bluuebunny/crossref_metadata_2025 huggingface dataset:
Price‐based spectrum sharing and rate allocation in the downlink of multihop multicarrier wireless networks
Authors: Fathi Mohammad
Published: January 2014

The author addresses the problem of subcarrier sharing with discrete rate allocation in the downlink of multicell and multihop orthogonal frequency division multiple access networks. The co‐channel interference makes the problem computationally intractable. The author therefore models the problem as a non‐cooperative game among the transmitting nodes with smaller scale problems. Each problem is solved using dual decomposition. Moreover, to mitigate the degradation effect of co‐channel interference in this game, the author additionally proposes a price‐based game. This game charges the nodes for their transmit power on subcarriers. Numerical results demonstrate that price‐based game outperforms the non‐cooperative game as a result of distributed interference avoidance. In addition, both the games with subcarrier sharing achieve higher sum‐rate in comparison with resource allocation schemes with no subcarrier sharing.
Comparative study of current‐mode controllers for a high‐order boost dc–dc converter
Authors: Chan Chok You
Published: January 2014

A comparative study of linear current‐mode controllers (using input and output inductor currents) for regulation of a high‐order boost dc–dc converter is presented. The high‐order boost converter gives a much higher output voltage as compared with that obtained from the conventional boost dc–dc converter. It is demonstrated that the current‐mode controller using the output inductor current is the most appropriate for the high‐order boost converter. Experimental results showing the effectiveness of the proposed controller in the presence of load disturbances are also presented.
On the design of human immunodeficiency virus treatment based on a non‐linear time‐delay model
Authors: Batmani Yazdan , Khaloozadeh Hamid
Published: January 2014

Mathematical modelling and methods from control theory can be employed to find appropriate drug regimens in human immunodeficiency virus (HIV) treatment. In this study, using a non‐linear time‐delay model, the authors design some suboptimal highly active antiretroviral therapy (HAART) [http://www.en.wikipedia.org/wiki/Protease_inhibitor_%28pharmacology%29] regimens for patients with HIV. The non‐linear delayed model is used to describe the dynamical interactions between HIV and human immune system in the presence of HAART. Based on the model, a set point tracking problem is defined in order to set the number of susceptible CD4+ T cells to a desired value. To solve this set point tracking problem in a suboptimal way, the authors introduce a new method which is able to consider constraints on the amount of drug dosage. It is proved that the proposed method is able to set the number of susceptible CD4+ T cells to the desired value. Simulation results confirm that the method is efficient even in the presence of parametric uncertainties.
Enhanced electrical and optoelectrical properties of cadmium selenide nanobelts by chlorine doping
Authors: Zhang Lijie , Yu Hongfei , Cao Wei , Zou Chao , Dong Youqing , Zhu Da‐Ming , Huang Shaoming
Published: January 2014

Single‐crystalline chlorine‐doped cadmium selenide (CdSe) nanobelts (NBs) with a wurtzite structure were synthesised by using CdSe and InCl3 powder as sources via a co‐evaporation approach. The investigation of the performance of the field‐effect transistors fabricated from Cl‐doped NBs shows n ‐type conduction behaviour and enhanced conductivity (1–70 S/cm). Furthermore, it is found that the photoconductivity (illuminated by a white light with a power density of 1.3 mW/cm2) increases with the enhancement of the conductivity. Photoconductive analysis reveals that the Cl‐doped NBs show excellent photoresponse properties, with responsivity of 8.87 × 105AW−1 and a corresponding external quantum efficiency of 1.74 × 106 when illuminated under a 650 nm light and biased 1 V. In addition, the electrical properties of the Cl‐doped NBs can be influenced by changing the ambiance, which is caused by their surface states.
Solvothermal fabrication and luminescent properties of nanoLuAG:Ce phosphors
Authors: Xing Lin , Qu Lianghui , He Qing , Tang Tong B. , Yang Linfeng
Published: January 2014

Nanosized Ce‐doped lutetium aluminium garnet (LuAG:Ce) phosphors have been synthesised by a solvothermal method using ethylenediamine as the solvent and metal nitrates as the starting materials. The phase development, the morphology and the luminescent properties of the prepared phosphors were investigated with X‐ray diffractometry, transmission electron microscopy and photoluminescence spectra, which showed that phosphors of high phase purity resulted after heating for 8 h at a low temperature of 230oC. This powder possesses good dispersivity, suffers little or no aggregation and has an average grain size of 220 nm with narrow size distribution, hence, it may be exploited for the fabrication of LuAG:Ce optical ceramics. Its excitation and emission spectra have also been examined, which confirms the transitions between the 4f and the 5d states of the Ce3+ ions as the photoluminescence mechanism. The photoluminescence decay showed almost identical components compared with the LuAG:Ce single crystal, which further proves that the obtained nanosized phosphors have been well crystallised.
Real-time observation of nanoscale topological transitions in epitaxial PbTe/CdTe heterostructures
Authors: Groiss H. , Daruka I. , Koike K. , Yano M. , Hesser G. , Springholz G. , Zakharov N. , Werner P. , Schäffler F.
Published: January 2014

The almost completely immiscible PbTe/CdTe heterostructure has recently become a prototype system for self-organized quantum dot formation based on solid-state phase separation. Here, we study by real-time transmission electron microscopy the topological transformations of two-dimensional PbTe-epilayers into, first, a quasi-one-dimensional percolation network and subsequently into zero-dimensional quantum dots. Finally, the dot size distribution coarsens by Ostwald ripening. The whole transformation sequence occurs during all stages in the fully coherent solid state by bulk diffusion. A model based on the numerical solution of the Cahn-Hilliard equation reproduces all relevant morphological and dynamic aspects of the experiments, demonstrating that this standard continuum approach applies to coherent solids down to nanometer dimensions. As the Cahn-Hilliard equation does not depend on atomistic details, the observed morphological transformations are general features of the model. To confirm the topological nature of the observed shape transitions, we developed a parameter-free geometric model. This, together with the Cahn-Hilliard approach, is in qualitative agreement with the experiments.
Strongly confining bare core CdTe quantum dots in polymeric microdisk resonators
Authors: Flatae Assegid , Grossmann Tobias , Beck Torsten , Wiegele Sarah , Kalt Heinz
Published: January 2014

We report on a simple route to the efficient coupling of optical emission from strongly confining bare core CdTe quantum dots (QDs) to the eigenmodes of a micro-resonator. The quantum emitters are embedded into QD/polymer sandwich microdisk cavities. This prevents photo-oxidation and yields the high dot concentration necessary to overcome Auger enhanced surface trapping of carriers. In combination with the very high cavity Q-factors, interaction of the QDs with the cavity modes in the weak coupling regime is readily observed. Under nanosecond pulsed excitation the CdTe QDs in the microdisks show lasing with a threshold energy as low as 0.33 μJ.
Time-dependent Density Functional-based Tight-bind Method Efficiently Implemented with OpenMP Parallel and GPU Acceleration
Authors: Fan Guo-hong , Han Ke-li , He Guo-zhong
Published: January 2014

The time-dependent density functional-based tight-bind (TD-DFTB) method is implemented on the multi-core and the graphical processing unit (GPU) system for excited state calculations of large system with hundreds or thousands of atoms. Sparse matrix and OpenMP multithreaded are used for building the Hamiltonian matrix. The diagonal of the eigenvalue problem in the ground state is implemented on the GPUs with double precision. The GPU-based acceleration fully preserves all the properties, and a considerable total speedup of 8.73 can be achieved. A Krylov-space-based algorithm with the OpenMP parallel and GPU acceleration is used for finding the lowest eigenvalue and eigenvector of the large TDDFT matrix, which greatly reduces the iterations taken and the time spent on the excited states eigenvalue problem. The Krylov solver with the GPU acceleration of matrix-vector product can converge quickly to obtain the final result and a notable speed-up of 206 times can be observed for system size of 812 atoms. The calculations on serials of small and large systems show that the fast TD-DFTB code can obtain reasonable result with a much cheaper computational requirement compared with the first-principle results of CIS and full TDDFT calculation.
Experimental and Theoretical Study of Reactions between Manganese Oxide Cluster Cations and Hydrogen Sulfide
Authors: Jia Mei-ye , He Sheng-gui , Ge Mao-fa
Published: January 2014

Manganese oxide cluster cations Mnm18On+ were prepared by laser ablation and reacted with hydrogen sulfide (H2S) in a fast flow reactor under thermal collision conditions. A time-of-flight mass spectrometer was used to detect the cluster distributions before and after the interactions with H2S. The experiments suggest that oxygen-for-sulfur (O/S) exchange reaction to release water took place in the reactor for most of the manganese oxide cluster cations: Mnm18On++H2S→Mnm18On−1S++H218O. Density functional theory calculations were performed for reaction mechanisms of Mn2O2++H2S, Mn2O3++H2S, and Mn2O4++H2S. The computational results indicate these O/S exchange reactions are both thermodynamically and kinetically favorable, thus in good agreement with the experimental observations. The O/S exchange reactions identified in this gas-phase cluster study parallel similar behavior of related condensed phase reaction systems.
Two-Dimensional Infrared Spectroscopy of the Photoproduct of π-Cyclopentadienyliron Dicarbonyl Dimer
Authors: Yang Fan , Yu Peng-yun , Shi Ji-pei , Zhao Juan , He Xue-mei , Wang Jian-ping
Published: January 2014

Equilibrium photoproduct of π-cyclopentadienyliron dicarbonyl dimer [CpFe(CO)2]2 in nonpolar solvent carbon tetrachloride (CCl4) is investigated using time-resolved 2D IR spectroscopy. One of the several possible visible-light-driven photoreaction pathways is confirmed and the product is found to contain a di-carbonyl group that exhibits quantum beating between two equivalent transitions in time-resolved 2D IR spectra, which turns out to be the anti-symmetric and symmetric stretching of the terminal carbonyl stretching modes of CpFe(CO)2Cl. This is the main product and its reaction pathway involves radical formation, followed by chloride addition. Quantum-chemistry computations support these experimental results. Our results indicate that 2D IR method can be used to identify in situ structures and dynamics of chemical species involved in condensed-phase chemical reactions.
Mapped Finite Element Discrete Variable Representation
Authors: Yu De-quan , Cong Shu-lin , Zhang Dong H. , Sun Zhi-gang
Published: January 2014

Efficient numerical solver for the Schrödinger equation is very important in physics and chemistry. The finite element discrete variable representation (FE-DVR) was first proposed by Rescigno and Mc-Curdy [Phys. Rev. A 62, 032706 (2000)] for solving quantum-mechanical scattering problems. In this work, an FE-DVR method in a mapped coordinate was proposed to improve the efficiency of the original FE-DVR method. For numerical demonstration, the proposed approach is applied for solving the electronic eigenfunctions and eigenvalues of the hydrogen atom and vibrational states of the electronic state 3Σg+ of the Cs2 molecule which has long-range interaction potential. The numerical results indicate that the numerical efficiency of the original FE-DVR has been improved much using our proposed mapped coordinate scheme.
Kinetochore assembly and heterochromatin formation occur autonomously in
Schizosaccharomyces pombe
Authors: Brown William R. A. , Thomas Geraint , Lee Nicholas C. O. , Blythe Martin , Liti Gianni , Warringer Jonas , Loose Matthew W.
Published: January 2014

Significance

This paper describes the use of natural variation to investigate a cell-autonomous function in the experimentally well-studied model
Schizosaccharomyces pombe.
We determined the genome structure of a natural isolate with four chromosomes, rather than the three present in the laboratory strain and in all other natural isolates studied to date. Two of the centromeres in this variant lack adjacent heterochromatin but assemble their kinetochores normally, demonstrating that kinetochore and heterochromatin assembly are autonomous in this organism.
Small business activity does not measure entrepreneurship
Authors: Henrekson Magnus , Sanandaji Tino
Published: January 2014

Significance

Schumpeterian entrepreneurship refers to growing and innovative firms. However, in empirical research the rate of entrepreneurship is commonly estimated using the self-employment rate or other measures of small business activity. We argue that this empirical strategy gives rise to misleading inferences regarding Schumpeterian entrepreneurship. To unambiguously identify this type of entrepreneur we focus on self-made billionaires on
Forbes Magazine’s
list who became wealthy by founding new firms. We identify 996 such billionaire entrepreneurs in over 50 countries. The rate of billionaire entrepreneurs correlates negatively with self-employment, small business ownership, and startup rates. Countries with higher income, higher trust, lower taxes, more venture capital investment, and lower regulatory burdens have higher entrepreneurship rates but less self-employment.
Toxin Kid uncouples DNA replication and cell division to enforce retention of plasmid R1 in
Escherichia coli
cells
Authors: Pimentel Belén , Nair Radhika , Bermejo-Rodríguez Camino , Preston Mark A. , Agu Chukwuma A. , Wang Xindan , Bernal Juan A. , Sherratt David J. , de la Cueva-Méndez Guillermo
Published: January 2014

Significance

Many plasmids disseminating antibiotic resistance in bacteria encode toxin-antitoxin (TA) pairs, which are generally assumed to function as postsegregational killing (PSK) systems. A shortage of antibiotic alternatives and the link of TA pairs to PSK have stimulated the opinion that premature toxin activation could be used to kill these recalcitrant organisms in the clinic. Following previous observations, we confirm here that toxin Kid (killing determinant) and antitoxin Kis (killing suppressor) function as a rescue system that enforces the retention of plasmid R1 by host cells, and not as a PSK system. Because the rescue system is conserved in clinically worrisome plasmids, our findings advise against the activation of this TA pair as an antibiotic strategy to fight pathogens carrying these extrachromosomal DNAs.
Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins
Authors: Rinaldi Silvia , Melaccio Federico , Gozem Samer , Fanelli Francesca , Olivucci Massimo
Published: January 2014

Significance

In this work, ab initio multiconfigurational quantum chemical computations are used to understand how light sensitivity is controlled in biological photoreceptors. The authors focus on melanopsin: the recently discovered nonvisual retina pigment responsible for the regulation of unconscious visual reflexes and the synchronization of endogenous physiological responses to the dawn/dusk cycle (circadian rhythms). The investigation indicates that the light-induced isomerization of melanopsin is up to several tens of femtoseconds faster than the analogue isomerization of invertebrate and vertebrate visual pigments. It is also revealed that its thermal isomerization is controlled by an energy barrier higher than the barrier of dim-light visual pigments. These properties support the hypothesis of an extreme light sensitivity of melanopsins.
Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles
Authors: Bajikar Sameer S. , Fuchs Christiane , Roller Andreas , Theis Fabian J. , Janes Kevin A.
Published: January 2014

Significance

Cell-to-cell variations in gene regulation occur in a number of biological contexts, such as development and cancer. Discovering regulatory heterogeneities in an unbiased manner is difficult owing to the population averaging that is required for most global molecular methods. Here, we show that we can infer single-cell regulatory states by mathematically deconvolving global measurements taken as averages from small groups of cells. This averaging-and-deconvolution approach allows us to quantify single-cell regulatory heterogeneities while avoiding the measurement noise of global single-cell techniques. Our method is particularly relevant to solid tissues, where single-cell dissociation and molecular profiling is especially problematic.
Gene-centric approach to integrating environmental genomics and biogeochemical models
Authors: Reed Daniel C. , Algar Christopher K. , Huber Julie A. , Dick Gregory J.
Published: January 2014

Significance

Modern molecular tools provide an invaluable window into the marine microbial world by identifying organisms and their metabolisms through the analysis of genetic material. Microbial communities are ubiquitous throughout the oceans and exert great influence over ocean chemistry, yet they are rarely included explicitly in models of marine biogeochemistry, such as those used to predict the response of the oceans to environmental problems (e.g., climate change). Here, we present a unique way of integrating genetic data from state-of-the-art molecular tools into biogeochemical models to improve their predictive power, better constrain geochemical processes—especially those that are not apparent from chemical measurements—and gain a deeper insight into ocean chemistry and microbiology.
Role of random electric fields in relaxors
Authors: Phelan Daniel , Stock Christopher , Rodriguez-Rivera Jose A. , Chi Songxue , Leão Juscelino , Long Xifa , Xie Yujuan , Bokov Alexei A. , Ye Zuo-Guang , Ganesh Panchapakesan , Gehring Peter M.
Published: January 2014

Significance

Relaxors are characterized by a frequency-dependent peak in the dielectric permittivity and are critical to modern technological applications because they exhibit large dielectric constants and unparalleled piezoelectric coefficients. Despite decades of study a fundamental understanding of the origin of relaxor behavior is lacking. Here we compare the structural, dynamical, dielectric, and piezoelectric properties of two highly similar piezoelectric lead-oxide materials: ferroelectric PbZr

1–
x

Ti

x

O
3
and relaxor Pb(Mg
1/3
Nb
2/3
)

1–
x

Ti

x

O
3
. Random electric fields are implicated as the genesis of relaxor behavior, and the diffuse scattering associated with short-range polar order is identified as the order parameter. The piezoelectric response is found to be greatly amplified in crystals that display this diffuse scattering.
Elevated expression of TANK-binding kinase 1 enhances tamoxifen resistance in breast cancer
Authors: Wei Congwen , Cao Yuan , Yang Xiaoli , Zheng Zirui , Guan Kai , Wang Qiang , Tai Yanhong , Zhang Yanhong , Ma Shengli , Cao Ye , Ge Xiaoxing , Xu Changzhi , Li Jia , Yan Hui , Ling Youguo , Song Ting , Zhu Lin , Zhang Buchang , Xu Quanbin , Hu Chengjin , Bian Xiu-wu , He Xiang , Zhong Hui
Published: January 2014

Significance

We investigated the possible role of TANK-binding kinase 1 (TBK1) protein in tamoxifen resistance and found that phosphorylation by TBK1 at the Ser-305 site stabilized estrogen receptor α (ERα) and modulated its transcriptional activity. Ectopic expression of TBK1 rendered breast cancer cells resistant to tamoxifen. TBK1 inhibition sensitized breast cancer cells to tamoxifen-induced cell death. The expression of TBK1 was increased in subjects with breast cancer and was positively correlated with ERα, ERα Ser-305, and cyclin D1 expression. Subjects with tumors that highly expressed TBK1 had poor responsiveness to tamoxifen treatment. Therefore, TBK1 is potentially a unique predictive marker of tamoxifen resistance and a potential therapeutic target for breast cancer.
PhoPQ regulates acidic glycerophospholipid content of the
Salmonella
Typhimurium outer membrane
Authors: Dalebroux Zachary D. , Matamouros Susana , Whittington Dale , Bishop Russell E. , Miller Samuel I.
Published: January 2014

Significance

The outer membrane (OM) of Gram-negative bacteria is composed of lipopolysaccharide (LPS) and glycerophospholipids (GPLs). Environmental regulation of LPS promotes bacterial resistance to host cationic antimicrobial peptides by altering surface charge and hydrophobicity. This work demonstrates that pathogenic
Salmonella
coordinately regulate GPL and LPS through the PhoPQ regulatory proteins and the OM palmitoyltransferase enzyme PagP. The broad conservation of PhoPQ and PagP in bacteria suggests that environmental regulation of OM GPL may be a conserved stress-response strategy for antimicrobial resistance. Improved understanding of OM GPL synthesis, transport, and modification could lead to new therapies that target the bacterial OM barrier.
Femtosecond pump-probe microscopy generates virtual cross-sections in historic artwork
Authors: Villafana Tana Elizabeth , Brown William P. , Delaney John K. , Palmer Michael , Warren Warren S. , Fischer Martin C.
Published: January 2014

Significance

We show that a nonlinear microscopy technique (femtosecond pump-probe microscopy) allows for nondestructive 3D imaging of paintings with molecular and structural contrast. Until now, studying the layering structure of a painting has generally required the physical removal of a cross-section sample. Pump-probe imaging has previously been shown on biological tissue, but applications to cultural heritage are more challenging: the variety of pigments in the artist’s palate is enormous compared with the biological pigments present in skin. Nonetheless, we show virtual cross-sectioning capabilities in mockup paintings and nondestructive imaging on an intact 14th century painting. This work represents a comprehensive collaborative effort between laser and biomedical imaging experts and scientists and conservators in national museums.
Decision-related pupil dilation reflects upcoming choice and individual bias
Authors: de Gee Jan Willem , Knapen Tomas , Donner Tobias H.
Published: January 2014

Significance

A number of studies reported that the pupil dilates (under constant illumination) during decision-making. Pupil dilation is also associated with the brain-wide release of modulatory neurotransmitters. It has remained unknown which specific elements of decision processes drive pupil dilation. Using a visual detection task, we here show that pupil dilation is primarily driven during, and not at the end of, a protracted decision. Further, pupil dilation differentiates between “yes” and “no” choices for conservative subjects deciding yes against their bias. Thus, pupil dilation reveals the content of the evolving decision and the decision maker’s attitude. These findings have important implications for interpreting decision-related brain activity. They also point to a possible role of neuromodulation in interacting with decision biases.
Highly sensitive electronic whiskers based on patterned carbon nanotube and silver nanoparticle composite films
Authors: Takei Kuniharu , Yu Zhibin , Zheng Maxwell , Ota Hiroki , Takahashi Toshitake , Javey Ali
Published: January 2014

Significance

Whiskers are hairlike tactile sensors used by certain mammals and insects to monitor wind and navigate around local obstacles. Here, we demonstrate artificial electronic whiskers that can respond to pressures as low as 1 Pa with high sensitivity. The active component is based on composites of carbon nanotubes and silver nanoparticles that are painted on high-aspect-ratio fibers. The resistivity of the composite films is highly sensitive to mechanical strain and can be readily tuned by changing the composition ratio of the components. As a proof of concept, arrays of electronic whiskers are fabricated for real-time two- and three-dimensional gas-flow mapping with high accuracy. This work may enable a wide range of applications in advanced robotics and human–machine interfacing.
PIKEis essential for oligodendroglia development and CNS myelination
Authors: Chan Chi Bun , Liu Xia , Zhao Lixia , Liu Guanglu , Lee Chi Wai , Feng Yue , Ye Keiqang
Published: January 2014

Significance

Accumulation of a lipid-rich substance (myelin sheath) around the axon of neurons enables the nerve cells to transmit information faster. However, the molecular mechanism that controls this important process is not well understood. Here, we report that the GTPase phosphoinositide 3-kinase enhancer is a regulator of myelin sheath formation during development and myelin repair.
Characterization of the IL-15 niche in primary and secondary lymphoid organs in vivo
Authors: Cui Guangwei , Hara Takahiro , Simmons Szandor , Wagatsuma Keisuke , Abe Akifumi , Miyachi Hitoshi , Kitano Satsuki , Ishii Masaru , Tani-ichi Shizue , Ikuta Koichi
Published: January 2014

Significance

IL-15 is a cytokine critical for development and maintenance of T lymphoid cells. However, the identity and distribution of IL-15–expressing cells in lymphoid organs are not well understood. The present study reveals, by using IL-15–CFP knock-in mice that IL-15 was expressed in subsets of thymic epithelial cells, bone marrow stromal cells, lymph node stromal cells, and blood endothelial cells, a unique perspective of IL-15 niche in immune microenvironment. Taken together with our previous observation on IL-7–producing cells, this study suggests that some stromal cells express IL-7 and IL-15 differentially. Thus, the immune microenvironment appears to be consisted of functionally distinct subsets of stromal cells, expressing different cytokines.
Nonautonomous contact guidance signaling during collective cell migration
Authors: Londono Camila , Loureiro M. Jimena , Slater Benjamin , Lücker Petra B. , Soleas John , Sathananthan Suthamathy , Aitchison J. Stewart , Kabla Alexandre J. , McGuigan Alison P.
Published: January 2014

Significance

Group cell migration in response to guidance signals is a critical process in determining tissue organization. Here we explore the response of groups of cells to topographic guidance signals and reveal that guidance information can be transmitted between cells within the group. Significantly, we show that guidance information transmission is not dependent on cell–cell junctions or tensional forces within cells. Instead, we propose that signal transmission arises from a volume exclusion-type mechanism and is an emergent property that can arise in dense cell populations.
TAp73 is required for spermatogenesis and the maintenance of male fertility
Authors: Inoue Satoshi , Tomasini Richard , Rufini Alessandro , Elia Andrew J. , Agostini Massimiliano , Amelio Ivano , Cescon Dave , Dinsdale David , Zhou Lily , Harris Isaac S. , Lac Sophie , Silvester Jennifer , Li Wanda Y. , Sasaki Masato , Haight Jillian , Brüstle Anne , Wakeham Andrew , Mckerlie Colin , Jurisicova Andrea , Melino Gerry , Mak Tak W.
Published: January 2014

Significance

Defects in spermatogenesis, many of which are unexplained, underlie the infertility problems of ∼20% of couples. Although specific roles for the p53 family members in female fertility have been described, their involvement in spermatogenesis is largely unexpected. Using gene-targeted mice, we have demonstrated that deficiency of TAp73, but not p53 or ∆Np73, leads to male infertility caused by severely impaired germ cell differentiation and maturation to viable sperms in the testes. Importantly, our work has established that TAp73, but not p53, regulates many genes involved in spermatogenesis. Thus, our results provide previously unidentified in vivo evidence that TAp73 is a “guardian” of male germ cells and may point toward a novel avenue for the diagnosis and management of male infertility.
Inheritance of Trans Chromosomal Methylation patterns from
Arabidopsis
F1 hybrids
Authors: Greaves Ian K. , Groszmann Michael , Wang Aihua , Peacock W. James , Dennis Elizabeth S.
Published: January 2014

Significance

Hybridization of two epigenetically distinct Arabidopsis accessions is associated with an altered methylome in the F1 hybrid brought about by the processes of Trans Chromosomal Methylation and deMethylation. In the loci studied, the altered F1 cytosine methylation (
m
C) patterns are inherited to the F2. These observations of trans-
m
C events are reminiscent of paramutation described in maize and may be common in hybridization events. In one locus, the altered
m
C states are associated with changed mRNA levels in the F1 hybrid and F2 plants. These events may contribute to F1 hybrid vigor and to the phenotypic heterogeneity and loss of vigor in the F2 through segregation of genetic and epigenetic determinants.
Differential expression of estrogen receptor α, β1, and β2 in lobular and ductal breast cancer
Authors: Huang Bo , Omoto Yoko , Iwase Hirotaka , Yamashita Hiroko , Toyama Tatsuya , Coombes Raoul Charles , Filipovic Aleksandra , Warner Margaret , Gustafsson Jan-Åke
Published: January 2014

Significance

Whether breast cancer will respond to the antiestrogen tamoxifen is determined by whether cellular proliferation is estrogen receptor (ER) α-mediated. As opposed to early ductal cancer, which is an ERα-rich, proliferating disease, in early lobular cancer both ERα and ERβ are abundantly expressed and proliferation is rare. In advanced lobular cancer, ERβ is lost, ERα is retained, and proliferation is high. Thus, tamoxifen may be an effective pharmaceutical in late but not early lobular cancer.
Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information
Authors: Cheng Ryan R. , Morcos Faruck , Levine Herbert , Onuchic José N.
Published: January 2014

Significance

Our study uses amino acid coevolutionary information to better understand how bacterial two-component signaling (TCS) proteins preferentially interact with their correct partners while avoiding interactions with nonpartners. We extract coevolutionary couplings from sequences of TCS partners and study how coevolution is necessary to maintain their ability to transfer signals with high specificity. We use these coevolving couplings to devise a metric, which can predict the effects of mutations in the quality of signal transmission observed in vitro and provide support to the hypothesis that hybrid TCS proteins have reduced specificity. Our metric can potentially be used to redesign a TCS protein to preferentially interact with a nonpartner. Furthermore, our study can potentially be extended to networks of interacting proteins.
Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass
Authors: Lee Young-Sam , Gregory Mark T. , Yang Wei
Published: January 2014

Significance

Although human DNA polymerase ζ (Pol ζ) is essential for DNA replication and cell proliferation, difficulties purifying active Pol ζ have hindered its biochemical characterization. We report here the first purification of an active form of human Pol ζ holoenzyme composed of Rev3, Rev7, PolD2, and PolD3, which opens up the possibility for detailed biochemical and structural studies of this essential enzyme. Based on genetic data, it has been postulated that two specialized DNA polymerases are needed for successful translesion synthesis. We show here that human Pol η inserts a nucleotide opposite the lesion, followed by Pol ζ extending the DNA primer; thus, the two complement each other to fully bypass the cisplatin cross-link.
The Evolving Institutional Structure of Public and Private Agricultural Research
Authors: Fuglie Keith O. , Toole Andrew A.
Published: January 2014

Over the past several decades, the private sector has assumed a larger role in developing improved technology for food and agriculture. Private companies fund nearly all food processing research and development (R&D) and perform a growing share of production‐oriented R&D for agriculture. In addition, institutional partnerships for public–private research collaboration are growing in the United States and other countries. This article outlines the major forces driving these changes and offers an interpretive framework to explore some of the implications for the volume and nature of research performed by the public and private sectors. One of the critical issues is whether public agricultural research complements and thereby stimulates additional private agricultural R&D investments. Another important issue concerns the role and contribution of alternative public–private partnership arrangements. To date, changes in the institutional structure of public and private agricultural research have outpaced systematic investigation, and new theoretical and empirical research is needed to help guide policy and address key societal challenges, such as climate change, clean energy, water scarcity, food safety, and health.
Morphological, Structural, and Thermal Properties of Starch Nanocrystals Affected by Different Botanic Origins
Authors: Xu Yixiang , Sismour Edward N. , Grizzard Cory , Thomas Melissa , Pestov Dmitry , Huba Zachary , Wang Tongwen , Bhardwaj Harbans L.
Published: January 2014

Six types of starch nanocrystals were prepared from corn, barley, potato, tapioca, chickpea, and mungbean starches with an acid hydrolysis method. The yields and morphological, structural, and thermal properties of starch nanocrystals were characterized. Starch nanocrystals had yields ranging from 8.8 to 35.7%, depending on botanical origin. During acid hydrolysis, amylose was effectively degraded, and no amylose was detected in any starch nanocrystal. Shape and size of native starch granules varied between starches, whereas there was no obvious difference in shape among different types of starch nanocrystals. The average particle size of starch nanocrystals was mainly related to crystalline type of native starches. Compared with their native starch counterparts, changes in crystalline diffraction patterns of starch nanocrystals depended on the original botanical source and crystalline structure. Degree of crystallinity, melting temperature, and enthalpy of starch nanocrystals increased, whereas their thermal decomposition temperature decreased. Of six produced starch nanocrystals, potato starch nanocrystal had the lowest yield, degree of crystallinity, and onset and melting temperatures, the largest particle size, and obvious changes in crystalline diffraction pattern.
The cAMP-PKA Pathway Regulates Growth, Sexual and Asexual Differentiation, and Pathogenesis in Fusarium graminearum
Authors: Hu Shuai , Zhou Xiaoying , Gu Xiaoying , Cao Shulin , Wang Chengfang , Xu Jin-Rong
Published: January 2014

Like many other filamentous ascomycetes, Fusarium graminearum contains two genes named CPK1 and CPK2 that encode the catalytic subunits of cyclic AMP (cAMP)-dependent protein kinase A (PKA). To determine the role of cAMP signaling in pathogenesis and development in F. graminearum, we functionally characterized these two genes. In addition, we generated and characterized the cpk1 cpk2 double and fac1 adenylate cyclase gene deletion mutants. The cpk1 mutant was significantly reduced in vegetative growth, conidiation, and deoxynivalenol production but it had increased tolerance to elevated temperatures. It was defective in the production of penetration branches on plant surfaces, colonization of wheat rachises, and spreading in flowering wheat heads. Deletion of CPK1 had no effect on perithecium development but the cpk1 mutant was defective in ascospore maturation and releasing. In contrast, the cpk2 mutant had no detectable phenotypes, suggesting that CPK2 contributes minimally to PKA activities in F. graminearum. Nevertheless, the cpk1 cpk2 double mutant had more severe defects in vegetative growth and rarely produced morphologically abnormal conidia. The double mutant, unlike the cpk1 or cpk2 mutant, was nonpathogenic and failed to form perithecia on self-mating plates. Therefore, CPK1 and CPK2 must have overlapping functions in vegetative growth, differentiation, and plant infection in F. graminearum. The fac1 mutant was also nonpathogenic and had growth defects similar to those of the cpk1 cpk2 mutant. However, deletion of FAC1 had no effect on conidium morphology. These results indicated that CPK1 is the major PKA catalytic subunit gene and that the cAMP-PKA pathway plays critical roles in hyphal growth, conidiation, ascosporogenesis, and plant infection in F. graminearum.
OxyR and SoxR Modulate the Inducible Oxidative Stress Response and Are Implicated During Different Stages of Infection for the Bacterial Phytopathogen Pantoea stewartii subsp. stewartii
Authors: Burbank Lindsey , Roper M. Caroline
Published: January 2014

Reactive oxygen species (ROS) from a variety of sources are often encountered by invading plant pathogens during the infection process. Pantoea stewartii subsp. stewartii, the etiological agent of Stewart's wilt, is a serious bacterial pathogen of sweet corn that colonizes both the apoplast and xylem tissues in which ROS are produced. The P. stewartii genome predicts the presence of two redox-sensing transcriptional regulators, OxyR and SoxR, which both activate gene expression in response to oxidative stress. ROS exposure in the form of hydrogen peroxide and the superoxide-generating compound paraquat initiates an induced stress response through OxyR and SoxR that includes activation of the ROS-detoxifying enzymes alkyl hydroperoxide reductase and superoxide dismutase. P. stewartii ΔsoxR was more sensitive to paraquat and was compromised in the ability to form water-soaked lesions, while ΔoxyR was more sensitive to hydrogen peroxide treatment and was deficient in exopolysaccharide production and the elicitation of wilting symptoms. This demonstrates that both SoxR and OxyR play an important role in virulence in the different niches that P. stewartii colonize during the infection process.
Effectiveness and Durability of the Rice Pi-ta Gene in Yunnan Province of China
Authors: Li Jinbin , Lu Lin , Jia Yulin , Li Chengyun
Published: January 2014

Rice blast is one of the most damaging diseases of rice worldwide. In the present study, we analyzed DNA sequence variation of avirulence (AVR) genes of AVR-Pita1 in field isolates of Magnaporthe oryzae in order to understand the effectiveness of the resistance gene Pi-ta in China. Genomic DNA of 366 isolates of M. oryzae collected from Yunnan province of China were used for polymerase chain reaction (PCR) amplification to examine the existence of AVR-Pita1 using gene-specific PCR markers. Results of PCR products revealed that 218 isolates of M. oryzae carry AVR-Pita1. Among of them, 62.5, 56.3, 58.5, 46.7, 72.4, and 57.4% of M. oryzae carry AVR-Pita1 from northeastern, southeast, western, northwest, southwestern, and central Yunnan province, respectively. The detection rate of AVR-Pita1 was, in order: southwestern > northeastern > western > central > southeastern > northwestern Yunnan province. Moreover, in total, 18 AVR-Pita1 haplotypes encoding 13 novel AVR-Pita1 variants were identified among 60 isolates. Most DNA sequence variation was found to occur in the exon region, resulting in amino acid substitution. Six virulent haplotypes of AVR-Pita1 to Pita were identified among 60 field isolates. The AVR-Pita1 has evolved to virulence from avirulent origins via base substitution. These findings demonstrate that AVR-Pita1 is under positive selection and mutations of AVR-Pita1 are responsible for defeating race-specific resistance in nature.
Landscape complexity influences route-memory formation in navigating pigeons
Authors: Mann Richard P. , Armstrong Chris , Meade Jessica , Freeman Robin , Biro Dora , Guilford Tim
Published: January 2014

Observations of the flight paths of pigeons navigating from familiar locations have shown that these birds are able to learn and subsequently follow habitual routes home. It has been suggested that navigation along these routes is based on the recognition of memorized visual landmarks. Previous research has identified the effect of landmarks on flight path structure, and thus the locations of potentially salient sites. Pigeons have also been observed to be particularly attracted to strong linear features in the landscape, such as roads and rivers. However, a more general understanding of the specific characteristics of the landscape that facilitate route learning has remained out of reach. In this study, we identify landscape complexity as a key predictor of the fidelity to the habitual route, and thus conclude that pigeons form route memories most strongly in regions where the landscape complexity is neither too great nor too low. Our results imply that pigeons process their visual environment on a characteristic spatial scale while navigating and can explain the different degrees of success in reproducing route learning in different geographical locations.
Predicting connectivity of green turtles at Palmyra Atoll, central Pacific: a focus on mtDNA and dispersal modelling
Authors: Naro-Maciel Eugenia , Gaughran Stephen J. , Putman Nathan F. , Amato George , Arengo Felicity , Dutton Peter H. , McFadden Katherine W. , Vintinner Erin C. , Sterling Eleanor J.
Published: January 2014

Population connectivity and spatial distribution are fundamentally related to ecology, evolution and behaviour. Here, we combined powerful genetic analysis with simulations of particle dispersal in a high-resolution ocean circulation model to investigate the distribution of green turtles foraging at the remote Palmyra Atoll National Wildlife Refuge, central Pacific. We analysed mitochondrial sequences from turtles (
n
= 349) collected there over 5 years (2008–2012). Genetic analysis assigned natal origins almost exclusively (approx. 97%) to the West Central and South Central Pacific combined Regional Management Units. Further, our modelling results indicated that turtles could potentially drift from rookeries to Palmyra Atoll via surface currents along a near-Equatorial swathe traversing the Pacific. Comparing findings from genetics and modelling highlighted the complex impacts of ocean currents and behaviour on natal origins. Although the Palmyra feeding ground was highly differentiated genetically from others in the Indo-Pacific, there was no significant differentiation among years, sexes or stage-classes at the Refuge. Understanding the distribution of this foraging population advances knowledge of green turtles and contributes to effective conservation planning for this threatened species.
Re-epithelialization: advancing epithelium frontier during wound healing
Authors: Ben Amar M. , Wu M.
Published: January 2014

The first function of the skin is to serve as a protective barrier against the environment. Its loss of integrity as a result of injury or illness may lead to a major disability and the first goal of healing is wound closure involving many biological processes for repair and tissue regeneration.In vivowound healing has four phases, one of them being the migration of the healthy epithelium surrounding the wound in the direction of the injury in order to cover it. Here, we present a theoretical model of the re-epithelialization phase driven by chemotaxis for a circular wound. This model takes into account the diffusion of chemoattractants both in the wound and the neighbouring tissue, the uptake of these molecules by the surface receptors of epithelial cells, the migration of the neighbour epithelium, the tension and proliferation at the wound border. Using a simple Darcy's law for cell migration transforms our biological model into a free-boundary problem, which is analysed in the simplified circular geometry leading to explicit solutions for the closure and making stability analysis possible. It turns out that for realistic wound sizes of the order of centimetres and from experimental data, the re-epithelialization is always an unstable process and the perfect circle cannot be observed, a result confirmed by fully nonlinear simulations and in agreement with experimental observations.
Improving controllable adhesion on both rough and smooth surfaces with a hybrid electrostatic/gecko-like adhesive
Authors: Ruffatto Donald , Parness Aaron , Spenko Matthew
Published: January 2014

This paper describes a novel, controllable adhesive that combines the benefits of electrostatic adhesives with gecko-like directional dry adhesives. When working in combination, the two technologies create a positive feedback cycle whose adhesion, depending on the surface type, is often greater than the sum of its parts. The directional dry adhesive brings the electrostatic adhesive closer to the surface, increasing its effect. Similarly, the electrostatic adhesion helps engage more of the directional dry adhesive fibrillar structures, particularly on rough surfaces. This paper presents the new hybrid adhesive's manufacturing process and compares its performance to three other adhesive technologies manufactured using a similar process: reinforced PDMS, electrostatic and directional dry adhesion. Tests were performed on a set of ceramic tiles with varying roughness to quantify its effect on shear adhesive force. The relative effectiveness of the hybrid adhesive increases as the surface roughness is increased. Experimental data are also presented for different substrate materials to demonstrate the enhanced performance achieved with the hybrid adhesive. Results show that the hybrid adhesive provides up to 5.1× greater adhesion than the electrostatic adhesive or directional dry adhesive technologies alone.