bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capacity of very noisy communication channels based on Fisher information
Authors: Duan Fabing , Chapeau-Blondeau François , Abbott Derek 
Published: June 2016

AbstractWe generalize the asymptotic capacity expression for very noisy communication channels to now include coloured noise. For the practical scenario of a non-optimal receiver, we consider the common case of a correlation receiver. Due to the central limit theorem and the cumulative characteristic of a correlation receiver, we model this channel noise as additive Gaussian noise. Then, the channel capacity proves to be directly related to the Fisher information of the noise distribution and the weak signal energy. The conditions for occurrence of a noise-enhanced capacity effect are discussed and the capacity difference between this noisy communication channel and other nonlinear channels is clarified.
A rapid and practical technique for real-time monitoring of biomolecular interactions using mechanical responses of macromolecules
Authors: Tarhan Mehmet C. , Lafitte Nicolas , Tauran Yannick , Jalabert Laurent , Kumemura Momoko , Perret Grégoire , Kim Beomjoon , Coleman Anthony W. , Fujita Hiroyuki , Collard Dominique 
Published: June 2016

AbstractMonitoring biological reactions using the mechanical response of macromolecules is an alternative approach to immunoassays for providing real-time information about the underlying molecular mechanisms. Although force spectroscopy techniques, e.g. AFM and optical tweezers, perform precise molecular measurements at the single molecule level, sophisticated operation prevent their intensive use for systematic biosensing. Exploiting the biomechanical assay concept, we used micro-electro mechanical systems (MEMS) to develop a rapid platform for monitoring bio/chemical interactions of bio macromolecules, e.g. DNA, using their mechanical properties. The MEMS device provided real-time monitoring of reaction dynamics without any surface or molecular modifications. A microfluidic device with a side opening was fabricated for the optimal performance of the MEMS device to operate at the air-liquid interface for performing bioassays in liquid while actuating/sensing in air. The minimal immersion of the MEMS device in the channel provided long-term measurement stability (>10 h). Importantly, the method allowed monitoring effects of multiple solutions on the same macromolecule bundle (demonstrated with DNA bundles) without compromising the reproducibility. We monitored two different types of effects on the mechanical responses of DNA bundles (stiffness and viscous losses) exposed to pH changes (2.1 to 4.8) and different Ag+ concentrations (1 μM to 0.1 M).
Dendrite Suppression by Shock Electrodeposition in Charged Porous Media
Authors: Han Ji-Hyung , Wang Miao , Bai Peng , Brushett Fikile R. , Bazant Martin Z. 
Published: June 2016

AbstractIt is shown that surface conduction can stabilize electrodeposition in random, charged porous media at high rates, above the diffusion-limited current. After linear sweep voltammetry and impedance spectroscopy, copper electrodeposits are visualized by scanning electron microscopy and energy dispersive spectroscopy in two different porous separators (cellulose nitrate, polyethylene), whose surfaces are modified by layer-by-layer deposition of positive or negative charged polyelectrolytes. Above the limiting current, surface conduction inhibits growth in the positive separators and produces irregular dendrites, while it enhances growth and suppresses dendrites behind a deionization shock in the negative separators, also leading to improved cycle life. The discovery of stable uniform growth in the random media differs from the non-uniform growth observed in parallel nanopores and cannot be explained by classic quasi-steady “leaky membrane” models, which always predict instability and dendritic growth. Instead, the experimental results suggest that transient electro-diffusion in random porous media imparts the stability of a deionization shock to the growing metal interface behind it. Shock electrodeposition could be exploited to enhance the cycle life and recharging rate of metal batteries or to accelerate the fabrication of metal matrix composite coatings.
Size-, electric-field- and frequency-dependent third-order nonlinear optical properties of hydrogenated silicon nanoclusters
Authors: Li Haipeng , Xu Hu , Shen Xiaopeng , Han Kui , Bi Zetong , Xu Runfeng 
Published: June 2016

AbstractWe investigated the electronic properties and second hyperpolarizabilities of hydrogenated silicon nanoclusters (H-SiNCs) by using the density functional theory method. The effects of cluster size, external electric field and incident frequency on the second hyperpolarizability were also examined, respectively. We found that small H-SiNCs exhibit large second hyperpolarizability. With the increase of the number of silicon atoms in H-SiNCs, the frontier molecular orbital energy gap decreases, attributed to the enhancement of the second hyperpolarizability. Interestingly, we also found the electric-field-induced gigantic enhancement of the second hyperpolarizability for H-SiNCs due to the change of electron density distributions. In addition, our results demonstrate a significant dependence on the frequency of incident light.
Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer
Authors: Dinpajooh Mohammadhasan , Martin Daniel R. , Matyushov Dmitry V. 
Published: June 2016

AbstractEnzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.
Endomembrane-associated RSD-3 is important for RNAi induced by extracellular silencing RNA in both somatic and germ cells of Caenorhabditis elegans
Authors: Imae Rieko , Dejima Katsufumi , Kage-Nakadai Eriko , Arai Hiroyuki , Mitani Shohei 
Published: June 2016

AbstractRNA silencing signals in C. elegans spread among cells, leading to RNAi throughout the body. During systemic spread of RNAi, membrane trafficking is thought to play important roles. Here, we show that RNAi Spreading Defective-3 (rsd-3), which encodes a homolog of epsinR, a conserved ENTH (epsin N-terminal homology) domain protein, generally participates in cellular uptake of silencing RNA. RSD-3 is previously thought to be involved in systemic RNAi only in germ cells, but we isolated several deletion alleles of rsd-3, and found that these mutants are defective in the spread of silencing RNA not only into germ cells but also into somatic cells. RSD-3 is ubiquitously expressed, and intracellularly localized to the trans-Golgi network (TGN) and endosomes. Tissue-specific rescue experiments indicate that RSD-3 is required for importing silencing RNA into cells rather than exporting from cells. Structure/function analysis showed that the ENTH domain alone is sufficient, and membrane association of the ENTH domain is required, for RSD-3 function in systemic RNAi. Our results suggest that endomembrane trafficking through the TGN and endosomes generally plays an important role in cellular uptake of silencing RNA.
An excellent navigation system and experience in craniomaxillofacial navigation surgery: a double-center study
Authors: Dai Jiewen , Wu Jinyang , Wang Xudong , Yang Xudong , Wu Yunong , Xu Bing , Shi Jun , Yu Hongbo , Cai Min , Zhang Wenbin , Zhang Lei , Sun Hao , Shen Guofang , Zhang Shilei 
Published: June 2016

AbstractNumerous problems regarding craniomaxillofacial navigation surgery are not well understood. In this study, we performed a double-center clinical study to quantitatively evaluate the characteristics of our navigation system and experience in craniomaxillofacial navigation surgery. Fifty-six patients with craniomaxillofacial disease were included and randomly divided into experimental (using our AccuNavi-A system) and control (using Strker system) groups to compare the surgical effects. The results revealed that the average pre-operative planning time was 32.32 mins vs 29.74 mins between the experimental and control group, respectively (p > 0.05). The average operative time was 295.61 mins vs 233.56 mins (p > 0.05). The point registration orientation accuracy was 0.83 mm vs 0.92 mm. The maximal average preoperative navigation orientation accuracy was 1.03 mm vs 1.17 mm. The maximal average persistent navigation orientation accuracy was 1.15 mm vs 0.09 mm. The maximal average navigation orientation accuracy after registration recovery was 1.15 mm vs 1.39 mm between the experimental and control group. All patients healed and their function and profile improved. These findings demonstrate that although surgeons should consider the patients’ time and monetary costs, our qualified navigation surgery system and experience could offer an accurate guide during a variety of craniomaxillofacial surgeries.
A Novel Long-term, Multi-Channel and Non-invasive Electrophysiology Platform for Zebrafish
Authors: Hong SoonGweon , Lee Philip , Baraban Scott C. , Lee Luke P. 
Published: June 2016

AbstractZebrafish are a popular vertebrate model for human neurological disorders and drug discovery. Although fecundity, breeding convenience, genetic homology and optical transparency have been key advantages, laborious and invasive procedures are required for electrophysiological studies. Using an electrode-integrated microfluidic system, here we demonstrate a novel multichannel electrophysiology unit to record multiple zebrafish. This platform allows spontaneous alignment of zebrafish and maintains, over days, close contact between head and multiple surface electrodes, enabling non-invasive long-term electroencephalographic recording. First, we demonstrate that electrographic seizure events, induced by pentylenetetrazole, can be reliably distinguished from eye or tail movement artifacts, and quantifiably identified with our unique algorithm. Second, we show long-term monitoring during epileptogenic progression in ascn1labmutant recapitulating human Dravet syndrome. Third, we provide an example of cross-over pharmacology antiepileptic drug testing. Such promising features of this integrated microfluidic platform will greatly facilitate high-throughput drug screening and electrophysiological characterization of epileptic zebrafish.
Birds have primate-like numbers of neurons in the forebrain
Authors: Olkowicz Seweryn , Kocourek Martin , Lučan Radek K. , Porteš Michal , Fitch W. Tecumseh , Herculano-Houzel Suzana , Němec Pavel 
Published: June 2016

Significance
Birds are remarkably intelligent, although their brains are small. Corvids and some parrots are capable of cognitive feats comparable to those of great apes. How do birds achieve impressive cognitive prowess with walnut-sized brains? We investigated the cellular composition of the brains of 28 avian species, uncovering a straightforward solution to the puzzle: brains of songbirds and parrots contain very large numbers of neurons, at neuronal densities considerably exceeding those found in mammals. Because these “extra” neurons are predominantly located in the forebrain, large parrots and corvids have the same or greater forebrain neuron counts as monkeys with much larger brains. Avian brains thus have the potential to provide much higher “cognitive power” per unit mass than do mammalian brains.
Late Cenozoic onset of the latitudinal diversity gradient of North American mammals
Authors: Marcot Jonathan D. , Fox David L. , Niebuhr Spencer R. 
Published: June 2016

SignificanceThe number of species declines from the Earth's equator to the poles—a pattern known as the latitudinal diversity gradient (LDG)—for nearly every group of living organisms in which the LDG has been studied. However, our analyses of fossil occurrences demonstrate that the LDG of terrestrial mammals was substantially weaker than it is today, if not absent entirely, for most of the past 65 My. We also show the strength of the LDG varies with global temperature and is weakest during globally warm periods. We find that the modern LDG became established sometime in only in the last 4 My, most likely as a result of declining global temperatures.
Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks
Authors: Willis Nicholas A. , Zhou Chunshui , Elia Andrew E. H. , Murray Johanne M. , Carr Antony M. , Elledge Stephen J. , Rhind Nicholas 
Published: June 2016

Significance
The cellular response to DNA damage during DNA replication promotes survival and genome maintenance. It involves a network of kinases that phosphorylate a variety of target proteins. Although the protein kinases involved have been studied extensively in fission yeast, only a handful of their targets have been identified. We used an unbiased approach to profile protein phosphorylation in response to DNA damage during DNA replication. We found target proteins involved in gene expression, stress response, regulation of mitosis and cytokinesis, and DNA replication and repair, many of which are required for resistance to DNA damage. These protein targets are conserved in budding yeast and human cells, demonstrating the deep conservation of the response.
Hepatitis C virus depends on E-cadherin as an entry factor and regulates its expression in epithelial-to-mesenchymal transition
Authors: Li Qisheng , Sodroski Catherine , Lowey Brianna , Schweitzer Cameron J. , Cha Helen , Zhang Fang , Liang T. Jake 
Published: June 2016

Significance
Hepatitis C virus (HCV) infects hepatocytes via an intricate series of interactions with the host cell machinery. Recently, we identified E-cadherin as a host dependency factor mediating HCV entry through integrative functional genomics studies. E-cadherin silencing restricted HCV entry and infection in hepatocytes. Mechanistic studies demonstrated that E-cadherin is a prerequisite for the cell-surface localization of claudin-1 and OCLN, two major HCV coreceptors. Moreover, HCV-induced loss of E-cadherin is associated with cancer-related cellular changes. Our study suggests that a dynamic interplay among E-cadherin, tight junction coreceptors, and epithelial-to-mesenchymal transition exists and plays an important role in regulating HCV entry. E-cadherin thereby represents a missing host factor in the comprehensive understanding of the molecular mechanisms and cellular regulatory events underlying HCV entry and pathogenesis.
Rational design and validation of a vanilloid-sensitive TRPV2 ion channel
Authors: Yang Fan , Vu Simon , Yarov-Yarovoy Vladimir , Zheng Jie 
Published: June 2016

Significance
Understanding how small molecules regulate activities of ion channels, which form the second largest family of drug targets, is important for both basic and translational research. By learning from how capsaicin activates TRPV1, we have introduced high-affinity binding of both capsaicin and resiniferatoxin to TRPV2 with only four point mutations. This successful outcome not only validated the working model for capsaicin–TRPV1 interactions but also suggested that vanilloids such as resiniferatoxin use a similar structural mechanism. Our findings further revealed previously unrecognized structural requirements for capsaicin-induced TRPV1 activation, which will guide future efforts to design drug candidates targeting this important pain sensor. In addition, the modified TRPV2–resiniferatoxin pair has the potential to be further engineered as a tool for chemogenetic studies.
Natural and anthropogenic drivers of calcium depletion in a northern forest during the last millennium
Authors: Leys Bérangère A. , Likens Gene E. , Johnson Chris E. , Craine Joseph M. , Lacroix Brice , McLauchlan Kendra K. 
Published: June 2016

Significance
This research breaks new ground by showing that, contrary to generally accepted theories of ecosystem development, calcium depletion has been occurring for millennia as a natural consequence of long-term ecosystem development. This natural process predisposed forest ecosystems in the region to detrimental responses to acid rain in the 20th century. We also show that nitrogen availability was increasing concurrently with the depletion of calcium. This is the first study, to our knowledge, to reconstruct continuous changes in nutrient availability for a northern forest ecosystem on the millennial time scale. The results alter our assessments of the speed and trajectory of nutrient limitation in forests and suggest that reformulation of global models of forest productivity may be necessary.
Asymmetric partitioning of transfected DNA during mammalian cell division
Authors: Wang Xuan , Le Nhung , Denoth-Lippuner Annina , Barral Yves , Kroschewski Ruth 
Published: June 2016

Significance
What happens to foreign DNA in mammalian cells during divisions? We provide evidence that the mitotic machinery helps cope with cytoplasmic clusters of plasmid DNA, a prototype of foreign DNA. The endoplasmic reticulum embraces these clusters, probably restricting their mobility and preventing them from interfering with chromosomal DNA. Subsequently, these clusters predominantly partition into the daughter cell with the young centrosome and with successive divisions end up in a decreasing fraction of cells within the growing population. This process is similar to the partition of noncentromeric DNA in budding yeast and cell fates in stem cells. The behavior difference of the two centrosomes documented here might also facilitate asymmetric partition of other cellular components.
Enhancing cellulase production by overexpression of xylanase regulator protein gene, xlnR, in Talaromyces cellulolyticus cellulase hyperproducing mutant strain
Authors: Okuda Naoyuki , Fujii Tatsuya , Inoue Hiroyuki , Ishikawa Kazuhiko , Hoshino Tamotsu 
Published: June 2016

Abstract
We obtained strains with the xylanase regulator gene, xlnR, overexpressed (HXlnR) and disrupted (DXlnR) derived from Talaromyces cellulolyticus strain C-1, which is a cellulase hyperproducing mutant. Filter paper degrading enzyme activity and cellobiohydrolase I gene expression was the highest in HXlnR, followed by C-1 and DXlnR. These results indicate that the enhancement of cellulase productivity was succeeded by xlnR overexpression.
On normal approximations to symmetric hypergeometric laws
Authors: Mattner Lutz , Schulz Jona 
Published: June 2016

The Kolmogorov distances between a symmetric hypergeometric law with standard deviation

σ
\sigma

and its usual normal approximations are computed and shown to be less than

1

/

(

8
π

σ
)

1/(\sqrt {8\pi }\,\sigma )

, with the order

1

/

σ

1/\sigma

and the constant

1

/

8
π

1/\sqrt {8\pi }

being optimal. The results of Hipp and Mattner (2007) for symmetric binomial laws are obtained as special cases.

Connections to Berry-Esseen type results in more general situations concerning sums of simple random samples or Bernoulli convolutions are explained.

Auxiliary results of independent interest include rather sharp normal distribution function inequalities, a simple identifiability result for hypergeometric laws, and some remarks related to Lévy’s concentration-variance inequality.
Permanent and Temporary Policy Incentives for Conservation under Stochastic Returns from Competing Land Uses
Authors: Shah Payal , Ando Amy W. 
Published: June 2016

AbstractRapid conversion of private land for agricultural and urban use has raised concern worldwide over the loss of ecological services. To inform conservation policy, we model privately optimal land use decisions using a real options framework that assumes both the ecological and commercial values of land are stochastic and that land conversion is irreversible. We analyze permanent and temporary land conservation policy incentives using this dynamic framework to guide policy makers interested in designing efficient payment mechanisms to achieve ecological preservation goals. We find that while the financial cost of temporary policy incentives is generally much lower than permanent policy incentives, this difference is very small in scenarios with high discount rates and lower uncertainties in conversion returns and lower expected trend in conservation returns. Alternately, the financial cost of temporary conservation is substantially lower than that of permanent conservation when the expected trend in conservation returns and uncertainties in conservation and conversion returns is high and the discount rate is low. Comparison with net present value and single‐source uncertainty models indicates that the presence of a second uncertainty increases the option value of delaying conversion, and shows that permanent and temporary policy incentives based on either of the two simpler models can be seriously misguided if multiple uncertainties are present. We illustrate the analytical results with a case study of tropical deforestation in Indonesia where private landowners can either conserve forests and earn carbon credits, or convert to palm oil agriculture and earn profits from the sale of palm oil.
Temperature Changes, Household Consumption, and Internal Migration: Evidence from Tanzania
Authors: Hirvonen Kalle 
Published: June 2016

AbstractLarge rural‐urban wage gaps observed in many developing countries are suggestive of barriers to migration that keep potential migrants in rural areas. Using long panel data spanning nearly two decades, I study the extent to which migration rates are constrained by liquidity constraints in rural Tanzania. The analysis begins by quantifying the impact of weather variation on household welfare. The results show how household consumption co‐moves with temperature, rendering households vulnerable to local weather events. These temperature‐induced income shocks are then found to inhibit long‐term migration among men, thus preventing them from tapping into the opportunities brought about by geographical mobility.
CONDOP: an R package for CONdition-Dependent Operon Predictions
Authors: Fortino Vittorio , Tagliaferri Roberto , Greco Dario 
Published: June 2016

Abstract
Summary: The use of high-throughput RNA sequencing to predict dynamic operon structures in prokaryotic genomes has recently gained popularity in bioinformatics. We provide the R implementation of a novel method that uses transcriptomic features extracted from RNA-seq transcriptome profiles to develop ensemble classifiers for condition-dependent operon predictions. The CONDOP package provides a deeper insight into RNA-seq data analysis and allows scientists to highlight the operon organization in the context of transcriptional regulation with a few lines of code.
Availability and Implementation: CONDOP is implemented in R and is freely available at CRAN.
Contact: vittorio.fortino@helsinki.fi
Supplementary information: Supplementary data are available at Bioinformatics online.