bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intravital imaging of cardiac function at the single-cell level
Authors: Aguirre Aaron D. , Vinegoni Claudio , Sebas Matt , Weissleder Ralph 
Published: July 2014

Significance
Despite advances in cardiac imaging technologies such as MRI, computed tomography, and ultrasound it has not been possible to image cardiac function in animal models at the cellular level owing to insufficient resolution and excess motion. As a result, our understanding of cardiac biology and function is derived from either whole-organ imaging techniques or from isolated in vitro heart preparations and cellular model systems. We demonstrate a technique for intravital optical microscopy that compensates for motion of the contracting heart and allows for measurement of contractile function at the single-cell level. These approaches will enable studies of complex and dynamic cellular physiology in the beating heart and should be widely useful for studying heart disease in animal models.
Arsenite oxidation by a facultative chemolithoautotrophicSinorhizobiumsp. KGO-5 isolated from arsenic-contaminated soil
Authors: Dong Dan , Ohtsuka Toshihiko , Dong Dian Tao , Amachi Seigo 
Published: July 2014

AbstractA chemolithoautotrophic arsenite-oxidizing bacterium, designated strain KGO-5, was isolated from arsenic-contaminated industrial soil. Strain KGO-5 was phylogenetically closely related with Sinorhizobium meliloti with 16S rRNA gene similarity of more than 99%, and oxidized 5 mM arsenite under autotrophic condition within 60 h with a doubling time of 3.0 h. Additions of 0.01–0.1% yeast extract enhanced the growth significantly, and the strain still oxidized arsenite efficiently with much lower doubling times of approximately 1.0 h. Arsenite-oxidizing capacities (11.2–54.1 μmol h−1 mg dry cells−1) as well as arsenite oxidase (Aio) activities (1.76–10.0 mU mg protein−1) were found in the cells grown with arsenite, but neither could be detected in the cells grown without arsenite. Strain KGO-5 possessed putative aioA gene, which is closely related with AioA of Ensifer adhaerens. These results suggest that strain KGO-5 is a facultative chemolithoautotrophic arsenite oxidizer, and its Aio is induced by arsenic.
Molecular cloning, expression profiles, and characterization of a novel polyphenol oxidase (PPO) gene in Hevea brasiliensis
Authors: Li Dejun , Deng Zhi , Liu Changren , Zhao Manman , Guo Huina , Xia Zhihui , Liu Hui 
Published: July 2014

Abstract
The polyphenol oxidase (PPO) is involved in undesirable browning in many plant foods. Although the PPOs have been studied by several researchers, the isolation and expression profiles of PPO gene were not reported in rubber tree. In this study, a new PPO gene, HbPPO, was isolated from Hevea brasiliensis. The sequence alignment showed that HbPPO indicated high identities to plant PPOs and belonged to dicot branch. The cis-acting regulatory elements related to stress/hormone responses were predicted in the promoter region of HbPPO. Real-time RT-PCR analyses showed that HbPPO expression varied widely depending on different tissues and developmental stages of leaves. Besides being associated with tapping panel dryness, the HbPPO transcripts were regulated by ethrel, wounding, H2O2, and methyl jasmonate treatments. Moreover, the correlation between latex coagulation rate and PPO activity was further confirmed in this study. Our results lay the foundation for further analyzing the function of HbPPO in rubber tree.
Enhanced protection of pathogenic Escherichia coli ingested by a soil nematode Caenorhabditis elegans against sanitizer treatments
Authors: Park Mi Ri , Oh Sangnam , Yun Hyun Sun , Kim Soon Han , Ko Young Ho , Ryu Jee-Hoon , Rhee Min Suk , Shin Ok Sarah , Kim Younghoon 
Published: July 2014

Abstract
We employed Caenorhabditis elegans as a model to study the effectiveness of sanitizers in killing pathogenic Escherichia coli strains ingested by free-living nematodes. Adult worms that had fed on six pathogenic E. coli strains (highly persistent in the nematode intestine) were treated with three chemical solutions. In planktonic cells, none of the H2O2 and acetic acid treatments influenced the survival of the pathogenic E. coli strains, whereas sodium hypochlorite critically decreased the viability of the strains. Importantly, the survival of the E. coli strains was dramatically increased by persistence in the C. elegans gut under 0.1% sodium hypochlorite, and several strains could survive at a concentration of 0.5%. In addition, all pathogenic E. coli strains in the C. elegans gut survived on the lettuce for 5 days even though they were washed with 0.1% sodium hypochlorite. Taken together, our results indicate that pathogenic E. coli ingested by C. elegans may be protected against washing treatment with commercial sanitizers on raw food materials.
Microtubule-associated protein (MAP) 4 interacts with microtubules in an intrinsically disordered manner
Authors: Hashi Yurika , Kawai Gota , Kotani Susumu 
Published: July 2014

AbstractWe previously used nuclear magnetic resonance (NMR) to analyze the structure of a synthetic tricosapeptide corresponding to an active site of microtubule-associated protein 4 (MAP4). To further the structural analysis, we have constructed a minimal active domain fragment of MAP4, encompassing the entire active site, and obtained its NMR spectra. The secondary structure prediction using partially assigned NMR data suggested that the fragment is largely unfolded. Two other independent techniques also demonstrated its unfolded nature, indicating that MAP4 belongs to the class of intrinsically disordered proteins (IDPs). The NMR spectra of the fragment-microtubule mixture revealed that the fragment binds to the microtubule using multiple binding sites, apparently contradicting our previous quantitative studies. Given that MAP4 is intrinsically disordered, we propose a mechanism in which any one of the binding sites is active at a time, which is one of the typical interaction mechanisms proposed for IDPs.
Comparison of Prior Authorization and Prospective Audit with Feedback for Antimicrobial Stewardship
Authors: Mehta Jimish M. , Haynes Kevin , Wileyto E. Paul , Gerber Jeffrey S. , Timko Daniel R. , Morgan Steven C. , Binkley Shawn , Fishman Neil O. , Lautenbach Ebbing , Zaoutis Theoklis 
Published: July 2014

(See the commentary by Van Schooneveld and Rupp, on pages1100–1102.)ObjectiveAlthough prior authorization and prospective audit with feedback are both effective antimicrobial stewardship program (ASP) strategies, the relative impact of these approaches remains unclear. We compared these core ASP strategies at an academic medical center.DesignQuasi-experimental study.MethodsWe compared antimicrobial use during the 24 months before and after implementation of an ASP strategy change. The ASP used prior authorization alone during the preintervention period, June 2007 through May 2009. In June 2009, many antimicrobials were unrestricted and prospective audit was implemented for cefepime, piperacillin/tazobactam, and vancomycin, marking the start of the postintervention period, July 2009 through June 2011. All adult inpatients who received more than or equal to 1 dose of an antimicrobial were included. The primary end point was antimicrobial consumption in days of therapy per 1,000 patient-days (DOT/1,000-PD). Secondary end points included length of stay (LOS).ResultsIn total, 55,336 patients were included (29,660 preintervention and 25,676 postintervention). During the preintervention period, both total systemic antimicrobial use (−9.75 DOT/1,000-PD per month) and broad-spectrum anti-gram-negative antimicrobial use (−4.00 DOT/1,000-PD) declined. After the introduction of prospective audit with feedback, however, both total antimicrobial use (+9.65 DOT/1,000-PD per month; P < .001) and broad-spectrum anti-gram-negative antimicrobial use (+4.80 DOT/1,000-PD per month; P < .001) increased significantly. Use of cefepime and piperacillin/tazobactam both significantly increased after the intervention (P = .03). Hospital LOS and LOS after first antimicrobial dose also significantly increased after the intervention (P = .016 and .004, respectively).ConclusionsSignificant increases in antimicrobial consumption and LOS were observed after the change in ASP strategy.Infect Control Hosp Epidemiol 2014;35(9):1092-1099
Multisite Exploration of Clinical Decision Making for Antibiotic Use by Emergency Medicine Providers Using Quantitative and Qualitative Methods
Authors: May Larissa , Gudger Glencora , Armstrong Paige , Brooks Gillian , Hinds Pamela , Bhat Rahul , Moran Gregory J. , Schwartz Lisa , Cosgrove Sara E. , Klein Eili Y. , Rothman Richard E. , Rand Cynthia 
Published: July 2014

Objectives.To explore current practices and decision making regarding antimicrobial prescribing among emergency department (ED) clinical providers.MethodsWe conducted a survey of ED providers recruited from 8 sites in 3 cities. Using purposeful sampling, we then recruited 21 providers for in-depth interviews. Additionally, we observed 10 patient-provider interactions at one of the ED sites. SAS 9.3 was used for descriptive and predictive statistics. Interviews were audio recorded, transcribed, and analyzed using a thematic, constructivist approach with consensus coding using NVivo 10.0. Field and interview notes collected during the observational study were aligned with themes identified through individual interviews.ResultsOf 150 survey respondents, 76% agreed or strongly agreed that antibiotics are overused in the ED, while half believed they personally did not overprescribe. Eighty-nine percent used a smartphone or tablet in the ED for antibiotic prescribing decisions. Several significant differences were found between attending and resident physicians. Interview analysis identified 42 codes aggregated into the following themes: (1) resource and environmental factors that affect care; (2) access to and quality of care received outside of the ED consult; (3) patient-provider relationships; (4) clinical inertia; and (5) local knowledge generation. The observational study revealed limited patient understanding of antibiotic use. Providers relied heavily upon diagnostics and provided limited education to patients. Most patients denied a priori expectations of being prescribed antibiotics.ConclusionsPatient, provider, and healthcare system factors should be considered when designing interventions to improve antimicrobial stewardship in the ED setting.Infect Control Hosp Epidemiol 2014;35(9):1114-1125
‘All the Trimmings?’: The Transfer of Theatre to Television in Adaptations of Shakespeare Stagings
Authors: Wyver John 
Published: July 2014

AbstractSince 1937, almost fifty British television productions of Shakespeare have been adapted from specific theatre stagings. This article surveys the history of these transmissions of previously staged performances of Shakespeare. It outlines the changing ways in which these adaptations have been important to television and it explores ideas about their status and effectivity. It argues that rather than being seen simply as ‘documentation’ and as the inferior traces of theatrical originals, these productions might more productively be regarded as doubled adaptations. That is, they can be understood as adaptations for the screen of a text—a staging of a Shakespeare play—that was previously, as a staged performance, an adaptation in itself. The interplay between the televisual, theatrical, and cinematic elements of these adaptations is considered and the history is set within in the context of the rapidly developing contemporary form of live cinema, exemplified by National Theatre Live and Live from Stratford-upon-Avon, which recreates as spectacle in a social context many of the approaches and concerns of television’s adaptations of Shakespeare stagings.
Monte Carlo algorithms for Brownian phylogenetic models
Authors: Horvilleur Benjamin , Lartillot Nicolas 
Published: July 2014

Abstract
Motivation : Brownian models have been introduced in phylogenetics for describing variation in substitution rates through time, with applications to molecular dating or to the comparative analysis of variation in substitution patterns among lineages. Thus far, however, the Monte Carlo implementations of these models have relied on crude approximations, in which the Brownian process is sampled only at the internal nodes of the phylogeny or at the midpoints along each branch, and the unknown trajectory between these sampled points is summarized by simple branchwise average substitution rates.
Results : A more accurate Monte Carlo approach is introduced, explicitly sampling a fine-grained discretization of the trajectory of the (potentially multivariate) Brownian process along the phylogeny. Generic Monte Carlo resampling algorithms are proposed for updating the Brownian paths along and across branches. Specific computational strategies are developed for efficient integration of the finite-time substitution probabilities across branches induced by the Brownian trajectory. The mixing properties and the computational complexity of the resulting Markov chain Monte Carlo sampler scale reasonably with the discretization level, allowing practical applications with up to a few hundred discretization points along the entire depth of the tree. The method can be generalized to other Markovian stochastic processes, making it possible to implement a wide range of time-dependent substitution models with well-controlled computational precision.
Availability : The program is freely available at www.phylobayes.org
Contact : nicolas.lartillot@univ-lyon1.fr
Incorporating the spatial access priorities of fishers into strategic
conservation planning and marine protected area design: reducing cost and
increasing transparency
Authors: Yates K. L. , Schoeman D. S. 
Published: July 2014

Abstract
Marine protected areas (MPAs) are increasingly used to address multiple marine management needs, and the incorporation of stakeholders into the MPA planning and designation processes is considered vital for success. Commercial fishers are often the stakeholder group most directly affected by spatial restrictions associated with MPAs, and the success of MPAs often depends, at least in part, on the behaviours and attitudes of fishers. MPA planning processes that incorporate fishers, and minimize the negative impact of MPA designation on the fishing community, should therefore have a greater chance of success. Here, the incorporation of both quantitative and qualitative fisher-derived data in MPA planning is investigated using strategic conservation planning software and multi-scenario analysis. We demonstrate the use of spatial access priority data as a cost layer, and suggest a process for incorporating fishers' MPA suggestions into planning scenarios in a transparent, but flexible, way. Results show that incorporating fisher-derived data, both quantitative and qualitative, can significantly reduce the cost of MPA planning solutions: enabling the development of MPA network designs that meet conservation targets with less detrimental impact to fishing community. Incorporating fishers and fisher-derived data in MPA planning processes can improve both the efficiency and defensibility of planning outcomes, as well as contribute to reducing potential conflicts between biodiversity conservation and the fishing industry.
Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome
Authors: Thévenin Annelyse , Ein-Dor Liat , Ozery-Flato Michal , Shamir Ron 
Published: July 2014

AbstractGenomes undergo changes in organization as a result of gene duplications, chromosomal rearrangements and local mutations, among other mechanisms. In contrast to prokaryotes, in which genes of a common function are often organized in operons and reside contiguously along the genome, most eukaryotes show much weaker clustering of genes by function, except for few concrete functional groups. We set out to check systematically if there is a relation between gene function and gene organization in the human genome. We test this question for three types of functional groups: pairs of interacting proteins, complexes and pathways. We find a significant concentration of functional groups both in terms of their distance within the same chromosome and in terms of their dispersal over several chromosomes. Moreover, using Hi-C contact map of the tendency of chromosomal segments to appear close in the 3D space of the nucleus, we show that members of the same functional group that reside on distinct chromosomes tend to co-localize in space. The result holds for all three types of functional groups that we tested. Hence, the human genome shows substantial concentration of functional groups within chromosomes and across chromosomes in space.
First Report of Aster Yellows Phytoplasma in Soybean in Michigan
Authors: Mollov D. , Chilvers M. I. , Jacobs J. L. 
Published: July 2014

During the summer of 2012, soybean plants in a commercial field in Clinton County, Michigan, exhibited symptoms characteristic of phytoplasmal diseases (1,2). Symptoms included extensive top dieback, stunting, purple stem surfaces, internal necrosis, leaf vein discoloration, and bud proliferation. Approximately 80% of plants in a half hectare along the southern edge of the field were symptomatic, although the majority of plants in the 4-ha field appeared symptomless. Total genomic DNA was extracted from one symptomatic and one asymptomatic leaf sample using a Qiagen DNeasy Plant Mini Kit (Qiagen, Germantown, MD) according to manufacturer's instructions. The DNA was used as template in direct PCR primed by the phytoplasma-universal primers P1/P7 followed by nested PCR primed by P1/AYint (3). Reactions containing template DNA from the symptomatic plant yielded ribosomal RNA gene amplicons of 1.8 kbp (P1/P7-primed) and 1.6 kbp (P1/AYint-primed), respectively. Reactions containing template DNA from the asymptomatic plant or water did not yield amplicons. The products of PCRs primed by P1/P7 were purified using PureLink PCR Purification kit (Life Technologies, Carlsbad, CA) and cloned in a pGem T-Easy vector system (Promega, Madison, WI). Three separate clones were sequenced using the sequencing primers M13For, M13Rev, SAYF nt 755, (5′-AAAGCGTGGGGAGCAAACAG), and SAYR nt 1159, (5′-TTTGACGTCGTCCCCACCTT). The sequences of all three clones were identical. A consensus (Sequencher 4.1, Gene Codes Corporation, Ann Arbor, MI) nucleotide sequence of 1,830 bp was deposited in GenBank under the accession number KF528320. A BLASTn similarity search revealed that the sequence shared 100% identity to rDNA of aster yellows phytoplasma (AF222063). Additionally, analysis of the 16Sr group/subgroup classification, based on in silico RFLP analyses using iPhyClassifier (4), indicated that the soybean phytoplasma is a member of subgroup 16SrI-B aster yellows phytoplasma subgroup. In a phylogenic tree deduced using the neighbor joining algorithm, the phytoplasma consensus sequence obtained from soybean in Michigan clustered with other group 16SrI (aster yellows phytoplasma) strains. While aster yellows phytoplasma has been previously reported in soybean in Wisconsin (2), to our knowledge, this is the first report of aster yellows in soybean in Michigan. References: (1) C. R. Grau et al. Compendium of Soybean Diseases, 4th ed. G. L. Hartman et al., eds. American Phytopathological Society, St. Paul, MN, 1999. (2) M. E. Lee et al. Can. J. Plant Pathol. 24:125, 2002. (3) C. D. Smart et al. Appl. Env. Microbiol. 62:2988, 1996. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
First Report of Grapevine leafroll-associated virus-2 and -3 in Texas Vineyards
Authors: Jones T. J. , Westover F. , Nita M. 
Published: July 2014

Grapevine leafroll disease (GLD), caused by the grapevine leafroll-associated viruses (GLRaVs, family Closteroviridae) is an important disease in all grapevine-growing regions of the world (2). It negatively affects vine vigor, fruit yield, and grape quality (e.g., sugar accumulation) (3). Typical disease symptoms include downward rolling of grape leaves accompanied by interveinal reddening in red-fruited varieties and interveinal chlorosis in white-fruited varieties (2). The state of Texas currently has over 275 commercial vineyards and acreage under grape production is expanding. Currently, there is limited information on the presence of either GLRaV-2 (genus Closterovirus) or GLRaV-3 (genus Ampelovirus) in this state. During the 2012 season, 19 individual, symptomatic grapevines (13 cv. Lenoir and 6 cv. Blanc du Bois) were sampled (14 petioles per vine) from one vineyard site in Richards, TX. Total nucleic acid was extracted from the samples as described before (5) and tested by RT-PCR using species specific primers to amplify a 334-bp fragment of the HSP70h gene of GLRaV-2 (L2 F: 5′-ATAATTCGGCGTACATCCCCACTT-3′ and U2 R: 5′-GCCCTCCGCGCAACTAATGACAG-3′) (1) and a 541-bp fragment of the HSP70h gene of GLRaV-3 (LC1 F: 5′-CGCTAGGGCTGTGGAAGTATT-3′ and LC2 R: 5′-GTTGTCCCGGGTACCAGATAT-3′) (4). Samples were also subjected to triple (TAS) and double (DAS) antibody sandwich ELISA for GLRaV-2 and GLRaV-3 using commercially available antibody test kits (AC Diagnostics, Fayetteville, AR). Five samples tested positive for GLRaV-2 and one for GLRaV-3, all from the variety Lenoir with no incidences of mixed infection. In addition to the RT-PCR and ELISA, the presence of GLRaV-2 and GLRaV-3 was confirmed by direct sequencing of select RT-PCR products, which was purified using the QIAquick PCR Purification kit (Qiagen Inc., CA). The sequencing took place at the Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA. GLRaV-2 isolate TX12 (GenBank Accession No. KF417612) and GLRaV-3 isolate TX9 (KJ545571) shared 85 to 100% and 94 to 100% nucleotide identity and 74 to 100% and 82 to 100% amino acid identity, respectively, with previously reported isolates from around the world. All samples tested negative for GLRaV-1, -4, -4 strain 5, and -4 strain 9 (4), suggesting that some of the symptomatic vines may have a different disease or abiotic disorder, such as a nutrient deficiency. To our knowledge, this is the first report of GLRaV-2 and GLRaV-3 in the state of Texas. References: (1) N. Bertazzon and E. Angelini. J. Plant Pathol. 86:283, 2004. (2) M. Fuchs et al. Plant Dis. 93:395, 2009. (3) L. Kovacs et al. Am. J. Enol. Vitic. 52:254, 2001. (4) F. Osman et al. J. Virol. Methods. 141:22, 2007. (5) A. Rowhani et al. Proc. ICVG (Adelaide). 13:82, 2000.