bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a novel sort of exponent-sine-shaped flexure hinges
Authors: Wang Rongqi , Zhou Xiaoqin , Zhu Zhiwei
Published: October 2013

Various types of flexure hinges have been developed to construct flexural mechanisms, however, all these hinges may have limited moving accuracies, blocking performance improvements of the flexural mechanisms. In this paper, a novel sort of exponent-sine-shaped flexure hinges (ESSFHs) with asymmetric structures is proposed to achieve much higher motion accuracy. To characterize elastic deformation behavior of the ESSFHs, a novel finite beam based matrix modeling (FBMM) method is employed to calculate the compliance matrix and the defined non-dimensional precision factors without executing laborious integration operations. Furthermore, finite element analysis is conducted and compared with the FBMM method, the maximum deviation of the obtained compliances and the precision factors by the two methods is less than 8%, well demonstrating the efficiency of the analytical method. Comparisons of the accuracies of the ESSFHs and certain state-of-the-art flexure hinges verify that the proposed ESSFHs can not only significantly improve the motion accuracy but also decrease the inherent parasitic motions of conventional flexure hinges. Based on the established analytical models, influences of the dimensional parameters on the compliances and the motion accuracy of the ESSFHs are well revealed. Finally, performances of the ESSFH and the efficiency of the analytical model are well investigated by means of experimental tests.
Adsorption of methylamine on mackinawite (FES) surfaces: A density functional theory study
Authors: Dzade N. Y. , Roldan A. , de Leeuw N. H.
Published: October 2013

We have used density functional theory calculations to investigate the interaction between methylamine (CH3NH2) and the dominant surfaces of mackinawite (FeS), where the surface and adsorption properties of mackinawite have been characterized using the DFT-D2 method of Grimme. Our calculations show that while the CH3NH2 molecule only interacts weakly with the most stable FeS(001), it adsorbs relatively strongly on the FeS(011) and FeS(100) surfaces releasing energies of 1.26 eV and 1.51 eV, respectively. Analysis of the nature of the bonding reveals that the CH3NH2 molecule interacts with the mackinawite surfaces through the lone-pair of electrons located on the N atom. The electron density built up in the bonding region between N and Fe is very much what one would expect of covalent type of bonding. We observe no significant adsorption-induced changes of the FeS surface structures, suggesting that amine capping agents would not distort the FeS nanoparticle surfaces required for active heterogeneous catalytic reactions. The vibrational frequencies and the infrared spectra of adsorbed methylamine have been calculated and assignments for vibrational modes are used to propose a kinetic model for the desorption process, yielding a simulated temperature programmed desorption with a relative desorption temperature of <140 K at the FeS(011) surface and <170 K at FeS(100) surface.
Photolabile xenon hydrides: A case study of HXeSH and HXeH
Authors: Ryazantsev Sergey V. , Kobzarenko Alexey V. , Feldman Vladimir I.
Published: October 2013

The photo-induced transformations of HXeSH and HXeH under the action of IR and visible light have been studied using FTIR spectroscopy. The xenon hydrides were produced by the X-ray induced decomposition of H2S and its isotopomers in a solid xenon matrix at 7.5 K followed by thermal annealing at the temperatures up to 45 K. Selective IR-induced photodissociation of HXeSH at 3500–2500 cm−1 was attributed to vibrational excitation of the 3νH–Xe mode. The IR-photodecomposed HXeSH molecules can be almost quantitative recovered below 22 K with very small effective activation energy (∼20 meV) indicating local character of this process. Analysis of the photoactivity of xenon hydrides in the visible region revealed previously unknown absorptions for HXeSH (in the region of 400–700 nm) and HXeH (above 700 nm). The decomposition of HXeH occurs due to both direct photolysis and reactions of “hot” H atoms produced from the photodissociation of HXeSH. The efficiency of thermal recovery for both xenon hydrides after photolysis with visible light was found to be dependent on the excitation wavelength, which was explained by the effect of photon energy on spatial distribution of the dissociation fragments.
Forces on aligned rising spherical bubbles at low-to-moderate Reynolds number
Authors: Ramírez-Muñoz J. , Baz-Rodríguez S. , Salinas-Rodríguez E. , Castellanos-Sahagún E. , Puebla H.
Published: October 2013

In this paper, the dynamic of a pair of equal-sized spherical gas bubbles rising in vertical line within a Newtonian liquid at low-to-moderate Reynolds numbers (Re ≤ 50) is studied. The dynamic momentum balance includes buoyancy, quasi-steady, and unsteady (history) drag, as well as inertial and added-mass body acceleration forces acting on the trailing bubble. This equation has been obtained under the following assumptions: (i) the bubble interaction occurs through the steady non-uniform wake induced by the leading bubble and (ii) the flow structure behind the leading bubble is known, so that proper expressions for the trailing bubble hydrodynamic force and its rising velocity can be derived. We propose an approximate analytical model for predicting the hydrodynamic force and the rise velocity of the trailing bubble. For this aim, we first use the well-known asymptotic far wake velocity solution (AWVS) for an axisymmetric body complementing it with an adequate drag expression. Then, the AWVS is modified via a Galilean transformation by introducing an artificial origin whose position is determined by fitting numerical data of known velocity profiles. Comparisons between the proposed models predictions with those reported experimental and numerical data for dimensionless distance between bubbles s/d in the interval 2 ≤ s/d ≤ 12.5 are presented. The results show that the added-mass body acceleration and the history forces are negligible compared to the other considered forces.
Electrowetting at a liquid metal-oxide-semiconductor junction
Authors: Arscott Steve
Published: October 2013

A voltage polarity dependent, voltage-induced wetting transition is demonstrated using a liquid metal-oxide-semiconductor (MOS) junction. A droplet of mercury can be made to spread out on an oxidized silicon wafer upon the application of a voltage. The wetting is seen to depend on the doping type and doping density of the silicon—a voltage polarity related asymmetrical electrowetting is observed. Impedance measurements on Al-SiO2-Si MOS capacitors link the space-charge effects with the electrowetting on the Hg-SiO2-Si MOS junction. A modified Young-Lippmann equation for electrowetting at a MOS junction is derived—the model agrees with the experiments.
Resistance and dopant profiling along freestanding GaAs nanowires
Authors: Korte Stefan , Steidl Matthias , Prost Werner , Cherepanov Vasily , Voigtländer Bert , Zhao Weihong , Kleinschmidt Peter , Hannappel Thomas
Published: October 2013

Resistance profiles along as-grown GaAs nanowires were measured with a multi-tip scanning tunneling microscope used as a nanoprober. The nanowires were grown in the vapor-liquid-solid growth mode in a two-temperature-step mode and doped with Zn. Using a transport model, the resistance profile was converted to a dopant profile. The dopant distribution along the nanowires was found to correlate with the temperature during different phases of nanowire growth. The nanowire base grown at higher temperature exhibits a decreased dopant concentration. Mechanical stress by intentional bending of a nanowire was shown not to influence nanowire conductance.
Sharp crack formation in low fluence hydrogen implanted Si0.75Ge0.25/B doped Si0.70Ge0.30/Si heterostructure
Authors: Chen Da , Zhang Miao , Liu Su , Wang Yongqiang , Nastasi Michael , Xue Zhongying , Wang Xi , Di Zengfeng
Published: October 2013

An approach to transfer a high-quality SiGe layer for the fabrication of SiGe-on-insulator wafers has been proposed based on the investigation of crack formation in H-implanted Si0.75Ge0.25/B-doped Si0.70Ge0.30/Si structures. The crack formation is found to be closely correlated to the concentration of B atoms doped in the buried Si0.70Ge0.30 layer. For H-implanted Si0.75Ge0.25/Si0.70Ge0.30/Si structures without B doping, no platelets or cracking is observed in the Si0.70Ge0.30 layer. Upon increasing the concentration of B doping in the buried Si0.70Ge0.30 layer to 2 × 1019/cm3, cracking occurs at the interfaces on both sides of Si0.70Ge0.30 interlayer, thus, resulting in the formation of continuous sharp crack confined in the ultrathin Si0.70Ge0.30 interlayer. With B doped ultrathin Si0.70Ge0.30 interlayer, the Si0.75Ge0.25 layer can be transferred to fabricate SiGe-on-insulator by H implantation with a fluence as low as 3 × 1016/cm2, which is only half of the typical fluence required for a conventional ion-cut process. Since cracking is confined in the ultrathin Si0.70Ge0.30 interlayer, the as-cut SiGe-on-insulator possesses a rather smooth surface with a roughness of 1.55 nm.
Free-standing terahertz chiral meta-foils exhibiting strong optical activity and negative refractive index
Authors: Wu Jianfeng , Ng Binghao , Turaga Shuvan P. , Breese Mark B. H. , Maier Stefan A. , Hong Minghui , Bettiol Andrew A. , Moser Herbert O.
Published: October 2013

A chiral meta-foil consisting of a self-supported square array of interconnected conjugated rosettes is demonstrated at terahertz frequencies. It exhibits strong optical activity and circular dichroism. Negative refractive index with a figure-of-merit as high as 4.2 is achieved, attributed to its free-standing nature. Experimental results are in good agreement with numerical simulation. Free-standing chiral meta-foils provide a unique approach to create a completely all-metal chiral metamaterial, which can be flexibly integrated into optical setups while eliminating dielectric insertion losses.
Magnetic and transport properties of Mn2CoAl oriented films
Authors: Jamer Michelle E. , Assaf Badih A. , Devakul Trithep , Heiman Don
Published: October 2013

The structure, magnetic, and transport properties of thin films of the Heusler ferrimagnet Mn2CoAl have been investigated for properties related to spin gapless semiconductors. Oriented films were grown by molecular beam epitaxy on GaAs substrates and the structure was found to transform from tetragonal to cubic for increasing annealing temperature. The anomalous Hall resistivity is found to be proportional to the square of the longitudinal resistivity and magnetization expected for a topological Berry curvature origin. A delicate balance of the spin-polarized carrier type when coupled with voltage gate-tuning could significantly impact advanced electronic devices.
Direct writing of ferroelectric domains on strontium barium niobate crystals using focused ultraviolet laser light
Authors: Boes Andreas , Crasto Tristan , Steigerwald Hendrik , Wade Scott , Frohnhaus Jakob , Soergel Elisabeth , Mitchell Arnan
Published: October 2013

We report ferroelectric domain inversion in strontium barium niobate (SBN) single crystals by irradiating the surface locally with a strongly focused ultraviolet (UV) laser beam. The generated domains are investigated using piezoresponse force microscopy. We propose a simple model that allows predicting the domain width as a function of the irradiation intensity, which indeed applies for both SBN and LiNbO3. Evidently, though fundamentally different, the domain structure of both SBN and LiNbO3 can be engineered through similar UV irradiation.
Organic magnetoresistance in ambipolar field-effect transistors
Authors: Pham Song-Toan , Kawasugi Yoshitaka , Tada Hirokazu
Published: October 2013

Magnetoresistance (MR) in ambipolar field-effect transistors (FETs) consisting of bilayers of pentacene (C22H14, PEN) and perfluoropentacene (C22F14, PFP) was studied. The ambipolar FET exhibits positive MR of approximately 1% at 100 mT and room temperature. This effect is considered to originate from the accumulated carriers at the interface between PEN and PFP. The gate voltage dependence showed that MR was enhanced with increasing number of electrons and holes accumulated at the PFP-PEN interface. The observed results support the proposed double-carrier models as the mechanism of organic magnetoresistance.
Finite time control of a class of time-varying unified chaotic systems
Authors: Ying Yang , Guopei Chen
Published: October 2013

This paper considers the problem of finite time control for a class of time-varying unified chaotic system. First, based on the finite-time stability theory, a novel adaptive control technique is presented to achieve finite-time stabilization for time-varying unified chaotic system. Comparing with the existing methods, the proposed controller only need to be added on one state variable of systems and it is easy to be implemented. Then, a finite time control technique is provided to realize the tracking of any target function with second-order derivatives. Finally, Simulation results are provided to show the effectiveness of the proposed method.
Magnetism of Co doped graphitic ZnO layers adsorbed on Si and Ag surfaces
Authors: Fernandes Marcelo , Schmidt Tome M.
Published: October 2013

The effect of the substrate on Co doped graphitic ZnO layers adsorbed on metallic and semiconductor surfaces are investigated. The first principles results reveal that the magnetic interactions are strongly affected by the substrate. While graphitic layers of ZnO:Co on the well controlled metallic Ag(111) surface present weak ferromagnetic stability, on the semiconductor Si(111) surface they are strongly ferromagnetic coupled. The presence of metallic states in ZnO:Co adsorbed on Ag(111) surface favors a superexchange mechanism, weakening the ferromagnetic interaction. On the other hand, the magnetism of few layers of ZnO:Co on Si(111) surface is governed by a direct exchange mechanism, favoring a ferromagnetic coupling. This confined II–VI system doped with transition metal on a semiconductor surface presents higher magnetic stability than III–V nanostructures, and it is desired for nanostructured oxide/semiconductor room temperature ferromagnetism, using silicon technology.
Achieving slow and fast light with high transmission by nanodiamond nitrogen-vacancy center coupling to photonic crystal cavity
Authors: Li J. H. , Yu R. , Yang X. X.
Published: October 2013

Using a single diamond nitrogen-vacancy (NV) center embedded in a waveguide-coupled photonic crystal (PC) nanocavity and driven by a classical laser field, we investigate optical transmission and group delay characteristics of the hybrid system operating in the weak-coupling regime. It is found that double electromagnetically induced-transparency (EIT) transmission peaks and slow- and fast-light propagation inside the EIT-like windows can be realized with practical system parameters. The double-frequency transparency of the input light expands the frequency range of EIT and may improve the controllability of EIT in this composite PC-NV system. The present system also provides a way to achieve integrated photonic slow- and fast-light devices for applications requiring multiple EIT effect in a PC platform.
In situ X-ray reflectivity of indium supplied on GaN templates by metal organic vapor phase epitaxy
Authors: Ju Guangxu , Fuchi Shingo , Tabuchi Masao , Takeda Yoshikazu
Published: October 2013

The indium supplied on c-plane GaN templates using Metal organic vapor phase epitaxy was studied by in situ X-ray reflectivity (XRR) at 800 °C. The presence of liquid indium layers on the GaN (0001) surface was demonstrated using data-fitting of XRR measurements, ex situ atomic force microscope, auger electron spectroscopy, and cross-sectional scanning electron microscope. These measurements demonstrated that a liquid indium layer coexisted with indium droplets on top of the GaN (0001) surface at 800 °C. The liquid indium film thicknesses increased with increasing TMIn supply time and did not change during cooling from 800 °C to room temperature.
Measuring the Hubble constant
Authors: Livio Mario , Riess Adam G.
Published: October 2013

Perhaps the fundamental parameter of cosmology, the ratio of an object’s recessional speed to its distance from us encodes information about the universe’s age, composition, and structure.
Change Blindness in a Dynamic Scene Due to Endogenous Override of Exogenous Attentional Cues
Authors: Smith Tim J , Lamont Peter , Henderson John M
Published: October 2013

Change blindness is a failure to detect changes if the change occurs during a mask or distraction. Without distraction, it is assumed that the visual transients associated with the change will automatically capture attention ( exogenous control), leading to detection. However, visual transients are a defining feature of naturalistic dynamic scenes. Are artificial distractions needed to hide changes to a dynamic scene? Do the temporal demands of the scene instead lead to greater endogenous control that may result in viewers missing a change in plain sight? In the present study we pitted endogenous and exogenous factors against each other during a card trick. Complete change blindness was demonstrated even when a salient highlight was inserted coincident with the change. These results indicate strong endogenous control of attention during dynamic scene viewing and its ability to override exogenous influences even when it is to the detriment of accurate scene representation.
Facial Coding is Disrupted at Equiluminance
Authors: Pearce Samuel L , Arnold Derek H
Published: October 2013

Human face recognition is disrupted by the reversal of luminance contrast polarity (ie photo negatives—see Galper 1970 Psychonomic Science19 207–208; Johnston et al 1992 Perception21 365–375), while recognition of other objects is less impacted (Nederhouser et al 2007 Vision Research47 2134–2142; Subramaniam and Biederman 1997 Investigative Ophthalmology & Visual Science38 998). This suggests that correct patterns of luminance contrast are important for facial coding. Here we investigate this further by minimising luminance contrast. We contrast peoples' ability to categorise cars and faces when images vary in luminance and when images are altered to predominantly contain differences in colour (equiluminance). Eliminating luminance contrast had a greater adverse impact on facial classifications relative to car categorisations. This was true even though precautions were taken to equate visibility, and despite equal levels of performance when images contained luminance contrast. These results were not due to images containing markedly different spectra, as the effect persisted for facial images altered to match car images in this regard, and performance in both tasks dropped off proportionally with increasing levels of image blur. Finally, consistent with previous observations, we show that facial coding is not only adversely impacted at equiluminance but becomes even worse when the polarity of luminance contrast is reversed. Our data show that the correct pattern of luminance contrast is very important for facial coding. We suggest that this is related to the role of luminance contrast in signalling 3-D shape from shading.
Receivers in American Football Use a Constant Optical Projection Plane Angle to Pursue and Catch Thrown Footballs
Authors: Shaffer Dennis M , Dolgov Igor , Maynor Andrew , Reed Cody
Published: October 2013

In the present work we test how well two interceptive strategies, which have been proposed for catching balls hit high in the air in baseball and cricket, account for receivers in American football catching footballs. This is an important test of the domain generality of these strategies as this is the first study examining a situation where the pursuer's locomotor axis is directed away from the origin of the ball, and because the flight characteristics of an American football are far different from targets studied in prior work. The first strategy is to elicit changes in the ball's lateral optical position that match changes in the vertical optical position so that the optical projection plane angle, ψ, remains constant, thus resulting in a linear optical trajectory (LOT). The second is keeping vertical optical ball velocity decreasing while maintaining constant lateral optical velocity (generalized optical acceleration cancellation, or GOAC). We found that the optical projection plane angle was maintained as constant significantly more often than maintaining vertical and lateral optical velocities as GOAC predicted. The present experiment extends previous research by showing that the constancy of ψ resulting in an LOT is used by humans pursuing American footballs and demonstrates the domain generality of the LOT heuristic.
Da Vinci's Mona Lisa Entering the Next Dimension
Authors: Carbon Claus-Christian , Hesslinger Vera M
Published: October 2013

For several of Leonardo da Vinci's paintings, such as The Virgin and Child with St Anne or the Mona Lisa, there exist copies produced by his own studio. In case of the Mona Lisa, a quite exceptional, rediscovered studio copy was presented to the public in 2012 by the Prado Museum in Madrid. Not only does it mirror its famous counterpart superficially; it also features the very same corrections to the lower layers, which indicates that da Vinci and the ‘copyist’ must have elaborated their panels simultaneously. On the basis of subjective (thirty-two participants estimated painter-model constellations) as well as objective data (analysis of trajectories between landmarks of both paintings), we revealed that both versions differ slightly in perspective. We reconstructed the original studio setting and found evidence that the disparity between both paintings mimics human binocular disparity. This points to the possibility that the two Giocondas together might represent the first stereoscopic image in world history.
Natural plant extracts and prebiotic compounds as alternatives to antibiotics in broiler chicken diets in a necrotic enteritis challenge model
Authors: Vidanarachchi J. K. , Mikkelsen L. L. , Constantinoiu C. C. , Choct M. , Iji P. A.
Published: October 2013

An experiment was conducted to determine the effects of two different water-soluble carbohydrate extracts (renga renga lily extract and Acacia extract), and two commercially available prebiotic compounds, Fibregum and Raftifeed-IPE, on the performance of broiler chickens subjected to a necrotic enteritis (NE) challenge model. These treatments were compared with negative control and a positive (Zn-bacitracin) control treatments. An overall 8.8% NE-related mortality was recorded, with mean jejunal and ileal lesion scores in dead birds ranging from 3.03 to 3.90 in all challenged groups except the positive control groups. NE-specific deaths or clinical abnormalities were not observed with unchallenged control and positive control groups. At 7 days post-challenge, the concentration of specific IgY antibodies against the α-toxin of Clostridium perfringens in the serum was lower (P < 0.05) in birds fed the positive control and Fibregum-supplemented diets than in the negative control group. However, birds fed Fibregum had increased (P < 0.05) IgM concentration compared with those fed Acacia extract and lily extract. The Fibregum-fed group also had higher (P < 0.05) IgA concentrations in serum than did the positive-control and lily extract-supplemented groups at 14 days but this effect did not persist to 21 days. The results from the present study demonstrated that supplementation with water-soluble carbohydrates from two plant sources was not effective in controlling NE. However, the prebiotic compound Fibregum was found to be having some immunomodulatory effects. Addition of Zn-bacitracin and monensin was highly effective in counteracting the negative effects of the disease challenge.
Computational study of the activated O
H
state in the catalytic mechanism of cytochrome
c
oxidase
Authors: Sharma Vivek , Karlin Kenneth D. , Wikström Mårten
Published: October 2013

Significance

Density functional theory studies on the O
H
state in the catalytic mechanism of cytochrome
c
oxidase are performed. The proposed structure of O
H
state and its calculated characteristics are found to comply with the experimental data. The presented hypothesis solves, at least in part, the dilemma of the O
H
and O states in the catalytic mechanism of cytochrome oxidase.
Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system
Authors: Okazaki Shin , Kaneko Takakazu , Sato Shusei , Saeki Kazuhiko
Published: October 2013

Significance

Root–nodule symbiosis between leguminous plants and rhizobia requires rhizobial Nod factors (NFs) and their leguminous receptors (NFRs). Here we show that symbiosis in the soybean rhizobium
Bradyrhizobium elkanii
is promoted by the type III secretion system (T3SS), which delivers virulence factors via pathogenic bacteria. Nodulation tests and expression analyses using mutants of both
B. elkanii
and soybean (
Glycine max
) revealed that rhizobial T3SS activates host nodulation signaling in the absence of NFs and NFRs. These results suggest that rhizobia have adopted a pathogenic system that stimulates their legume hosts to initiate symbiotic programs.
Origins of correlated spiking in the mammalian olfactory bulb
Authors: Gerkin Richard C. , Tripathy Shreejoy J. , Urban Nathaniel N.
Published: October 2013

Significance

Neurons exhibit temporally correlated patterns of activity, and the brain is believed to process information in part by exploiting these correlations. Here we use new analytic tools to show that in the olfactory bulb, the first processing station for smell in mammals, these correlations emerge primarily from the animal’s own breathing pattern, and also from the sparse connectivity of the cells that ultimately transmit olfactory information to higher brain areas. These results inform our understanding of how, and how well, the brain can represent information about smell and provide insight into the importance of active sampling processes in sensory coding.
Synergistic inhibition of natural killer cells by the nonsignaling molecule CD94
Authors: Cheent Kuldeep S. , Jamil Khaleel M. , Cassidy Sorcha , Liu Mengya , Mbiribindi Berenice , Mulder Arend , Claas Frans H. J. , Purbhoo Marco A. , Khakoo Salim I.
Published: October 2013

Significance

Natural killer (NK) cell function is critically regulated by inhibitory receptors for MHC class I. This work shows that peptides derived from both host and viruses can engage CD94 in the absence of a signalling partner and augment inhibition of NK cells expressing NK cell receptor gene 2A. This result establishes CD94 as a receptor that binds HLA-E in a peptide-dependent fashion. It also demonstrates that NK cells expressing inhibitory receptors from the killer cell immunoglobulin-like receptor or C-type lectin-like receptor families respond with different stoichiometries to changes in the levels of cell-surface MHC class I. Thus these two receptor families may have distinct but complementary functions in recognizing changes in MHC class I.
CRL4A-FBXW5–mediated degradation of DLC1 Rho GTPase-activating protein tumor suppressor promotes non-small cell lung cancer cell growth
Authors: Kim Tai Young , Jackson Sarah , Xiong Yue , Whitsett Timothy G. , Lobello Janine R. , Weiss Glen J. , Tran Nhan Le , Bang Yung-Jue , Der Channing J.
Published: October 2013

Significance

The
DLC1
tumor suppressor gene is commonly lost in cancer by genomic deletion or epigenetic silencing, leading to loss of gene transcription.
DLC1
encodes a GTPase-activating protein for the RhoA small GTPase, and DLC1 loss of expression results in aberrant RhoA activation and signaling. Unexpectedly, we found that a subset of non-small cell lung cancer patient tumors and cell lines retained
DLC1
mRNA but not protein expression. We determined that the CUL4A–DDB1–FBXW5 E3 ubiquitin ligase complex is responsible for loss of DLC1 protein expression. Suppression of FBXW5 function restored DLC1-dependent lung cancer cell growth suppression. Our observations identify a mechanism for posttranslational loss of DLC1 function in cancer and substrate for CRL4A-FBXW5–driven cancer growth.
Discovery of novel chemoeffectors and rational design of
Escherichia coli
chemoreceptor specificity
Authors: Bi Shuangyu , Yu Daqi , Si Guangwei , Luo Chunxiong , Li Tongqing , Ouyang Qi , Jakovljevic Vladimir , Sourjik Victor , Tu Yuhai , Lai Luhua
Published: October 2013

Significance

Chemotaxis is a universal phenomenon whereby motile cells, like motile bacteria, navigate by following chemical gradients in their environment. Bacterial chemoreceptors can bind with specific chemoeffectors and transfer environmental signals to the cell. However, the molecular mechanisms for chemoeffector binding and signaling are not fully understood, and rational design of bacteria to respond to new chemicals has been challenging. In this study, by using a combined experimental and computational approach, we discovered novel antagonists and attractants for the
Escherichia coli
chemoreceptor Tar. The interaction differences of the novel antagonists and attractants with Tar provide clues to alter Tar–ligand specificity. Based on these understandings,
E. coli
strain was successfully engineered to sense
l
-arginine, a ligand unrecognized before.
Stigmergy, collective actions, and animal social spacing
Authors: Giuggioli Luca , Potts Jonathan R. , Rubenstein Daniel I. , Levin Simon A.
Published: October 2013

Significance

Marking animals avoid locations recently visited by others. We conceptualized this time nonlocal avoidance behavior as stigmergy, a form of mediated interaction that gives rise to coordinated behavior from seemingly independent individuals. In so doing, the concept of stigmergy is used beyond the realm of eusocial insects. To link the population spatiotemporal patterns that emerge from the individual nonlocal rules of interaction, we construct a collective movement model whereby randomly moving animals have the tendency to avoid marks left by a conspecific, depending on the age of the mark. As a result, we are able to quantify animal decision-making processes in terms of current and past locations of other individuals, linking behavior to history-dependent actions.
The gated induction system of a systemic floral inhibitor, antiflorigen, determines obligate short-day flowering in chrysanthemums
Authors: Higuchi Yohei , Narumi Takako , Oda Atsushi , Nakano Yoshihiro , Sumitomo Katsuhiko , Fukai Seiichi , Hisamatsu Tamotsu
Published: October 2013

Significance

Photoperiodic floral initiation is thought to be regulated by a systemic flowering inducer (florigen) and inhibitor (antiflorigen) produced in the leaves. Here, we show the discovery of an antiflorigen (CsAFT) from chrysanthemum, which is produced in the leaves under a noninductive photoperiod to systemically inhibit flowering. This antiflorigen production system prevents precocious flowering and enables the year-round supply of marketable flowers by manipulation of day length.
Hydration dynamics as an intrinsic ruler for refining protein structure at lipid membrane interfaces
Authors: Cheng Chi-Yuan , Varkey Jobin , Ambroso Mark R. , Langen Ralf , Han Songi
Published: October 2013

Significance

The structural properties of a membrane-associating protein at the water–membrane interfaces are intimately linked to its biological function, but they are difficult to characterize using existing biophysical tools. We identify the existence of a distinct intrinsic gradient of water diffusion across the lipid bilayer, encompassing a thick surface hydration layer above the lipid membrane surface, and debut an approach to exploit this gradient as a highly sensitive ruler to determine the topology, immersion depth, and location of a membrane associating protein, including the segments residing well above the membrane surface, that are otherwise difficult to resolve. This study demonstrates a potential of a broadly applicable approach for the structure–dynamics–function study of membrane proteins, membrane systems, and beyond.
Structure–function analysis of ribonucleotide bypass by B family DNA replicases
Authors: Clausen Anders R. , Murray Michael S. , Passer Andrew R. , Pedersen Lars C. , Kunkel Thomas A.
Published: October 2013

Significance

More than a million ribonucleotides may be incorporated into the mammalian nuclear genome during each round of DNA replication. When these ribonucleotides are not removed, they persist in the DNA template used for the next round of replication. Here we show that replicases stall when attempting to bypass ribonucleotides in DNA templates, with stalling increasing as the number of consecutive ribonucleotides increases from one to four. Structural analysis reveals that stalling is associated with displacement of a conserved tyrosine residue that is important for template strand interactions and with an unpreferred C2´-endo conformation for the ribose. Replication fork stalling during ribonucleotide bypass is likely to be relevant to both negative and positive consequences of ribonucleotides in DNA.
Deficits in dopaminergic transmission precede neuron loss and dysfunction in a new Parkinson model
Authors: Janezic Stephanie , Threlfell Sarah , Dodson Paul D. , Dowie Megan J. , Taylor Tonya N. , Potgieter Dawid , Parkkinen Laura , Senior Steven L. , Anwar Sabina , Ryan Brent , Deltheil Thierry , Kosillo Polina , Cioroch Milena , Wagner Katharina , Ansorge Olaf , Bannerman David M. , Bolam J. Paul , Magill Peter J. , Cragg Stephanie J. , Wade-Martins Richard
Published: October 2013

Significance

Elevated expression of the presynaptic protein α-synuclein underlies familial and sporadic Parkinson disease (PD). However, our understanding of how increases in α-synuclein levels drive the sequence of events leading to PD is incomplete. Here, we apply a multidisciplinary longitudinal analysis to a new α-synuclein transgenic mouse model. We show that early-stage decreases in dopamine release and vesicle reclustering precede late-stage changes in neuronal firing properties, measured by in vivo recordings from vulnerable neurons. Accumulated deficits in dopamine neurotransmission and altered neuronal firing are associated with cell death and motor abnormalities, in the absence of protein aggregation in the substantia nigra. These findings have important implications for developing therapies.
Loss of metabotropic glutamate receptor 2 escalates alcohol consumption
Authors: Zhou Zhifeng , Karlsson Camilla , Liang Tiebing , Xiong Wei , Kimura Mitsuru , Tapocik Jenica D. , Yuan Qiaoping , Barbier Estelle , Feng Austin , Flanigan Meghan , Augier Eric , Enoch Mary-Anne , Hodgkinson Colin A. , Shen Pei-Hong , Lovinger David M. , Edenberg Howard J. , Heilig Markus , Goldman David
Published: October 2013

Significance

Gene identification for complex behavioral traits, alcoholism in particular, has been largely unsuccessful, in part because of the rarity of many causative variants and the heterogeneity and small effect size of the causal loci. Artificially selected animals may be valuable in gene identification. We identified a causal role of metabotropic glutamate receptor 2 (mGluR2) in altered alcohol preference via genomic sequencing of selectively bred rats, linkage analysis in the F2 rats, and function validation in mGluR2 null mice. Our findings represent a valuable contribution to understanding the neurobiology of alcoholism and a strategy for gene identification for complex behavior traits.
Inter- and intrasubunit interactions between transmembrane helices in the open state of P2X receptor channels
Authors: Heymann Gabriel , Dai Jian , Li Mufeng , Silberberg Shai D. , Zhou Huan-Xiang , Swartz Kenton J.
Published: October 2013

Significance

The opening of P2X receptor channels by extracellular ATP underlies purinergic signaling in many tissues. Here we use computational and functional approaches to study helix interactions within the transmembrane domain of P2X receptors. Our results suggest that the intersubunit crevices observed in the X-ray structure of detergent-solubilized ATP-bound receptors are nonnative but confirm helix interactions within individual subunits observed in both apo and ATP-bound receptors and identify a hot spot within a narrow internal region where the gating and permeation properties can be readily tuned.
Reexposure to nicotine during withdrawal increases the pacemaking activity of cholinergic habenular neurons
Authors: Görlich Andreas , Antolin-Fontes Beatriz , Ables Jessica L. , Frahm Silke , Ślimak Marta A. , Dougherty Joseph D. , Ibañez-Tallon Inés
Published: October 2013

Significance

According to the World Health Organization, tobacco consumption causes the death of close to 6 million people each year, yet successful attempts to quit smoking are very rare. The present study identifies a group of neurons in the brain that respond differently to nicotine after a period of abstinence, suggesting that altered activity of these neurons may contribute to difficulties with smoking cessation.
Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage
Authors: Azpurua Jorge , Ke Zhonghe , Chen Iris X. , Zhang Quanwei , Ermolenko Dmitri N. , Zhang Zhengdong D. , Gorbunova Vera , Seluanov Andrei
Published: October 2013

Significance

Molecular mechanisms responsible for differences in longevity between animal species are largely unknown. Here we show that the longest-lived rodent, the naked mole-rat, has more accurate protein translation than the mouse. Furthermore, we show that the naked mole-rat has a unique fragmented ribosomal RNA structure. Such cleaved ribosomal RNA has been reported for only one other species of mammal. This article suggests the importance of protein translation in aging and provides insight into the mechanisms of longevity.
In vitro evolution of α-hemolysin using a liposome display
Authors: Fujii Satoshi , Matsuura Tomoaki , Sunami Takeshi , Kazuta Yasuaki , Yomo Tetsuya
Published: October 2013

Significance

The directed evolution of proteins in vitro has generated highly functional proteins and has contributed to elucidating the sequence–function relationship of proteins. However, the available methods consider globular proteins, not membrane proteins, despite the biological and pharmaceutical importance of the latter. We report the development of a method called liposome display, which enables the in vitro evolution of membrane proteins. We applied the method to evolve the pore-forming activity of α-hemolysin from
Staphylococcus aureus
and obtained a mutant with 30-fold higher activity than the WT. Given its high degree of controllability, liposome display allows for the rapid and efficient evolution of a wide range of membrane proteins, thereby improving the field of membrane protein engineering.
Personalized genomic disease risk of volunteers
Authors: Gonzalez-Garay Manuel L. , McGuire Amy L. , Pereira Stacey , Caskey C. Thomas
Published: October 2013

Significance

Replacing traditional methods for genetic testing of inheritable disorders with next-generation sequencing (NGS) will reduce the cost of genetic testing and increase the information available for the patients. NGS will become an invaluable resource for the patient and physicians, especially if the sequencing information is stored properly and reanalyzed as bioinformatics tools and annotations improve. NGS is still at the early stages of development, and it is full of false-positive and -negative results and requires infrastructure and specialized personnel to properly analyze the results. This paper will explain our experience with an adult population, our bioinformatics analysis, and our clinical decisions to assure that our genetic diagnostics were accurate to detect carrier status and serious medical conditions in our volunteers.
Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in
Arabidopsis
Authors: Hua Zhihua , Pool John E. , Schmitz Robert J. , Schultz Matthew D. , Shiu Shin-Han , Ecker Joseph R. , Vierstra Richard D.
Published: October 2013

Significance

Gene families significantly influence organismal diversity and adaptation, but how they evolved and are controlled is not fully clear. Using the
Arabidopsis
F-Box protein superfamily as a model, we show that both genomic and epigenomic forces are consequential with reversible, suppressive chromatin marks potentially helping dampen the adverse effects of altered gene dosage and the emergence of deleterious alleles. Such forces might be relevant to other highly polymorphic gene families impacted by genomic drift evolution.
Supervisor social skill and supervision outcome
Authors: Bambling Matthew , King Robert
Published: October 2013

Background: The practice of clinical supervision is considered an effective procedure to achieve a variety of professional outcomes for supervisees. Supervisory alliance mediates many of the learning outcomes thought important for effective supervision. Therefore, it is important to identity supervisor characteristics that relate to the capacity to develop a positive supervisory alliance and achieve supervision outcome. Aim: Supervisor interpersonal skill was investigated as a characteristic involved with both supervisee assessment of supervisory alliance and learning outcomes of supervision. Method: Forty supervisors completed assessments for interpersonal skill and provided 8 sessions of supervision to 50 supervisees. Supervisees completed assessments for supervisory alliance and supervision evaluation. Findings: Supervisor interpersonal skill predicted supervisee rated supervisory alliance and supervision outcome. Implications: Supervisor interpersonal skill is important for the capacity to develop a positive supervisory alliance and manage the learning environment of supervision.
The Mechanical Philosophy and Newton’s Mechanical Force
Authors: Kochiras Hylarie
Published: October 2013

How does Newton approach the challenge of mechanizing gravity and, more broadly, natural philosophy? By adopting the simple machine tradition’s mathematical approach to a system’s covarying parameters of change, he retains natural philosophy’s traditional goal while specifying it in a novel way as the search for impressed forces. He accordingly understands the physical world as a divinely created machine possessing intrinsically mathematical features and mathematical methods as capable of identifying its real features. The gravitational force’s physical cause remains an outstanding problem, however, as evidenced by Newton’s onetime reference to active principles as the “genuine principles of the mechanical philosophy.”
Congruence-Association Model of music and multimedia: Origin and evolution
Authors: Cohen Annabel J.
Published: October 2013

The evolution of the Congruence-Association Model (CAM) is presented in a cognitive-scientific and historical context. Iteration 1 of CAM proposed a bottom-up process for analysis of musical and film stimuli in terms of ‘Congruence’ (audiovisual structural overlap) and ‘Association’ (contingency-base meaning). Iteration 2 added speech and top-down inference to create the best match with bottom-up processing. Adding sound effects and text, Iteration 3 referred to the best match between top-down and bottom-up information as the conscious ‘working narrative.’ A developmental version of CAM was also proposed to accommodate cohort-specific multimedia experience at critical periods. Iteration 4 incorporated a kinesthetic channel, supporting a mirror system and embodied meaning. The chapter illustrates how psychological experiments increase understanding of the role of music in multimedia, and aims to help set the stage for further empirical work and progress.
Understanding the impact of surround sound in multimedia
Authors: Kerins Mark
Published: October 2013

This chapter explores the effects of multichannel sound presentation (e.g., surround sound) on music listening and on the experience of multimedia, focusing especially on comparing 5.1-channel surround—the standard soundtrack format for movies and television—with traditional two-channel stereo. The chapter organizes research on this topic into three categories: studies based on distinguishing between sound systems, studies based on listeners indicating their sound system preferences, and studies based on independent group ratings (i.e., do participants rate different presentation modes differently when they cannot directly compare them?). For each category, the chapter outlines methods, conclusions, strengths, and limitations of extant work; across categories, it demonstrates that slight differences in experimental method yield divergent results, making it difficult to come to general conclusions about the impact of multichannel presentation. As a whole, the existing research reveals that whether and how multichannel sound affects the audience experience is heavily dependent on the specific content used and the context in which it is presented.
The Perils of Peace
Authors: Reinisch Jessica
Published: October 2013

When the war was over in 1945, Germany was a country with no government, little functioning infrastructure, millions of refugees and homeless people, and huge foreign armies living largely off the land. Large parts of the country were covered in rubble, with no clean drinking water, electricity, or gas. Hospitals overflowed with patients, but were short of beds, medicines, and medical personnel. In these conditions, the potential for epidemics and public health disasters was severe. This is a study of how the four occupiers—Britain, France, the Soviet Union, and the United States—attempted to keep their own troops and the ex-enemy population alive. While the war was still being fought, German public health was a secondary consideration for them, an unaffordable and undeserved luxury. But once fighting ceased and the occupation began, it rapidly turned into a urgent priority. Public health was now recognized as an indispensable component of creating order, keeping the population governable, and facilitating the reconstruction of German society. But they faced a number of insoluble problems in the process: Which Germans could be trusted to work with the occupiers, and how were they to be identified? Who could be tolerated because of a lack of alternatives? How, if at all, could former Nazis be reformed and reintegrated into German society? What was the purpose of the occupation anyway? This is the first carefully researched comparison of the four occupation zones which looks at the occupation through the prism of public health, an essential service fundamentally shaped by political and economic criteria, and which in turn was to determine the success or failure of the occupation.