bluuebunny/crossref_metadata_2025_split huggingface dataset:
MicroRNA-33 regulates sterol regulatory element-binding protein 1 expression in mice
Authors: Horie Takahiro , Nishino Tomohiro , Baba Osamu , Kuwabara Yasuhide , Nakao Tetsushi , Nishiga Masataka , Usami Shunsuke , Izuhara Masayasu , Sowa Naoya , Yahagi Naoya , Shimano Hitoshi , Matsumura Shigenobu , Inoue Kazuo , Marusawa Hiroyuki , Nakamura Tomoyuki , Hasegawa Koji , Kume Noriaki , Yokode Masayuki , Kita Toru , Kimura Takeshi , Ono Koh 
Published: December 2013

AbstractMicroRNAs (miRs) are small non-protein-coding RNAs that bind to specific mRNAs and inhibit translation or promote mRNA degradation. Recent reports have indicated that miR-33, which is located within the intron of sterol regulatory element-binding protein (SREBP) 2, controls cholesterol homoeostasis and may be a potential therapeutic target for the treatment of atherosclerosis. Here we show that deletion of miR-33 results in marked worsening of high-fat diet-induced obesity and liver steatosis. Using miR-33−/−Srebf1+/− mice, we demonstrate that SREBP-1 is a target of miR-33 and that the mechanisms leading to obesity and liver steatosis in miR-33−/− mice involve enhanced expression of SREBP-1. These results elucidate a novel interaction between SREBP-1 and SREBP-2 mediated by miR-33 in vivo.
A proposal for a novel impact factor as an alternative to the JCR impact factor
Authors: Yang Zu-Guo , Zhang Chun-Ting 
Published: December 2013

AbstractOne disadvantage of the JCR impact factor, the most commonly used assessment tool for ranking and evaluating scientific journals, is its inability in distinguishing among different shapes of citation distribution curves, leading to unfair evaluation of journals in some cases. This paper aims to put forward an alternative impact factor (IF′) that can properly reflect citation distributions. The two impact factors are linearly and positively correlated and have roughly the same order of magnitude. Because of the ability of IF′ in distinguishing among different shapes of citation distribution curves, IF′ may properly reflect the academic performance of a scientific journal in a way that is different from the JCR impact factor with some unique features that reward journals with highly cited papers. Therefore, it is suggested that IF′ could be used to complement the JCR impact factor.
A novel reduced leakage current modulation technique for Z‐source inverter used in photovoltaic systems
Authors: Erginer Volkan , Sarul Mustafa Hadi 
Published: December 2013

In this study a novel modulation technique is proposed to reduce common mode leakage current in a three‐phase Z‐Source inverter used in a photovoltaic (PV) system. The proposed method reduces common mode current as well as common mode voltage (CMV); moreover, it reduces inverter output current total harmonic distortion at high switching frequencies. At first, previously presented techniques are summarised. Then, proposed technique is presented theoretically. Finally, conventional space vector modulation and the proposed modulation technique are simulated for a 10 kW PV power generation system. The validity of the proposed modulation technique is verified through MATLAB/Simulink. Simulations are performed for different load power factors and switching frequencies with considering real application parameters to provide a certain comparison between conventional and proposed modulation techniques. The results are analysed considering both CMV, leakage current and inverter output current quality, and the results verify effectiveness of the proposed technique.
Laplace-Runge-Lenz vector in quantum mechanics in noncommutative space
Authors: Gáliková Veronika , Kováčik Samuel , Prešnajder Peter 
Published: December 2013

The main point of this paper is to examine a “hidden” dynamical symmetry connected with the conservation of Laplace-Runge-Lenz vector (LRL) in the hydrogen atom problem solved by means of non-commutative quantum mechanics (NCQM). The basic features of NCQM will be introduced to the reader, the key one being the fact that the notion of a point, or a zero distance in the considered configuration space, is abandoned and replaced with a “fuzzy” structure in such a way that the rotational invariance is preserved. The main facts about the conservation of LRL vector in both classical and quantum theory will be reviewed. Finally, we will search for an analogy in the NCQM, provide our results and their comparison with the QM predictions. The key notions we are going to deal with are non-commutative space, Coulomb-Kepler problem, and symmetry.
Regulation of Son of sevenless by the membrane-actin linker protein ezrin
Authors: Geißler Katja J. , Jung M. Juliane , Riecken Lars Björn , Sperka Tobias , Cui Yan , Schacke Stephan , Merkel Ulrike , Markwart Robby , Rubio Ignacio , Than Manuel E. , Breithaupt Constanze , Peuker Sebastian , Seifert Reinhard , Kaupp Ulrich Benjamin , Herrlich Peter , Morrison Helen 
Published: December 2013

Significance
Activity of the small GTPase Ras (rat sarcoma) needs to be tightly regulated because aberrant activity has a potent oncogenic effect, causing several forms of cancer as well as developmental disorders known as RASopathies. We have identified the ezrin, radixin, and moesin protein family as a previously unknown component in the control of Ras activity. Ezrin functions in the assembly of a protein complex that facilitates the encounter of Ras with its activating enzyme, Son of sevenless. Thus ezrin mediates a spatiotemporal control of Ras activity that helps coordinate and safeguard Ras signaling output.
Phosphorylated K-Ras limits cell survival by blocking Bcl-xL sensitization of inositol trisphosphate receptors
Authors: Sung Pamela J. , Tsai Frederick D. , Vais Horia , Court Helen , Yang Jun , Fehrenbacher Nicole , Foskett J. Kevin , Philips Mark R. 
Published: December 2013

Significance
K-Ras is mutated more often than any other oncogene, making the protein and the pathways it regulates attractive targets for anticancer drug discovery. We have shown that phosphorylation of serine 181 in the membrane-targeting region of K-Ras causes the protein to translocate from plasma membrane to intracellular membranes. Translocation is associated with toxicity but the mechanism has remained undefined. Here we show that phospho–K-Ras associates with inositol trisphosphate receptors (IP3Rs) on the endoplasmic reticulum (ER) and thereby blocks one of the prosurvival activities of Bcl-xL, which is to sensitize IP3Rs and thereby allow constitutive transfer of calcium from ER to mitochondria where it is required for efficient respiration. This pathway could be exploited to limit the oncogenic activity of mutant K-Ras.
Resolving the roles of immunity, pathogenesis, and immigration for rabies persistence in vampire bats
Authors: Blackwood Julie C. , Streicker Daniel G. , Altizer Sonia , Rohani Pejman 
Published: December 2013

SignificanceBats are a frequent source of pathogen spillover to humans and livestock, and a reservoir for emerging infectious diseases. Transmission mechanisms within bat populations remain enigmatic, precluding effective management of zoonotic infections. Vampire bats transmit rabies virus throughout Latin America, causing lethal human rabies and thousands of livestock deaths every year. By selecting among competing transmission models applied to spatially replicated, longitudinal field data, we find that most rabies virus exposures are nonlethal and instead immunize bats, thus facilitating viral persistence. Further, frequent interactions among bats from different colonies are necessary to maintain the chain of transmission. We also evaluate the efficacy of bat culling and demonstrate that it has minimal effects on seroprevalence when spatially coordinated control is absent.
Presynaptic mitochondrial morphology in monkey prefrontal cortex correlates with working memory and is improved with estrogen treatment
Authors: Hara Yuko , Yuk Frank , Puri Rishi , Janssen William G. M. , Rapp Peter R. , Morrison John H. 
Published: December 2013

Significance
Human and nonhuman primates are vulnerable to age- and menopause-related decline in working memory, a cognitive function reliant on the energy-demanding excitation of prefrontal cortex (PFC) neurons. The number and strength of presynaptic boutons providing inputs to these PFC neurons regulate their excitability. We show that poor working memory in rhesus monkeys is associated with a higher incidence of presynaptic boutons harboring malformed, donut-shaped mitochondria that form abnormally small synaptic contacts. Surgically induced menopause results in working memory impairment and a concomitant increase in presynaptic donut-shaped mitochondria, both of which are reversed by estradiol treatment. Our findings suggest that hormone replacement therapy benefits cognitive aging, in part, by promoting mitochondrial and synaptic health in the PFC.
Structural snapshots illustrate the catalytic cycle of β-galactocerebrosidase, the defective enzyme in Krabbe disease
Authors: Hill Chris H. , Graham Stephen C. , Read Randy J. , Deane Janet E. 
Published: December 2013

Significance
Defects in the enzyme β-galactocerebrosidase (GALC) result in the devastating neurodegenerative disorder Krabbe disease. GALC is responsible for the degradation and recycling of glycosphingolipids that form the primary lipid component of the myelin sheath that insulates nerve cells. A detailed understanding of how GALC processes substrate will facilitate the development of new drug therapies for Krabbe disease. This study reveals a series of structural snapshots of GALC captured during different steps of the catalytic cycle. These structures identify specific residues within the active site that undergo significant movements during substrate cleavage, providing key insight into the catalytic mechanism of GALC.
Bioluminescent imaging of drug efflux at the blood–brain barrier mediated by the transporter ABCG2
Authors: Bakhsheshian Joshua , Wei Bih-Rong , Chang Ki-Eun , Shukla Suneet , Ambudkar Suresh V. , Simpson R. Mark , Gottesman Michael M. , Hall Matthew D. 
Published: December 2013

Significance
The blood–brain barrier (BBB) prevents ingress of small molecules into the brain partly by expression of drug efflux transporters. Although several transporters are known to be involved, the role ABCG2 plays in this process is not clear. We demonstrate the ability to image ABCG2 function at the BBB by using luciferin in a luciferase-expressing mouse. This represents a direct measurement of ABCG2 function at the BBB, and demonstrates that ABCG2 does play a functional role at the BBB.
Protein recognition and selection through conformational and mutually induced fit
Authors: Wang Qian , Zhang Pengzhi , Hoffman Laurel , Tripathi Swarnendu , Homouz Dirar , Liu Yin , Waxham M. Neal , Cheung Margaret S. 
Published: December 2013

Significance
Protein–protein interactions drive most every biological process, but in many instances the domains mediating recognition are disordered. How specificity in binding is attained in the absence of defined structure is a fascinating problem but not well understood. Calmodulin presents a unique opportunity to investigate mechanisms for selectivity given that it interacts with several hundred different potential targets. In our work, a combined experimental and theoretical approach is taken to define how target selectivity occurs at the molecular level. Our study shows that the binding interactions require mutually induced conformational changes in both calmodulin and the target protein, and broadly informs how intrinsically disordered proteins can achieve both high affinity and high specificity.
Mantle–slab interaction and redox mechanism of diamond formation
Authors: Palyanov Yuri N. , Bataleva Yuliya V. , Sokol Alexander G. , Borzdov Yuri M. , Kupriyanov Igor N. , Reutsky Vadim N. , Sobolev Nikolai V. 
Published: December 2013

Significance
The primary question that we address in this study is what happens when a carbonate-bearing crust is subducted to depths where the Earth’s mantle is metal saturated. Subduction plays an important role in the evolution of the Earth’s interiors, but the mechanism of the interaction between the oxidized slab and reduced mantle remains unclear. Here we report the results of high-pressure redox-gradient experiments on the interaction between Mg-Ca-carbonate and metallic iron, modeling the processes at the mantle–slab boundary, and present mechanisms of diamond formation ahead of and behind the redox front. We demonstrate that the redox mechanism revealed in this study can explain the contrasting heterogeneity of natural diamonds on the composition of inclusions, carbon isotopic composition, and nitrogen impurity content.
Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds
Authors: Projecto-Garcia Joana , Natarajan Chandrasekhar , Moriyama Hideaki , Weber Roy E. , Fago Angela , Cheviron Zachary A. , Dudley Robert , McGuire Jimmy A. , Witt Christopher C. , Storz Jay F. 
Published: December 2013

SignificanceHummingbirds have exceedingly high oxygen demands because of their elevated rates of aerobic metabolism, and yet they thrive in high-altitude environments in the Andes where oxygen is scarce. Here we report the finding that when hummingbird species colonized new elevational zones, evolutionary changes in the respiratory properties of hemoglobin were repeatedly mediated by the same amino acid replacements. Specifically, ancestral sequence reconstruction and protein engineering experiments revealed that parallel adaptation of hemoglobin function in multiple species is attributable to repeated amino acid replacements at a single pair of interacting sites. This striking parallelism at the molecular level suggests a surprising degree of reproducibility and predictability in adaptive protein evolution.
Coevolutionary signals across protein lineages help capture multiple protein conformations
Authors: Morcos Faruck , Jana Biman , Hwa Terence , Onuchic José N. 
Published: December 2013

Significance
We show that directly coupled evolutionary residue pairs provide a distinct footprint of conformational diversity in protein families. This is revealed as competing residue contacts unique to distinct configurations of proteins with multiple conformations. We demonstrate that combining this information with physical models of proteins is sufficient to uncover conformational diversity for several protein families. We discovered that such directly coupled residues not only allow us to accurately transition between apo and holo conformations but also help to uncover intermediate states that are not easily accessible to experimental or other computational methods. This enhanced sampling of the functional conformational space of proteins may have broad implications in protein structure determination and the design of ligands that can trap intermediate states.
Stoichiometry for activation of neuronal α7 nicotinic receptors
Authors: Andersen Natalia , Corradi Jeremías , Sine Steven M. , Bouzat Cecilia 
Published: December 2013

Significance
Nicotinic α7 receptors are neurotransmitter-gated ion channels that participate in cognitive, cytoprotective, and anti-inflammatory processes and have emerged as targets for neurological disorders and therapeutic drugs. They are associated with extrasynaptic volume transmission where they are exposed to low ACh concentrations and thus function with partial occupancy of their five identical binding sites. By generating α7 receptors with different numbers of functional ACh binding sites and measuring open-channel lifetimes of individual receptors, we find that occupancy of one site produces a maximal response and that the additional sites enhance agonist sensitivity. Thus, ACh occupancy of only one of five sites in α7 produces a maximal response, adapting it to extrasynaptic volume transmission in neuronal and nonneuronal cells.
Formation of highly porous aerosol particles by atmospheric freeze-drying in ice clouds
Authors: Adler Gabriela , Koop Thomas , Haspel Carynelisa , Taraniuk Ilya , Moise Tamar , Koren Ilan , Heiblum Reuven H. , Rudich Yinon 
Published: December 2013

Significance
Aerosols cycling through clouds affect particle morphological and chemical properties, thus modifying aerosol effects on cloud microphysics and climate. Previous studies have focused on aerosol processing in warm clouds via aqueous-phase reactions. Here we investigate the physical modifications of aerosols following processing within ice clouds using a unique laboratory setup that simulates ice cloud processes. The processed particles have a porous structure due to phase separation upon freezing, subsequent glass transition, and ice sublimation. Such modified aerosols can be better ice and cloud condensation nuclei and scatter less light. These changes have implications for aerosol–cloud interactions and optical properties of aerosols in the vicinity of clouds.
Relaxin-3/RXFP3 system regulates alcohol-seeking
Authors: Ryan Philip J. , Kastman Hanna E. , Krstew Elena V. , Rosengren K. Johan , Hossain Mohammed Akhter , Churilov Leonid , Wade John D. , Gundlach Andrew L. , Lawrence Andrew J. 
Published: December 2013

Significance
Relapse and hazardous drinking represent the most difficult clinical problems in treating patients with alcohol use disorders. Increasing our understanding of the brain circuits and chemicals that regulate alcohol intake and relapse offers the potential for more targeted therapeutic approaches to assist in relapse prevention. Using a rat model of alcohol use and alcohol-seeking, we provide the first evidence that a neuropeptide, namely relaxin-3, acts upon specific receptors (relaxin family peptide 3) within the brain to regulate alcohol self-administration and relapse-like behavior. In the case of relapse-like alcohol-seeking, this system appears particularly involved in stress-mediated relapse via actions within a brain region called the bed nucleus of the stria terminalis.
Role for regulated phosphatase activity in generating mitotic oscillations in
Xenopus
cell-free extracts
Authors: Zhang Tongli , Tyson John J. , Novák Béla 
Published: December 2013

Significance
A long-standing puzzle in the cell-cycle field is how it can be that the anaphase-promoting complex/cyclosome (APC/C) gets activated only when cyclin-dependent kinase 1 (Cdk1) activity reaches a very high level in metaphase but stays active even after Cdk1 activity drops to much lower levels as cells exit mitosis. In this manuscript, we propose that the regulation of a protein phosphatase 2A (PP2A:B55δ) by Greatwall kinase might provide a solution to this puzzle. Our proposal is consistent with what is already known about the regulation of Cdk1 and PP2A:B55δ in frog eggs, and it leads to testable predictions.
Optical control of an ion channel gate
Authors: Lemoine Damien , Habermacher Chloé , Martz Adeline , Méry Pierre-François , Bouquier Nathalie , Diverchy Fanny , Taly Antoine , Rassendren François , Specht Alexandre , Grutter Thomas 
Published: December 2013

Significance
Engineered light-sensitive ion channels offer the opportunity to govern electrical activity of neurons. To date, developed strategies have relied on specific actions on either ligand-binding or permeation pathways. Here we developed a unique and versatile method, in which the gating machinery of an ATP-activated channel (purinergic P2X receptor) was reprogrammed to respond to light. We found that channels covalently modified by azobenzene-containing reagents at the transmembrane segments could be reversibly turned on and off by light, without the need of the natural ligand (here ATP). We demonstrate photocontrol of neuronal activity by a light-gated P2X receptor, in which the natural sensitivity to ATP was genetically removed. These light-gated P2X receptors represent valuable tools for investigating their physiological functions.
Couple Bargaining or Socio-Economic Status?
Authors: Baizán Pau , Domínguez Marta , González María José 
Published: December 2013

ABSTRACT
The quality of time dedicated to child care has potentially positive effects on children's life chances. However, the determinants of parental time allocation to child care remain largely unexplored. We assess two main explanations for differences among parents in the amount of time spent with children. The first, based on the relative resources hypothesis, links variation in time spent with children to the relative attributes (occupation, education or income) of one partner with the other. The second, derived from the social status hypothesis, suggests that variation in time spent with children can be attributed to the relative social position of the couple (i.e. higher status couples spend more time with children regardless of within-couple difference). To investigate these questions, we use a sample of parents living in a partnership with children younger than 10 years old from the 2002 to 2003 Spanish Time Use Survey (STUS) (n = 7438). We find little support for the ‘relative resources hypothesis’, although it has some explanatory power on supervisory and routine activities performed with children. Instead, consistent with the ‘social status hypothesis’, we find that time spent on child care is attributable to the social position of the couple, regardless of between-parent differences in income or education. The ‘social status hypothesis’ is especially relevant for explaining the time that parents devote to activities that have a higher potential for the development of the child's cognitive and social capabilities.
NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
Authors: Leggett Richard M. , Clavijo Bernardo J. , Clissold Leah , Clark Matthew D. , Caccamo Mario 
Published: December 2013

Abstract
Summary: Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assemblies and other downstream bioinformatics analyses such as the characterization of structural variants. However, LMP libraries are intrinsically noisy and to maximize their value, post-sequencing data analysis is required. Standardizing laboratory protocols and the selection of sequenced reads for downstream analysis are non-trivial tasks. NextClip is a tool for analyzing reads from LMP libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads.
Availability and implementation: Source code, user guide and example data are available from https://github.com/richardmleggett/nextclip/.
Contact: Richard.Leggett@tgac.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
The implications of the declining energy return on investment of oil production
Authors: Murphy David J. 
Published: December 2013

Declining production from conventional oil resources has initiated a global transition to unconventional oil, such as tar sands. Unconventional oil is generally harder to extract than conventional oil and is expected to have a (much) lower energy return on (energy) investment (EROI). Recently, there has been a surge in publications estimating the EROI of a number of different sources of oil, and others relating EROI to long-term economic growth, profitability and oil prices. The following points seem clear from a review of the literature: (i) the EROI of global oil production is roughly 17 and declining, while that for the USA is 11 and declining; (ii) the EROI of ultra-deep-water oil and oil sands is below 10; (iii) the relation between the EROI and the price of oil is inverse and exponential; (iv) as EROI declines below 10, a point is reached when the relation between EROI and price becomes highly nonlinear; and (v) the minimum oil price needed to increase the oil supply in the near term is at levels consistent with levels that have induced past economic recessions. From these points, I conclude that, as the EROI of the average barrel of oil declines, long-term economic growth will become harder to achieve and come at an increasingly higher financial, energetic and environmental cost.