin subunits (LMW-GS). Breeding increased the frequency of the LMW-GS combination aaa, which was present in 75% of all intermediate cultivars and in 100% of the modern Italian cultivars. A LMW-GS combination not previously reported (d?b) was identified in two modern Spanish cultivars. Breeding programs were also successful in increasing the stability of gluten strength and the sedimentation index.
Establishing the carrying capacity of the grasslands of China: a review
Authors: Zhang Y. J. , Zhang X. Q. , Wang X. Y. , Liu N. , Kan H. M.
Published: January 2014

China is rich in grassland resources, with 400 × 106 ha of natural grasslands and 18 main types, mostly distributed in the north-east, north, Qinghai-Tibet Plateau and Xinjiang regions. Grassland-based livestock production is the foundation of the economy in these rural areas. Degradation of grassland has occurred to varying degrees in these regions. Mean overgrazing rates across the whole country were estimated to be ~30% in 2009. Considerable amounts of research have focussed, especially since 2000, on developing better ways of managing Chinese grasslands. Research concerning the relationship between forage production and animal performance, is reviewed for three important national grassland regions. For the three major grassland (steppes) types of Inner Mongolia, the stocking rates proposed as a result of research were 1.0–2.2 sheep units (SU) ha–1 for the western, drier Stipa breviflora desert steppe; 2.0–3.8 SU ha–1 for the steppe of Artemisia frigida and Stipa grandis; and 1.8–4.0 SU ha–1 for the eastern higher-rainfall Leymus chinensis meadow steppe in Hulunbeir. In the Qinghai-Tibetan alpine meadows, the stocking rate of grassland dominated by Edelweiss-Potentilla and Kobresia parva, proposed on the basis of research, was 1.0–5.8 SU ha–1. In Xinjiang’s desert steppe, the stocking rates of Seriphidium transiliense desert steppe were proposed on the basis of research were 1.2 SU ha–1 in spring and 1.8 SU ha–1 in autumn for non-degraded pasture, and 0.3 and 1.2 SU ha–1 for moderate-degraded pasture, respectively. These stocking rates were based on either annual net primary production or desired levels of livestock production and it is argued that there is a need to develop carrying capacities based on a wider range of sustainability criteria and with the most appropriate grazing systems.
Introduction of Dorper sheep into Australian rangelands: implications for production and natural resource management
Authors: Alemseged Yohannes , Hacker Ronald B.
Published: January 2014

The growing popularity of the Dorper breed of sheep potentially may have implications for the ecological sustainability of the semiarid and arid rangelands of southern Australia. The implications are heightened by forecasts of a warming and drying climate in these rangelands, which may in itself place native vegetation under increasing stress. While the Dorper breed of sheep offers important production advantages, little is known from research under Australian conditions about their grazing ecology and management requirements from a natural resource perspective. Key factors identified from this review of literature from other countries include a high fertility and fecundity, a generalist feeding strategy, a high growth rate and a capacity to survive and reproduce under low-rainfall conditions. The wider range of plant species selected by the Dorper compared with the traditional Merino breed of sheep potentially creates both opportunities and risks for rangeland condition. Less selective grazing may reduce pressure on some species but the capacity to harvest sufficient nutrients over a smaller area could concentrate grazing and promote resource degradation. High reproductive efficiency under a wide range of seasonal conditions may lead to more rapid onset of overgrazing and will require close attention to both natural resources and animal marketing if resource degradation is to be avoided.
Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in
Arabidopsis
roots
Authors: Muraro Daniele , Mellor Nathan , Pound Michael P. , Help Hanna , Lucas Mikaël , Chopard Jérôme , Byrne Helen M. , Godin Christophe , Hodgman T. Charlie , King John R. , Pridmore Tony P. , Helariutta Ykä , Bennett Malcolm J. , Bishopp Anthony
Published: January 2014

Significance

The vascular tissues form a continuous network providing the long-distance transport of water and nutrients in all higher plants (tracheophytes). To incorporate separate organs into this network, it is essential that the position of different vascular cell types is tightly regulated. Several factors required for root vascular patterning (including hormones and gene products) have previously been identified in the model plant
Arabidopsis
. We have now established a mathematical model formulizing the interaction between these factors, allowing us to identify a minimal regulatory network capable of maintaining a stable vascular pattern in
Arabidopsis
roots. We envisage that this model will help future researchers understand how similar regulatory units can be applied to create alternative patterns in other species.
Computational design of a pH-sensitive IgG binding protein
Authors: Strauch Eva-Maria , Fleishman Sarel J. , Baker David
Published: January 2014

Significance

Protein–protein interactions are part of almost every biological process; hence, the ability to manipulate and design protein binding has widespread applications. Here, we describe an approach to designing pH-dependent protein interfaces and use it to design a protein that binds antibodies at high pH but poorly at low pH. The designed protein should be useful for antibody affinity purification and diagnostic devices.
Analysis and modeling of mitotic spindle orientations in three dimensions
Authors: Jüschke Christoph , Xie Yunli , Postiglione Maria Pia , Knoblich Juergen A.
Published: January 2014

Significance

During development, three-dimensional tissues with defined architecture are generated from one single cell. To achieve this, cells divide with specific orientations to ensure correct placement of their daughter cells. Because the direction of cell division is determined by the orientation of the mitotic spindle apparatus, precise methodology for determining spindle orientation in three-dimensional tissues is crucial to understanding developmental processes. Here, we describe a method for the analysis of spindle orientation in three dimensions. We use mathematical modeling to demonstrate that our method can avoid systematic errors that are intrinsic to conventional 2D analysis of the process. Using experimental data from the developing mouse brain, we show that our method can distinguish between mechanistically different models for spindle orientation.
Harnessing evolutionary fitness in
Plasmodium falciparum
for drug discovery and suppressing resistance
Authors: Lukens Amanda K. , Ross Leila Saxby , Heidebrecht Richard , Javier Gamo Francisco , Lafuente-Monasterio Maria J. , Booker Michael L. , Hartl Daniel L. , Wiegand Roger C. , Wirth Dyann F.
Published: January 2014

Significance

Drug resistance is a major problem in treating malaria infections. Resistance pathways are limited by evolutionary fitness constraints, and these pathways can be anticipated and preemptively blocked. We identified compounds selective for mutant malaria parasites that are resistant to either clinically used (chloroquine) or in-development dihydroorotate dehydrogenase (DHODH) inhibitor therapies. In both cases, resistance selections of mutant parasites with the matching mutant-selective drug led to a reversion to the wild-type phenotype. Additionally, combination selection of wild-type parasites with paired wild-type and mutant-type DHODH inhibitors failed to produce resistant parasites. These findings indicate that pairing inhibitors that target the bulk wild-type population and the small, emerging resistant population can suppress the rise and spread of drug resistance.
Endothelial cellular senescence is inhibited by liver X receptor activation with an additional mechanism for its atheroprotection in diabetes
Authors: Hayashi Toshio , Kotani Hitoshi , Yamaguchi Tomoe , Taguchi Kumiko , Iida Mayu , Ina Koichiro , Maeda Morihiko , Kuzuya Masafumi , Hattori Yuichi , Ignarro Louis J.
Published: January 2014

Significance

Our studies demonstrate that the regulation of endothelial cellular senescence emerges as an additional mechanism underlying the antiatherogenic properties of liver X receptor (LXR) agents. Furthermore, our data suggest that combination therapy with LXR agents and metformin may provide a clinically useful therapeutic strategy to alleviate an LXR activation-mediated adverse effect on liver triglyceride metabolism. The beneficial effects of LXR activation appear to be reduced reactive oxygen species levels and increased endothelial NO synthase activity, both of which will lead to increased NO actions. Among the elderly population, atherosclerosis is a growing problem, leading to an increased risk of mortality by cardiovascular events. Adoption of combination therapy with LXR agents and widely prescribed metformin may be of clinical significance.
Toso controls encephalitogenic immune responses by dendritic cells and regulatory T cells
Authors: Brenner Dirk , Brüstle Anne , Lin Gloria H. Y. , Lang Philipp A. , Duncan Gordon S. , Knobbe-Thomsen Christiane B. , St. Paul Michael , Reardon Colin , Tusche Michael W. , Snow Bryan , Hamilton Sara R. , Pfefferle Aline , Gilani Syed O. , Ohashi Pamela S. , Lang Karl S. , Mak Tak W.
Published: January 2014

Significance

More than 1 million people worldwide suffer from the debilitating neurological disorder multiple sclerosis (MS). The initiation of MS is associated with sustained inflammation and an autoimmune T-cell response targeting the central nervous system. The activities of Th1 and Th17 effector T cells, which are the main pathogenic drivers of MS, are balanced by regulatory T cells, which dampen inflammation and mitigate disease. Our study describes an important role for the surface receptor Toso in balancing these T-cell subsets and controlling inflammation. Using an animal model of MS, we have developed a preclinical treatment strategy in which Toso-Fc fusion protein ameliorates the inflammatory symptoms of experimental autoimmune encephalomyelitis, an MS-like disease.
School sports and identity formation: Socialisation or selection?
Authors: Pot Niek , Schenk Niels , van Hilvoorde Ivo
Published: January 2014

It seems common knowledge that school sport participation leads to all kinds of social, educational and health outcomes. However, it may also be that students with a certain predisposition, sometimes referred to as sporting habitus, are more inclined to participate in school sports and that the ‘outcomes’ were already present before participation. Several studies indicated that identity formation mediates between sport participation and the outcomes described. Therefore, a longitudinal survey study was used to investigate whether participation in an elementary school sport competition brought about changes in the formation of sport identity and student identity of students. The results of the study showed that participation in the competition was not related to changes in the sport identity and student identity of the children. In contrast to commonplace assumptions about the socialising effects of school sport participation, the results indicate that participating in this school sport competition did not influence the student identity and sport identity of children. It may be that a selected, predisposed group of children with a strong sport identity participates in school sports, although future research is necessary to test this hypothesis.
Relevance, Not Invariance, Explanatoriness, Not Manipulability: Discussion of Woodward’s Views on Explanatory Relevance
Authors: Imbert Cyrille
Published: January 2014

According to Woodward’s causal model of explanation, explanatory information is relevant for manipulation purposes and indicates by means of invariant causal relations how to change the value of certain target explanandum variables by intervening on others. Therefore, the depth of an explanation is evaluated through the size of the domain of invariance of the generalization involved. In this article, I argue that Woodward’s account of explanatory relevance is still unsatisfactory and claim that the depth of an explanation should be explicated in terms of the size of the domain of circumstances which it designates as leaving the explanandum unchanged.
The attenuated inflammation of MPL is due to the lack of CD14-dependent tight dimerization of the TLR4/MD2 complex at the plasma membrane
Authors: Tanimura Natsuko , Saitoh Shin-ichiroh , Ohto Umeharu , Akashi-Takamura Sachiko , Fujimoto Yukari , Fukase Koichi , Shimizu Toshiyuki , Miyake Kensuke
Published: January 2014

TLR4/MD-2 senses lipid A, activating the MyD88-signaling pathway on the plasma membrane and the TRIF-signaling pathway after CD14-mediated TLR4/MD-2 internalization into endosomes. Monophosphoryl lipid A (MPL), a detoxified derivative of lipid A, is weaker than lipid A in activating the MyD88-dependent pathway. Little is known, however, about mechanisms underlying the attenuated activation of MyD88-dependent pathways. We here show that MPL was impaired in induction of CD14-dependent TLR4/MD-2 dimerization compared with lipid A. Impaired TLR4/MD-2 dimerization decreased CD14-mediated TNFα production. In contrast, MPL was comparable to lipid A in CD14-independent MyD88-dependent TNFα production and TRIF-dependent responses including cell surface CD86 up-regulation and IFNβ induction. Although CD86 up-regulation is dependent on TRIF signaling, it was induced by TLR4/MD-2 at the plasma membrane. These results revealed that the attenuated MPL responses were due to CD14-initiated responses at the plasma membrane, but not just to responses initiated by MyD88, that is, MPL was specifically unable to induce CD14-dependent TLR4/MD-2 dimerization that selectively enhances MyD88-mediated responses at the plasma membrane.
Sufficient observables for large-scale structure in galaxy surveys
Authors: Carron J. , Szapudi I.
Published: January 2014

Beyond the linear regime, the power spectrum and higher order moments of the matter field no longer capture all cosmological information encoded in density fluctuations. While non-linear transforms have been proposed to extract this information lost to traditional methods, up to now, the way to generalize these techniques to discrete processes was unclear; ad hoc extensions had some success. We pointed out in Carron and Szapudi's paper that the logarithmic transform approximates extremely well the optimal ‘sufficient statistics’, observables that extract all information from the (continuous) matter field. Building on these results, we generalize optimal transforms to discrete galaxy fields. We focus our calculations on the Poisson sampling of an underlying lognormal density field. We solve and test the one-point case in detail, and sketch out the sufficient observables for the multipoint case. Moreover, we present an accurate approximation to the sufficient observables in terms of the mean and spectrum of a non-linearly transformed field. We find that the corresponding optimal non-linear transformation is directly related to the maximum a posteriori Bayesian reconstruction of the underlying continuous field with a lognormal prior as put forward in the paper of Kitaura et al.. Thus, simple recipes for realizing the sufficient observables can be built on previously proposed algorithms that have been successfully implemented and tested in simulations.
An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage
Authors: Fine Eli J. , Cradick Thomas J. , Zhao Charles L. , Lin Yanni , Bao Gang
Published: January 2014

Although engineered nucleases can efficiently cleave intracellular DNA at desired target sites, major concerns remain on potential ‘off-target’ cleavage that may occur throughout the genome. We developed an online tool: predicted report of genome-wide nuclease off-target sites (PROGNOS) that effectively identifies off-target sites. The initial bioinformatics algorithms in PROGNOS were validated by predicting 44 of 65 previously confirmed off-target sites, and by uncovering a new off-target site for the extensively studied zinc finger nucleases (ZFNs) targeting C-C chemokine receptor type 5. Using PROGNOS, we rapidly interrogated 128 potential off-target sites for newly designed transcription activator-like effector nucleases containing either Asn-Asn (NN) or Asn-Lys (NK) repeat variable di-residues (RVDs) and 3- and 4-finger ZFNs, and validated 13 bona fide off-target sites for these nucleases by DNA sequencing. The PROGNOS algorithms were further refined by incorporating additional features of nuclease–DNA interactions and the newly confirmed off-target sites into the training set, which increased the percentage of bona fide off-target sites found within the top PROGNOS rankings. By identifying potential off-target sites in silico, PROGNOS allows the selection of more specific target sites and aids the identification of bona fide off-target sites, significantly facilitating the design of engineered nucleases for genome editing applications.
Long-term cycles in the carbon reservoir of the Quaternary ocean: a perspective from the South China Sea
Authors: Wang PinXian , Li QianYu , Tian Jun , Jian ZhiMin , Liu ChuanLian , Li Li , Ma WenTao
Published: January 2014

In recent years, long-term, high-resolution records from the deep sea and ice-cores have offered new research opportunities for Quaternary science. Paleoclimate studies are no longer restricted to individual glacial cycles, but extend to long-term (≥105 yr) processes across those cycles. Ocean Drilling Program Leg 184 of the South China Sea in 1999 uncovered well-preserved sediment sections, in which three long-term cycles in Pleistocene carbon isotope (δ13C) sequence have been found and demonstrated to be common in the global ocean. Subsequent discoveries confirm the existence of long-term processes of 105 yr in both the hydrologic (ice-sheet changes) and carbon (biogeochemical changes) cycles, posing the question whether the two processes are related. The present review shows that the long-eccentricity cycles prevail throughout the δ13C and other biogeochemical records in geologic history, and 400-kyr cycles in the oceanic δ13C sequence before the Quaternary can be hypothetically explained by changes in ratio between particulate and dissolved organic carbon (POC/DOC) in the ocean, depending on the monsoon-controlled nutrient supply. This is a ‘DOC hypothesis’. However, ocean restructuring at 1.6 Ma marked by the isolation of a sluggish abyss under the Southern Ocean has obscured the long-eccentricity 400-kyr signal in oceanic δ13C. The last million-year period has experienced two major changes in the climate regime, namely the mid-Pleistocene transition (MPT) centered at 0.9 Ma and the mid-Brunhes event (MBE) around 0.4 Ma. The MPT and MBE were preluded by δ13C maxima-III (δ13Cmax-III) ∼ 1.0 Ma and δ13Cmax-II ∼ 0.5 Ma, respectively. Together with similar hydroclimatic phenomena over corresponding glacial cycles, the two groups of hydrologic and biogeochemical events appear to have been driven largely by oceanographic changes in the Southern Ocean. Therefore, we interpret that the long-term biogeochemical processes originating from the Southern Ocean must have played a crucial role in Quaternary ice-sheet waxing and waning.
Pathogenesis Implication for Necrotizing Enterocolitis Prevention in Preterm Very‐Low‐Birth‐Weight Infants
Authors: Chen An‐Chyi , Chung Mei‐Yung , Chang Jui Hsing , Lin Hung‐Chih
Published: January 2014

Recent reports show that the incidence of and deaths caused by necrotizing enterocolitis (NEC) in preterm very‐low‐birth‐weight (PVLBW) infants are on the rise. Unfortunately, NEC often rapidly progresses from early signs of intestinal inflammation to extensive necrosis within a matter of hours, making treatment and secondary prevention extremely difficult to achieve. Primary prevention should thus be the priority. Recent studies provide information that enhances our understanding of the pathophysiology and provides more practical options for the prevention of NEC. The most accepted hypothesis at present is that enteral feeding (providing substrate) in the presence of abnormal intestinal colonization by pathogens provokes an inappropriately heightened inflammatory response in immature intestinal epithelial cells of PVLBW infants. Seventy‐four relevant articles were reviewed. Our focus was on the present understanding of the pathophysiology of NEC in the context of developing optimal strategies to prevent NEC in PVLBW infants. Strategies such as antenatal glucocorticoids, postnatal breast milk feeding, and cautious approach to enteral feeding failed to eliminate NEC in PVLBW infants because these strategies did not address the complexity of the pathogenesis. Probiotics seem to be the most significant advance in NEC prevention at present because of the significant range of beneficial effects at various levels of gut function and defense mechanism and the present evidence based on 19 randomized controlled trials.
Predicting bycatch hotspots for endangered leatherback turtles on longlines in the Pacific Ocean
Authors: Roe John H. , Morreale Stephen J. , Paladino Frank V. , Shillinger George L. , Benson Scott R. , Eckert Scott A. , Bailey Helen , Tomillo Pilar Santidrián , Bograd Steven J. , Eguchi Tomoharu , Dutton Peter H. , Seminoff Jeffrey A. , Block Barbara A. , Spotila James R.
Published: January 2014

Fisheries bycatch is a critical source of mortality for rapidly declining populations of leatherback turtles,
Dermochelys coriacea
. We integrated use-intensity distributions for 135 satellite-tracked adult turtles with longline fishing effort to estimate predicted bycatch risk over space and time in the Pacific Ocean. Areas of predicted bycatch risk did not overlap for eastern and western Pacific nesting populations, warranting their consideration as distinct management units with respect to fisheries bycatch. For western Pacific nesting populations, we identified several areas of high risk in the north and central Pacific, but greatest risk was adjacent to primary nesting beaches in tropical seas of Indo-Pacific islands, largely confined to several exclusive economic zones under the jurisdiction of national authorities. For eastern Pacific nesting populations, we identified moderate risk associated with migrations to nesting beaches, but the greatest risk was in the South Pacific Gyre, a broad pelagic zone outside national waters where management is currently lacking and may prove difficult to implement. Efforts should focus on these predicted hotspots to develop more targeted management approaches to alleviate leatherback bycatch.
Hippocampal motifs
Authors: Aghajan Zahra M. , Acharya Lavanya , Cushman Jesse , Vuong Cliff , Moore Jason , Mehta Mayank R.
Published: January 2014

Dorsal Hippocampal neurons provide an allocentric map of space1, characterized by three key properties. First, their firing is spatially selective1–3, termed a rate code. Second, as animals traverse through place fields, neurons sustain elevated firing rates for long periods, however this has received little attention. Third the theta-phase of spikes within this sustained activity varies with animal’s location, termed phase-precession or a temporal code4–10. The precise relationship between these properties and the mechanisms governing them are not understood, although distal visual cues (DVC) are thought to be sufficient to reliably elicit them2,3. Hence, we measured rat CA1 neurons’ activity during random foraging in two-dimensional VR—where only DVC provide consistent allocentric location information— and compared it with their activity in real world (RW). Surprisingly, we found little spatial selectivity in VR. This is in sharp contrast to robust spatial selectivity commonly seen in one-dimensional RW and VR7–11, or two-dimensional RW1–3. Despite this, neurons in VR generated approximately two-second long phase precessing spike sequences, termed “hippocampal motifs”. Motifs, and “Motif-fields”, an aggregation of all motifs of a neuron, had qualitatively similar properties including theta-scale temporal coding in RW and VR, but the motifs were far less spatially localized in VR. These results suggest that intrinsic, network mechanisms generate temporally coded hippocampal motifs, which can be dissociated from their spatial selectivity. Further, DVC alone are insufficient to localize motifs spatially to generate a robust rate code.
Functions of Multiple Genes Encoding ADP-Glucose Pyrophosphorylase Subunits in Maize Endosperm, Embryo, and Leaf
Authors: Huang Binquan , Hennen-Bierwagen Tracie A. , Myers Alan M.
Published: January 2014

ADP-glucose pyrophosphorylase (AGPase) provides the nucleotide sugar ADP-glucose and thus constitutes the first step in starch biosynthesis. The majority of cereal endosperm AGPase is located in the cytosol with a minor portion in amyloplasts, in contrast to its strictly plastidial location in other species and tissues. To investigate the potential functions of plastidial AGPase in maize (Zea mays) endosperm, six genes encoding AGPase large or small subunits were characterized for gene expression as well as subcellular location and biochemical activity of the encoded proteins. Seven transcripts from these genes accumulate in endosperm, including those from shrunken2 and brittle2 that encode cytosolic AGPase and five candidates that could encode subunits of the plastidial enzyme. The amino termini of these five polypeptides directed the transport of a reporter protein into chloroplasts of leaf protoplasts. All seven proteins exhibited AGPase activity when coexpressed in Escherichia coli with partner subunits. Null mutations were identified in the genes agpsemzm and agpllzm and shown to cause reduced AGPase activity in specific tissues. The functioning of these two genes was necessary for the accumulation of normal starch levels in embryo and leaf, respectively. Remnant starch was observed in both instances, indicating that additional genes encode AGPase large and small subunits in embryo and leaf. Endosperm starch was decreased by approximately 7% in agpsemzm- or agpllzm- mutants, demonstrating that plastidial AGPase activity contributes to starch production in this tissue even when the major cytosolic activity is present.
SWEET17, a Facilitative Transporter, Mediates Fructose Transport across the Tonoplast of Arabidopsis Roots and Leaves
Authors: Guo Woei-Jiun , Nagy Reka , Chen Hsin-Yi , Pfrunder Stefanie , Yu Ya-Chi , Santelia Diana , Frommer Wolf B. , Martinoia Enrico
Published: January 2014

Fructose (Fru) is a major storage form of sugars found in vacuoles, yet the molecular regulation of vacuolar Fru transport is poorly studied. Although SWEET17 (for SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTERS17) has been characterized as a vacuolar Fru exporter in leaves, its expression in leaves is low. Here, RNA analysis and SWEET17-β-glucuronidase/-GREEN FLUORESCENT PROTEIN fusions expressed in Arabidopsis (Arabidopsis thaliana) reveal that SWEET17 is highly expressed in the cortex of roots and localizes to the tonoplast of root cells. Expression of SWEET17 in roots was inducible by Fru and darkness, treatments that activate accumulation and release of vacuolar Fru, respectively. Mutation and ectopic expression of SWEET17 led to increased and decreased root growth in the presence of Fru, respectively. Overexpression of SWEET17 specifically reduced the Fru content in leaves by 80% during cold stress. These results intimate that SWEET17 functions as a Fru-specific uniporter on the root tonoplast. Vacuoles overexpressing SWEET17 showed increased [14C]Fru uptake compared with the wild type. SWEET17-mediated Fru uptake was insensitive to ATP or treatment with NH4Cl or carbonyl cyanide m-chlorophenyl hydrazone, indicating that SWEET17 functions as an energy-independent facilitative carrier. The Arabidopsis genome contains a close paralog of SWEET17 in clade IV, SWEET16. The predominant expression of SWEET16 in root vacuoles and reduced root growth of mutants under Fru excess indicate that SWEET16 also functions as a vacuolar transporter in roots. We propose that in addition to a role in leaves, SWEET17 plays a key role in facilitating bidirectional Fru transport across the tonoplast of roots in response to metabolic demand to maintain cytosolic Fru homeostasis.
Prolapse surgery with or without stress incontinence surgery for pelvic organ prolapse: a systematic review and meta‐analysis of randomised trials
Authors: van der Ploeg JM , van der Steen A , Oude Rengerink K , van der Vaart CH , Roovers JP
Published: January 2014

Objectives

The combination of prolapse surgery with an incontinence procedure can reduce the incidence of stress urinary incontinence (SUI) after surgery, but may increase adverse events. We compared the effectiveness and safety of prolapse surgery versus combined prolapse and incontinence surgery in women with pelvic organ prolapse.

Design and setting

Pubmed, EMBASE, DARE, the Cochrane Library and the register of Current Controlled Trials were searched for randomised trials (restricted to Burch colposuspension and midurethral sling as incontinence procedure) from 1995 to 2013 limited to the English literature.

Methods

Two reviewers selected eligible articles and extracted the data. Pooling for SUI was based on three patient groups: (1) women with coexisting SUI; (2) women asymptomatic for SUI; and (3) women with occult SUI. For adverse events, pooling was based on incontinence procedure.

Main outcome measures

The primary outcome was SUI. The secondary outcomes were treatment for SUI, bladder storage symptoms, obstructive voiding and adverse events.

Results

Seven trials were included. Pooling for women with coexisting SUI was possible for objective SUI with two studies and showed no difference. Statistical (I2 = 95%) and clinical heterogeneity was, however, high. The largest study showed a lower incidence of persisting SUI (5% versus 23%) and treatment for this (0% versus 57%) in women who underwent prolapse repair with a midurethral sling. The second study did not find a difference in women undergoing a sacrocolpopexy with or without Burch colposuspension. In asymptomatic women, combination surgery resulted in a lower incidence of de novo subjective SUI (two studies; 24% versus 41%; relative risk [RR], 0.6; 95% confidence interval [CI], 0.3–0.9; I2 = 36%) and the need for subsequent anti‐incontinence surgery (three studies; 2% versus 7%; RR, 0.4; 95% CI, 0.2–0.8; I2 = 13%). For the outcome objective SUI, pooling was possible for five studies, but statistical heterogeneity was high (I2 = 82%) and the difference was not statistically significant. In the subgroup of women with occult stress incontinence, we found a lower incidence of objective SUI after combination surgery (two studies; 22% versus 52%; RR, 0.4; 95% CI, 0.3–0.8; I2 = 32%). There were no differences in bladder storage symptoms, urgency incontinence or long‐term obstructive voiding symptoms. Adverse events (two studies; 15% versus 10%; RR, 1.6; 95% CI, 1.0–2.5; I2 = 0%) and prolonged catheterisation (three studies; 6% versus 1%; RR, 4.5; 95% CI, 1.5–13.3; I2 = 0%) were more frequent after vaginal prolapse repair with a midurethral sling.

Conclusions

Combination surgery reduces the risk of postoperative stress incontinence, but short‐term voiding difficulties and adverse events were more frequent after combination surgery with a midurethral sling.
Progress and Progressivism: Thoughts on an Elusive Term
Authors: Freeden Michael
Published: January 2014

Michael Freeden responds to the debate in this issue on progressivism and its contested manifestations. He asks, first, is there a cluster of policies that collectively merits the designation ‘progressive'? Second, what are the rhetorical usages and power of the term and is it the case that those usages override or deflect its substantive content? And finally, are the multiple understandings of progressivism equally ‘legitimate’ or culturally resonant, and with what effect does the term mutate among its various meanings?