bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enantio-Relay Catalysis Constructs Chiral Biaryl Alcohols over Cascade Suzuki Cross-Coupling-Asymmetric Transfer Hydrogenation
Authors: Zhang Dacheng , Gao Xiaoshuang , Cheng Tanyu , Liu Guohua 
Published: May 2014

AbstractThe construction of chiral biaryl alcohols using enantio-relay catalysis is a particularly attractive synthetic method in organic synthesis. However, overcoming the intrinsic incompatibility of distinct organometallic complexes and the reaction conditions used are significant challenges in asymmetric catalysis. To overcome these barriers, we have taken advantage of an enantio-relay catalysis strategy and a combined dual-immobilization approach. We report the use of an imidazolium-based organopalladium-functionalized organic–inorganic hybrid silica and ethylene-coated chiral organoruthenium-functionalized magnetic nanoparticles to catalyze a cascade Suzuki cross-coupling–asymmetric transfer hydrogenation reaction to prepare chiral biaryl alcohols in a two-step, one-pot process. As expected, the site-isolated active species, salient imidazolium phase-transfer character and high ethylene-coated hydrophobicity can synergistically boost the catalytic performance. Furthermore, enantio-relay catalysis has the potential to efficiently prepare a variety of chiral biaryl alcohols. Our synthetic strategy is a general method that shows the potential of developing enantio-relay catalysis towards environmentally benign and sustainable organic synthesis.
Losing the left side of the world: Rightward shift in human spatial attention with sleep onset
Authors: Bareham Corinne A. , Manly Tom , Pustovaya Olga V. , Scott Sophie K. , Bekinschtein Tristan A. 
Published: May 2014

AbstractUnilateral brain damage can lead to a striking deficit in awareness of stimuli on one side of space called Spatial Neglect. Patient studies show that neglect of the left is markedly more persistent than of the right and that its severity increases under states of low alertness. There have been suggestions that this alertness-spatial awareness link may be detectable in the general population. Here, healthy human volunteers performed an auditory spatial localisation task whilst transitioning in and out of sleep. We show, using independent electroencephalographic measures, that normal drowsiness is linked with a remarkable unidirectional tendency to mislocate left-sided stimuli to the right. The effect may form a useful healthy model of neglect and help in understanding why leftward inattention is disproportionately persistent after brain injury. The results also cast light on marked changes in conscious experience before full sleep onset.
Investigating the Impact of Asp181 Point Mutations on Interactions between PTP1B and Phosphotyrosine Substrate
Authors: Liu Mengyuan , Wang Lushan , Sun Xun , Zhao Xian 
Published: May 2014

AbstractProtein tyrosine phosphatase 1B (PTP1B) is a key negative regulator of insulin and leptin signaling, which suggests that it is an attractive therapeutic target in type II diabetes and obesity. The aim of this research is to explore residues which interact with phosphotyrosine substrate can be affected by D181 point mutations and lead to increased substrate binding. To achieve this goal, molecular dynamics simulations were performed on wild type (WT) and two mutated PTP1B/substrate complexes. The cross-correlation and principal component analyses show that point mutations can affect the motions of some residues in the active site of PTP1B. Moreover, the hydrogen bond and energy decomposition analyses indicate that apart from residue 181, point mutations have influence on the interactions of substrate with several residues in the active site of PTP1B.
Coding for Mild Cognitive Impairment
Authors: Kinder Renee 
Published: May 2014

Appropriate coding when providing skilled therapy interventions for individuals with Mild Cognitive Impairment (MCI) begins by obtaining an adequate understanding of the diagnostic criteria for the disorder.
Current diagnostic criteria for MCI include:
a. reported change in cognition, which is preferably corroborated by an informant in comparison with previous level with concern of patient, family, or clinician with one or more impaired cognitive domains for age and education.
b. decline which is evident over time and greater than expected for age and education in a variety of domains including memory, executive function, attention, language, visuospatial skills, and episodic memory.
c. not normal, not demented.
d. intact activities of daily living (Albert et al., 2011). Individual may present with mild problems with complex tasks such as paying bills, preparing a meal, and shopping and may require more time and be less efficient, with more errors during tasks.
Control of catalytic efficiency by a coevolving network of catalytic and noncatalytic residues
Authors: McMurrough Thomas A. , Dickson Russell J. , Thibert Stephanie M. F. , Gloor Gregory B. , Edgell David R. 
Published: May 2014

Significance
Maximizing structural and functional information from multiple sequence alignments is difficult for protein families that exhibit extreme sequence variation. We addressed this issue by identifying covarying positions within the sequence alignment to predict networks of coevolving amino acid residues in LAGLIDADG homing endonucleases, enzymes used for genome-engineering applications. Intriguingly, the predicted coevolving network with the highest score includes the active-site metal-binding residues and adjacent residues. We were able to modulate catalytic efficiency ∼100-fold by substitution of residues in the network. Our data show that the evolutionary trajectory and fitness landscape of LAGLIDADG active sites is constrained by a barrier of coevolving residues and imply that generating an optimal coevolving network is an important consideration when engineering these endonucleases.
Visualizing synaptic vesicle turnover and pool refilling driven by calcium nanodomains at presynaptic active zones of ribbon synapses
Authors: Vaithianathan Thirumalini , Matthews Gary 
Published: May 2014

Significance
Sensory synapses in the retina are characterized by special structures at the site of neurotransmitter release called synaptic ribbons, which transmit information about both sustained and rapidly changing visual stimuli. Because rapid signaling is important for detecting spatial and temporal contrast, we investigated the mechanism of fast neurotransmitter release at ribbon synapses, using high-resolution imaging of synaptic vesicle turnover and calcium responses. We find that nanodomains of high calcium at ribbons drive exocytosis of membrane-associated synaptic vesicles within milliseconds, accounting for the rapid component of neurotransmitter release, whereas replacement of lost vesicles occurs at membrane-distal sites on the ribbon. The results provide insight into synaptic mechanisms that enhance detection of contrast, a fundamental aspect of visual processing.
Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes
Authors: Szczelkun Mark D. , Tikhomirova Maria S. , Sinkunas Tomas , Gasiunas Giedrius , Karvelis Tautvydas , Pschera Patrizia , Siksnys Virginijus , Seidel Ralf 
Published: May 2014

Significance
Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide adaptive immunity for bacteria and archaea. They use a protein complex that targets invading nucleic acids using a bound RNA that hybridizes to complementary sequence stretches. On DNA targets, the resulting structure is an R-loop. By twisting single DNA molecules, we can directly observe R-loop formation and dissociation in two distinct types of CRISPR-Cas system. This allows us to investigate the role of different elements of the target sequence. Whereas upstream elements control the actual R-loop formation, downstream elements ensure R-loop stability, suggesting a directional R-loop formation. This provides insight into the recognition process by these enzymes, which is the crucial step to understand targeting in the rapidly emerging genetic engineering applications of CRISPR-Cas systems.
Prosurvival Bcl-2 family members affect autophagy only indirectly, by inhibiting Bax and Bak
Authors: Lindqvist Lisa M. , Heinlein Melanie , Huang David C. S. , Vaux David L. 
Published: May 2014

Significance
It is widely accepted that prosurvival B-cell lymphoma 2 (Bcl-2) family members not only inhibit apoptosis but also negatively regulate autophagy by binding to Beclin 1. Herein, we challenge this view and provide genetic and biochemical evidence that the effects of prosurvival Bcl-2 family members on autophagy are instead an indirect consequence of their inhibition of apoptosis mediators Bcl-2–associated X (Bax) and Bcl-2 homologous antagonist/killer (Bak). We show that in the absence of Bax and Bak, antagonizing or altering the levels of prosurvival Bcl-2 family members has no detectable impact on autophagy. Because several inhibitors of both autophagy and Bcl-2 are in clinical trials for the treatment of cancer, it is important to understand the cross-talk between these pathways.
Characterization and development of photoactivatable fluorescent proteins for single-molecule–based superresolution imaging
Authors: Wang Siyuan , Moffitt Jeffrey R. , Dempsey Graham T. , Xie X. Sunney , Zhuang Xiaowei 
Published: May 2014

Significance
Photoactivatable fluorescent proteins (PAFPs) are important probes for superresolution fluorescence microscopy, which allows the spatial organization of proteins in living cells to be probed with sub–diffraction-limit resolution. Here, we compare four properties of PAFPs that are critical for superresolution imaging and report two new PAFPs that exhibit excellent performance in all four properties.
Commonness and rarity in the marine biosphere
Authors: Connolly Sean R. , MacNeil M. Aaron , Caley M. Julian , Knowlton Nancy , Cripps Ed , Hisano Mizue , Thibaut Loïc M. , Bhattacharya Bhaskar D. , Benedetti-Cecchi Lisandro , Brainard Russell E. , Brandt Angelika , Bulleri Fabio , Ellingsen Kari E. , Kaiser Stefanie , Kröncke Ingrid , Linse Katrin , Maggi Elena , O’Hara Timothy D. , Plaisance Laetitia , Poore Gary C. B. , Sarkar Santosh K. , Satpathy Kamala K. , Schückel Ulrike , Williams Alan , Wilson Robin S. 
Published: May 2014

SignificanceTests of biodiversity theory have been controversial partly because alternative formulations of the same theory seemingly yield different conclusions. This has been a particular challenge for neutral theory, which has dominated tests of biodiversity theory over the last decade. Neutral theory attributes differences in species abundances to chance variation in individuals’ fates, rather than differences in species traits. By identifying common features of different neutral models, we conduct a uniquely robust test of neutral theory across a global dataset of marine assemblages. Consistently, abundances vary more among species than neutral theory predicts, challenging the hypothesis that community dynamics are approximately neutral, and implicating species differences as a key driver of community structure in nature.
Chaos–order transition in foraging behavior of ants
Authors: Li Lixiang , Peng Haipeng , Kurths Jürgen , Yang Yixian , Schellnhuber Hans Joachim 
Published: May 2014

Significance
We have studied the foraging behavior of group animals that live in fixed colonies (especially ants) as an important problem in ecology. Building on former findings on deterministic chaotic activities of single ants, we uncovered that the transition from chaotic to periodic regimes results from an optimization scheme of the self-organization of such an animal colony. We found that an effective foraging of ants mainly depends on their nest as well as their physical abilities and knowledge due to experience. As an important outcome, the foraging behavior of ants is not represented by random, but rather by deterministic walks, in a random environment: Ants use their intelligence and experience to navigate.
Synthesis of terephthalic acid via Diels-Alder reactions with ethylene and oxidized variants of 5-hydroxymethylfurfural
Authors: Pacheco Joshua J. , Davis Mark E. 
Published: May 2014

Significance
Current, plant-based polyethylene terephthalate (PET) is produced from biomass-derived ethylene glycol [the terephthalic acid (PTA) used is not from biomass]. To have a 100% biomass-derived PET, PTA must be produced from biomass. Here, pathways for the production of renewable PTA, using Diels-Alder reactions between ethylene and oxidized derivatives of 5-hydroxymethylfurfural, a biomass-derived chemical, are reported. These pathways are enabled by new catalytic chemistry that may provide routes for the production of 100% biomass-derived PET.
Collagen peptide and vitamin C additively attenuate age-related skin atrophy in Sod1-deficient mice
Authors: Shibuya Shuichi , Ozawa Yusuke , Toda Toshihiko , Watanabe Kenji , Tometsuka Chisa , Ogura Takayuki , Koyama Yoh-ichi , Shimizu Takahiko 
Published: May 2014

Abstract
Age-related skin thinning is correlated with a decrease in the content of collagen in the skin. Accumulating evidence suggests that collagen peptide (CP) and vitamin C (VC) transcriptionally upregulate type I collagen in vivo. However, the additive effects of CP and VC on age-related skin changes remain unclear. We herein demonstrate that CP and a VC derivative additively corrected age-related skin thinning via reduced oxidative damage in superoxide dismutase 1 (Sod1)-deficient mice. Co-treatment with these compounds significantly normalized the altered gene expression of Col1a1, Has2, and Ci1, a proton-coupled oligopeptide transporter, in Sod1−/− skin. The in vitro analyses further revealed that collagen oligopeptide, a digestive product of ingested CP, significantly promoted the bioactivity of the VC derivative with respect to the migration and proliferation of Sod1−/− fibroblasts. These findings suggest that combined treatment with CP and VC is effective in cases of age-related skin pathology.
Isolation of diploid baker’s yeast capable of strongly activating immune cells and analyses of the cell wall structure
Authors: Takada Yuki , Mizobuchi Ayano , Kato Takayuki , Kasahara Emiko , Ito Chinatsu , Watanabe Hajime , Kanzaki Ken , Kitagawa Seiichi , Tachibana Taro , Azuma Masayuki 
Published: May 2014

Abstract
Diploid baker’s yeast capable of strongly activating a mouse macrophage was constructed based on haploid mutant AQ-37 obtained previously. The obtained strain BQ-55 activated also human immune cells. To clarify a factor for the activation, the cell wall structure, especially the β-glucan structure, was analyzed, suggesting that the length of branching, β-1,6-glucan, may be one of the factors.
Characterization and genetic analyses of a carbazole-degrading gram-positive marine isolate, Janibacter sp. strain OC11
Authors: Oba Shintaro , Suzuki Toshihiro , Maeda Rintaro , Omori Toshio , Fuse Hiroyuki 
Published: May 2014

Abstract
Strain OC11 was isolated from seawater sampled at the coast of Chiba, Japan, in artificial seawater medium with carbazole (CAR) as the sole carbon source. Its 16S ribosomal RNA gene sequence suggested that strain OC11 belongs to the genus Janibacter. The CAR-degradation genes (car genes) of strain OC11 were PCR amplified, using degenerate primers designed based on the car gene sequences of other CAR-degrading bacteria. Complete nucleotide sequences encoding six complete open reading frames were determined, and the first known ferredoxin reductase gene (carAd) was found from a CAR-degrading bacterium isolated from the marine environment. An experiment using a mutant strain suggested that the car genes of strain OC11 are functional in CAR degradation. Southern hybridization indicated that strain OC11 had one car gene cluster in vivo. RT-PCR revealed that transcription of carOC11 constitutes an operon.
keeSeek: searching distant non-existing words in genomes for PCR-based applications
Authors: Falda Marco , Fontana Paolo , Barzon Luisa , Toppo Stefano , Lavezzo Enrico 
Published: May 2014

Abstract
Summary: The search for short words that are absent in the genome of one or more organisms (neverwords, also known as nullomers) is attracting growing interest because of the impact they may have in recent molecular biology applications. keeSeek is able to find absent sequences with primer-like features, which can be used as unique labels for exogenously inserted DNA fragments to recover their exact position into the genome using PCR techniques. The main differences with respect to previously developed tools for neverwords generation are (i) calculation of the distance from the reference genome, in terms of number of mismatches, and selection of the most distant sequences that will have a low probability to anneal unspecifically; (ii) application of a series of filters to discard candidates not suitable to be used as PCR primers. KeeSeek has been implemented in C++ and CUDA (Compute Unified Device Architecture) to work in a General-Purpose Computing on Graphics Processing Units (GPGPU) environment.
Availability and implementation: Freely available under the Q Public License at http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=keeseek
Contact: stefano.toppo@unipd.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Novel Natural Product Discovery from Marine Sponges and their Obligate Symbiotic Organisms
Authors: Monaco Regina R. , Quinlan Rena F. 
Published: May 2014

AbstractDiscovery of novel natural products is an accepted method for the elucidation of pharmacologically active molecules and drug leads. Best known sources for such discovery have been terrestrial plants and microbes, accounting for about 85% of the approved natural products in pharmaceutical use (1), and about 60% of approved pharmaceuticals and new drug applications annually (2). Discovery in the marine environment has lagged due to the difficulty of exploration in this ecological niche. Exploration began in earnest in the 1950’s, after technological advances such as scuba diving allowed collection of marine organisms, primarily at a depth to about 15m.Natural products from filter feeding marine invertebrates and in particular, sponges, have proven to be a rich source of structurally unique pharmacologically active compounds, with over 16,000 molecules isolated thus far (3, 1) and a continuing pace of discovery at hundreds of novel bioactive molecules per year. All classes of pharmaceuticals have been represented in this discovery process, including antiprotazoals, pesticides, TGF-beta inhibitors, cationic channel blockers, anticancer, cytotoxic, antiviral, anti-inflammatory and antibacterial compounds. Important biosynthetic pathways found in sponges which give rise to these compounds include the terpenoid (4), fatty acid, polyketoid, quinone reductase, alkaloid, isoprenoid (5), and non-ribosomal protein synthase pathways.
Reconstructing Austronesian population history in Island Southeast Asia
Authors: Lipson Mark , Loh Po-Ru , Patterson Nick , Moorjani Priya , Ko Ying-Chin , Stoneking Mark , Berger Bonnie , Reich David 
Published: May 2014

AbstractAustronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the “Austronesian expansion,” which began 4–5 thousand years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, focusing primarily on Island Southeast Asia, we analyze genome-wide data from 56 populations using new methods for tracing ancestral gene flow. We show that all sampled Austronesian groups harbor ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.
The conditions and potential of RMB as an international reserve currency
Authors: Wu Jun , Pan Yingli , Zhu Qi 
Published: May 2014

Purpose– The purpose of this paper is to identify the determinants for currency internationalization and forecast the potential of RMB as an international reserve currency.Design/methodology/approach– This paper performs linear or non-linear regressions of the shares of eight major international reserve currencies as the reserve assets in global central banks on the macro economic and financial variables of their corresponding countries to identify the determinants for their international positions, and conducts an “counter-factual simulation” for the potential of RMB as an international reserve currency.Findings– This paper finds that the economic size and the “network externalities” are the most important determinants for the international status of a reserve currency; that exchange rate volatility has negative impacts; the conditions for the RMB internationalization are basically available. The simulation for the potential of RMB as an international reserve currency reveals that the international role of RMB could surpass that of the Japanese Yen and the British Pound, and get close to Euro in the coming 15 years. Based on the empirical evidence, this paper suggests a promoting strategy for RMB internationalization.Research limitations/implications– This paper has not taken the influence of economic systemic and political factors on the process of RMB internationalization into account.Practical implications– RMB internationalization promotion should follow the strategy of “stably create RMB international demand in the initial period and dramatically release the RMB overseas supply in the latter period” in the coming 15 years.Originality/value– The conclusions and policy implications are from the results of the empirical analysis on the 45-year historical experience on the eight main international currencies.