bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heisenberg-scaling measurement of the single-photon Kerr non-linearity using mixed states
Authors: Chen Geng , Aharon Nati , Sun Yong-Nan , Zhang Zi-Huai , Zhang Wen-Hao , He De-Yong , Tang Jian-Shun , Xu Xiao-Ye , Kedem Yaron , Li Chuan-Feng , Guo Guang-Can 
Published: January 2018

AbstractImproving the precision of measurements is a significant scientific challenge. Previous works suggest that in a photon-coupling scenario the quantum fisher information shows a quantum-enhanced scaling of N2, which in theory allows a better-than-classical scaling in practical measurements. In this work, utilizing mixed states with a large uncertainty and a post-selection of an additional pure system, we present a scheme to extract this amount of quantum fisher information and experimentally attain a practical Heisenberg scaling. We performed a measurement of a single-photon’s Kerr non-linearity with a Heisenberg scaling, where an ultra-small Kerr phase of ≃6 × 10−8 rad was observed with a precision of ≃3.6 × 10−10 rad. From the use of mixed states, the upper bound of quantum fisher information is improved to 2N2. Moreover, by using an imaginary weak-value the scheme is robust to noise originating from the self-phase modulation.
Auditory opportunity and visual constraint enabled the evolution of echolocation in bats
Authors: Thiagavel Jeneni , Cechetto Clément , Santana Sharlene E. , Jakobsen Lasse , Warrant Eric J. , Ratcliffe John M. 
Published: January 2018

AbstractSubstantial evidence now supports the hypothesis that the common ancestor of bats was nocturnal and capable of both powered flight and laryngeal echolocation. This scenario entails a parallel sensory and biomechanical transition from a nonvolant, vision-reliant mammal to one capable of sonar and flight. Here we consider anatomical constraints and opportunities that led to a sonar rather than vision-based solution. We show that bats’ common ancestor had eyes too small to allow for successful aerial hawking of flying insects at night, but an auditory brain design sufficient to afford echolocation. Further, we find that among extant predatory bats (all of which use laryngeal echolocation), those with putatively less sophisticated biosonar have relatively larger eyes than do more sophisticated echolocators. We contend that signs of ancient trade-offs between vision and echolocation persist today, and that non-echolocating, phytophagous pteropodid bats may retain some of the necessary foundations for biosonar.
High temperature limit of photosynthetic excitons
Authors: Rätsep Margus , Muru Renata , Freiberg Arvi 
Published: January 2018

AbstractExcitons in light-harvesting complexes are known to significantly improve solar-energy harnessing. Here we demonstrate photosynthetic excitons at super-physiological temperatures reaching 60–80 °C in different species of mesophilic photosynthetic bacteria. It is shown that the survival of light-harvesting excitons in the peripheral LH2 antennae is restricted by thermal decomposition of the pigment–protein complex rather than by any intrinsic property of excitons. The regular spatial organization of the bacteriochlorophyllapigments supporting excitons in this complex is lost upon the temperature-induced breakdown of its tertiary structure. Secondary structures of the complexes survive even higher temperatures. The discovered pivotal role of the protein scaffold in the stabilization of excitons comprises an important aspect of structure–function relationship in biology. These results also intimately entangle the fundamental issues of quantum mechanical concepts in biology and in the folding of proteins.
Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components
Authors: Razew Michal , Warkocki Zbigniew , Taube Michal , Kolondra Adam , Czarnocki-Cieciura Mariusz , Nowak Elzbieta , Labedzka-Dmoch Karolina , Kawinska Aleksandra , Piatkowski Jakub , Golik Pawel , Kozak Maciej , Dziembowski Andrzej , Nowotny Marcin 
Published: January 2018

AbstractNuclease and helicase activities play pivotal roles in various aspects of RNA processing and degradation. These two activities are often present in multi-subunit complexes from nucleic acid metabolism. In the mitochondrial exoribonuclease complex (mtEXO) both enzymatic activities are tightly coupled making it an excellent minimal system to study helicase–exoribonuclease coordination. mtEXO is composed of Dss1 3′-to-5′ exoribonuclease and Suv3 helicase. It is the master regulator of mitochondrial gene expression in yeast. Here, we present the structure of mtEXO and a description of its mechanism of action. The crystal structure of Dss1 reveals domains that are responsible for interactions with Suv3. Importantly, these interactions are compatible with the conformational changes of Suv3 domains during the helicase cycle. We demonstrate that mtEXO is an intimate complex which forms an RNA-binding channel spanning its entire structure, with Suv3 helicase feeding the 3′ end of the RNA toward the active site of Dss1.
Regulatory feedback response mechanisms to phosphate starvation in rice
Authors: Ajmera Ishan , Shi Jing , Giri Jitender , Wu Ping , Stekel Dov J. , Lu Chungui , Hodgman T. Charlie 
Published: January 2018

AbstractPhosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding of the molecular mechanisms underlying phosphate uptake by investigating the transcriptional dynamics of two regulators: the Ubiquitin ligase PHO2 and the long non-coding RNA IPS1. Temporal measurements of RNA levels have been integrated into mechanistic mathematical models using advanced statistical techniques. Models based solely on current knowledge could not adequately explain the temporal expression profiles. Further modeling and bioinformatics analysis have led to the prediction of three regulatory features: the PHO2 protein mediates the degradation of its own transcriptional activator to maintain constant PHO2 mRNA levels; the binding affinity of the transcriptional activator ofPHO2is impaired by a phosphate-sensitive transcriptional repressor/inhibitor; and the extremely high levels of IPS1 and its rapid disappearance upon Pi re-supply are best explained by Pi-sensitive RNA protection. This work offers both new opportunities for plant phosphate research that will be essential for informing the development of phosphate efficient crop varieties, and a foundation for the development of models integrating phosphate with other stress responses.
Short heatwaves during fluctuating incubation regimes produce females under temperature-dependent sex determination with implications for sex ratios in nature
Authors: Carter A. W. , Sadd B. M. , Tuberville T. D. , Paitz R. T. , Bowden R. M. 
Published: January 2018

AbstractPatterns of temperature fluctuations in nature affect numerous biological processes, yet, empirical studies often utilize constant temperature treatments. This can limit our understanding of how thermally sensitive species respond to ecologically relevant temperatures. Research on turtles with temperature-dependent sex determination (TSD) provides good examples of this, since nest temperatures from many populations rarely exceed those necessary to produce females under constant laboratory conditions. We hypothesized that exposure to brief periods of warm temperatures (i.e., heat waves) are integral to sex determination in species with TSD, which requires tests that move beyond constant temperatures. We exposedTrachemys scriptaembryos from multiple populations and across the nesting season to heat waves of variable durations and quantified sex ratios. We found that embryos from all populations were highly sensitive to brief exposures to female producing temperatures; only 7.9 days of exposure produced a 50:50 sex ratio, but the response varied across the nesting season. From these findings, a model was developed to estimate sex ratios from field temperature traces, and this model outperformed traditional methods. Overall, these results enhance our understanding of TSD and emphasize the importance of using biologically relevant temperatures when studying thermally sensitive processes.
Adipocyte-activated oxidative and ER stress pathways promote tumor survival in bone via upregulation of Heme Oxygenase 1 and Survivin
Authors: Herroon Mackenzie K. , Rajagurubandara Erandi , Diedrich Jonathan D. , Heath Elisabeth I. , Podgorski Izabela 
Published: January 2018

AbstractMetastatic tumor cells engage the local tumor microenvironment and activate specific pro-survival mechanisms to thrive and progress in the harsh bone marrow niche. Here we show that the major contributors to the survival of carcinoma cells that have colonized the bone marrow are the adipocyte-induced oxidative stress and ER stress pathways. We demonstrate that upon exposure to adipocyte-rich environments in vitro or in vivo, bone-trophic prostate and breast tumor cells upregulate the oxidative stress enzyme, HO-1. We also show that HO-1 levels are significantly increased in human metastatic prostate cancer tissues and that stable HO-1 overexpression in tumor cells promotes growth and invasiveness. Co-incident with the adipocyte-induced expression of HO-1, there is an upregulation of ER chaperone BIP and splicing of XBP1, indicating adipocyte-driven unfolded protein response, a process that we show to be sensitive to antioxidant treatment. Importantly, we also demonstrate that triggering of the oxidative stress and ER stress responses, or HO-1 induction by adipocyte exposure result in the activation of pro-survival pathways, involving survivin. Collectively, our findings reveal a new link between HO-1 and survivin expression in tumor cells, and provide a new insight into potentially targetable survival pathways in bone-metastatic disease.
Shikonin Protects PC12 Cells Against β-amyloid Peptide-Induced Cell Injury Through Antioxidant and Antiapoptotic Activities
Authors: Tong Yuna , Bai Lan , Gong Rong , Chuan Junlan , Duan Xingmei , Zhu Yuxuan 
Published: January 2018

AbstractExcessive accumulation of β-amyloid (Aβ) is thought to be a major causative factor in the pathogenesis of Alzheimer’s disease (AD). Pretreating Aβ-induced neurotoxicity is a potential therapeutic approach to ameliorate the progression and development of AD. The present study aimed to investigate the neuroprotective effect of shikonin, a naphthoquinone pigment isolated from the roots of the traditional Chinese herb Lithospermum erythrorhizon, on Aβ1–42-treated neurotoxicity in PC12 cells. Pretreating cells with shikonin strongly improved cell viability, decreased the malondialdehyde and reactive oxygen species (ROS) content, and stabilized the mitochondrial membrane potential in Aβ1–42-induced PC12 cells. In addition, shikonin strongly improved the response of the antioxidant system to ROS by increasing the levels of superoxidedismutase, catalase and glutathione peroxidase. Furthermore, shikonin has the ability to reduce proapoptotic signaling by reducing the activity of caspase-3 and moderating the ratio of Bcl-2/Bax. These observations indicate that shikonin holds great potential for neuroprotection via inhibition of oxidative stress and cell apoptosis.
Poppers use and Sexual Partner Concurrency Increase the HIV Incidence of MSM: a 24-month Prospective Cohort Survey in Shenyang, China
Authors: Chu Zhen-xing , Xu Jun-jie , Zhang Yong-hui , Zhang Jing , Hu Qing-hai , Yun Ke , Wang Hong-yi , Jiang Yong-jun , Geng Wen-qing , Shang Hong 
Published: January 2018

AbstractThe use of poppers is highly prevalent in MSM, but little is known about the association between their use and HIV incidence in China. A prospective cohort study was conducted from 2011 to 2013 in MSM in Shenyang. 475(79.6%) of eligible HIV-negative MSM participated in this prospective survey and near one fourth MSM (23.4%) ever used poppers. About one-third of the participants had condomless anal intercourse, half had multiple sexual partners and 10.5% were syphilis positive. The HIV incidence densities were15.5 (95% CI:9.4–23.4)/100 PY[person-years]) and 4.6 (95% CI:2.9–7.0)/100 PY in poppers-users and non-poppers-users, respectively. Predictors of HIV seroconversion included poppers-using-behavior, having had more than two male partners, practicing group sex, unprotected anal intercourse(UAI) with male partners, and baseline syphilis positivity (all P < 0.05). In conclusion, the use of poppers, high-risk-sexual behaviors and syphilis infection significantly increase the HIV incidence among Shenyang MSM. It is essential for policy makers to add poppers to the official controlled illicit drug list to reduce HIV transmission among the MSM community. A comprehensive strategy should also be implemented to control both their high-risk-sexual behaviors and risk of syphilis infection, since these may represent novel ways to prevent new HIV infections in these MSM.
Hydroacoustics as a tool to examine the effects of Marine Protected Areas and habitat type on marine fish communities
Authors: Egerton J. P. , Johnson A. F. , Turner J. , LeVay L. , Mascareñas-Osorio I. , Aburto-Oropeza O. 
Published: January 2018

AbstractHydroacoustic technologies are widely used in fisheries research but few studies have used them to examine the effects of Marine Protected Areas (MPAs). We evaluate the efficacy of hydroacoustics to examine the effects of closure to fishing and habitat type on fish populations in the Cabo Pulmo National Park (CPNP), Mexico, and compare these methods to Underwater Visual Censuses (UVC). Fish density, biomass and size were all significantly higher inside the CPNP (299%, 144% and 52% respectively) than outside in non-MPA control areas. These values were much higher when only accounting for the reefs within the CPNP (4715%, 6970% and 97% respectively) highlighting the importance of both habitat complexity and protection from fishing for fish populations. Acoustic estimates of fish biomass over reef-specific sites did not differ significantly from those estimated using UVC data, although acoustic densities were less due to higher numbers of small fish recorded by UVC. There is thus considerable merit in nesting UVC surveys, also providing species information, within hydroacoustic surveys. This study is a valuable starting point in demonstrating the utility of hydroacoustics to assess the effects of coastal MPAs on fish populations, something that has been underutilised in MPA design, formation and management.
Theory for Perfect Transmodal Fabry-Perot Interferometer
Authors: Yang Xiongwei , Kweun Joshua M. , Kim Yoon Young 
Published: January 2018

AbstractWe establish the theory for perfect transmodal Fabry-Perot interferometers that can convert longitudinal modes solely to transverse modes and vice versa, reaching up to 100% efficiency. Two exact conditions are derived for plane mechanical waves: simultaneous constructive interferences of each of two coupled orthogonal modes, and intermodal interference at the entrance and exit sides of the interferometer with specific skew polarizations. Because the multimodal interferences and specific skew motions require unique anisotropic interferometers, they are realized by metamaterials. The observed peak patterns by the transmodal interferometers are similar to those found in the single-mode Fabry-Perot resonance, but multimodality complicates the involved mechanics. We provide their design principle and experimented with a fabricated interferometer. This theory expands the classical Fabry-Perot resonance to the realm of mode-coupled waves, having profound impact on general wave manipulation. The transmodal interferometer could sever as a device to transfer wave energy freely between dissimilar modes.
The Coupled Straintronic-Photothermic Effect
Authors: Rahneshin Vahid , Ziolkowska Dominika A. , McClelland Arthur , Cromwell Jaya , Jasinski Jacek B. , Panchapakesan Balaji 
Published: January 2018

AbstractWe describe the coupled straintronic-photothermic effect where coupling between bandgap of the 2D layered semiconductor under localized strains, optical absorption and the photo-thermal effect results in a large chromatic mechanical response in TMD-nanocomposites. Under the irradiation of visible light (405 nm to 808 nm), such locally strained atomic thin films based on 2H-MoS2embedded in an elastomer such as poly (dimethyl) siloxane matrix exhibited a large amplitude of photo-thermal actuation compared to their unstrained counterparts. Moreover, the locally strain engineered nanocomposites showed tunable mechanical response giving rise to higher mechanical stress at lower photon energies. Scanning photoluminescence spectroscopy revealed a change in bandgap of 30 meV between regions encompassing highly strained compared to the unstrained few layers. For 1.6% change in the bandgap, the macroscopic photo-thermal response increased by a factor of two. Millimeter scale bending actuators based on the locally strained 2H-MoS2resulted in significantly enhanced photo-thermal actuation displacements compared to their unstrained counterparts at lower photon energies and operated up to 30 Hz. Almost 1 mN photo-activated force was obtained at 50 mW and provided long-term stability. This study demonstrates a new mechanism in TMD-nanocomposites that would be useful for developing broad range of transducers.
A study of the influence of measurement timescale on internal resistance characterisation methodologies for lithium-ion cells
Authors: Barai Anup , Uddin Kotub , Widanage W. D. , McGordon Andrew , Jennings Paul 
Published: January 2018

AbstractThe power capability of a lithium ion battery is governed by its resistance, which changes with battery state such as temperature, state of charge, and state of health. Characterizing resistance, therefore, is integral in defining battery operational boundaries, estimating its performance and tracking its state of health. There are many techniques that have been employed for estimating the resistance of a battery, these include: using DC pulse current signals such as pulse power tests or Hybrid Pulse Power Characterization (HPPC) tests; using AC current signals, i.e., electrochemical impedance spectroscopy (EIS) and using pulse-multisine measurements. From existing literature, these techniques are perceived to yield differing values of resistance. In this work, we apply these techniques to 20 Ah LiFePO4/C6 pouch cells and use the results to compare the techniques. The results indicate that the computed resistance is strongly dependent on the timescales of the technique employed and that when timescales match, the resistances derived via different techniques align. Furthermore, given that EIS is a perturbative characterisation technique, employing a spectrum of perturbation frequencies, we show that the resistance estimated from any technique can be identified – to a high level of confidence – from EIS by matching their timescales.
Putative functional genes in idiopathic dilated cardiomyopathy
Authors: Nair Nishanth Ulhas , Das Avinash , Amit Uri , Robinson Welles , Park Seung Gu , Basu Mahashweta , Lugo Alex , Leor Jonathan , Ruppin Eytan , Hannenhalli Sridhar 
Published: January 2018

AbstractIdiopathic dilated cardiomyopathy (DCM) is a complex disorder with a genetic and an environmental component involving multiple genes, many of which are yet to be discovered. We integrate genetic, epigenetic, transcriptomic, phenotypic, and evolutionary features into a method – Hridaya, to infer putative functional genes underlying DCM in a genome-wide fashion, using 213 human heart genomes and transcriptomes. Many genes identified by Hridaya are experimentally shown to cause cardiac complications. We validate the top predicted genes, via five different genome-wide analyses: First, the predicted genes are associated with cardiovascular functions. Second, their knockdowns in mice induce cardiac abnormalities. Third, their inhibition by drugs cause cardiac side effects in human. Fourth, they tend to have differential exon usage between DCM and normal samples. Fifth, analyzing 213 individual genotypes, we show that regulatory polymorphisms of the predicted genes are associated with elevated risk of cardiomyopathy. The stratification of DCM patients based on cardiac expression of the functional genes reveals two subgroups differing in key cardiac phenotypes. Integrating predicted functional genes with cardiomyocyte drug treatment experiments reveals novel potential drug targets. We provide a list of investigational drugs that target the newly identified functional genes that may lead to cardiac side effects.
Combined shRNA over CRISPR/cas9 as a methodology to detect off-target effects and a potential compensatory mechanism
Authors: Peretz Liat , Besser Elazar , Hajbi Renana , Casden Natania , Ziv Dan , Kronenberg Nechama , Gigi Liat Ben , Sweetat Sahar , Khawaled Saleh , Aqeilan Rami , Behar Oded 
Published: January 2018

AbstractInhibition of genes is a powerful approach to study their function. While RNA interference is a widely used method to achieve this goal, mounting evidence indicates that such an approach is prone to off-target effects. An alternative approach to gene function inhibition is genetic mutation, such as the CRISPR/cas9 method. A recent report, however, demonstrated that genetic mutation and inhibition of gene expression do not always give corresponding results. This can be explained by off-target effects, but it was recently shown, at least in one case, that these differences are the result of a compensatory mechanism induced only by genetic mutation. We present here a combination of RNA inhibition and CRISPR/cas9 methods to identify possible off targets as well as potential compensatory effects. This approach is demonstrated by testing a possible role for Sema4B in glioma biology, in which our results implicate Sema4B as having a critical function. In stark contrast, by using shRNA over CRISPR/cas9 combined methodology, we clearly demonstrate that the Sema4B targeted shRNA effects on cell proliferation is the result of off-target effects. Nevertheless, it also revealed that certain splice variants of Sema4B are important for the ability of glioma cells to grow as individual clones.
Veiled symmetry of disordered Parity-Time lattices: protected PT-threshold and the fate of localization
Authors: Harter Andrew K. , Onanga Franck Assogba , Joglekar Yogesh N. 
Published: January 2018

AbstractOpen, non-equilibrium systems with balanced gain and loss, known as parity-time ($${\mathscr{P}}{\mathscr{T}}$$
P
T
)-symmetric systems, exhibit properties that are absent in closed, isolated systems. A key property is the $${\mathscr{P}}{\mathscr{T}}$$
P
T
-symmetry breaking transition, which occurs when the gain-loss strength, a measure of the openness of the system, exceeds the intrinsic energy-scale of the system. We analyze the fate of this transition in disordered lattices with non-Hermitian gain and loss potentials ±iγ at reflection-symmetric sites. Contrary to the popular belief, we show that the $${\mathscr{P}}{\mathscr{T}}$$
P
T
-symmetric phase is protected in the presence of a periodic disorder which leads to a positive $${\mathscr{P}}{\mathscr{T}}$$
P
T
-symmetry breaking threshold. We uncover a veiled symmetry of such disordered systems that is instrumental for the said protection, and show that this symmetry leads to new localization behavior across the $${\mathscr{P}}{\mathscr{T}}$$
P
T
-symmetry breaking transition. We elucidate the interplay between such localization and the $${\mathscr{P}}{\mathscr{T}}$$
P
T
-symmetry breaking phenomena in disordered $${\mathscr{P}}{\mathscr{T}}$$
P
T
-symmetric lattices, with Hermitian disorder or gain-loss disorder, and support our conclusions with a beampropagation- method analysis. Our theoretical predictions provide avenues for experimental realizations of -symmetric systems with engineered disorder.