bluuebunny/crossref_metadata_2025_split huggingface dataset:
HEAVY AND LIGHT BODY PARTS: THE WEIGHING METAPHOR IN EARLY CHINESE DIALOGUES
Authors: Defoort Carine 
Published: May 2015

AbstractThe article analyses the metaphorical use of weighing body parts such as fingers, arms, or a head. Our understanding of the weighing metaphor has been much influenced by A. C. Graham's characterization of its rhetorical mechanism, followed by Griet Vankeerberghen in her description of one type of weighing (quanB). The basis of this understanding are two corrupt textual fragments in the dialectical chapters of theMozi. SeveralLü shi chunqiuchapters, however, contain a set of argumentative stories in which body parts are weighed in terms of light and heavy. These stories always argue in favor of life and health, they have a relatively consistent structure, and they may have constituted the core of a larger set of related arguments. Insight into their working can therefore enlighten our reading of other texts.
Interindividual Contacts and Carriage of Methicillin-ResistantStaphylococcus aureus: A Nested Case-Control Study
Authors: Obadia Thomas , Opatowski Lulla , Temime Laura , Herrmann Jean-Louis , Fleury Éric , Boëlle Pierre-Yves , Guillemot Didier 
Published: May 2015

BACKGROUNDReducing the spread of multidrug-resistant bacteria in hospitals remains a challenge. Current methods are screening of patients, isolation, and adherence to hygiene measures among healthcare workers (HCWs). More specific measures could rely on a better characterization of the contacts at risk of dissemination.OBJECTIVETo quantify how close-proximity interactions (CPIs) affectedStaphylococcus aureusdissemination.DESIGNNested case-control study.SETTINGFrench long-term care facility in 2009.PARTICIPANTSPatients (n=329) and HCWs (n=261).METHODSWe recorded CPIs using electronic devices together withS. aureusnasal carriage during 4 months in all participants. Cases consisted of patients showing incidentS. aureuscolonization and were paired to 8 control patients who did not exhibit incident colonization at the same date. Conditional logistic regression was used to quantify associations between incidence and exposure to demographic, network, and carriage covariables.RESULTSThe local structure of contacts informed on methicillin-resistantS. aureus(MRSA) carriage acquisition: CPIs with more HCWs were associated with incident MRSA colonization in patients (odds ratio [OR], 1.10 [95% CI, 1.04–1.17] for 1 more HCW), as well as longer CPI durations (1.03 [1.01–1.06] for a 1-hour increase). Joint analysis of carriage and contacts showed increased carriage acquisition in case of CPI with another colonized individual (OR, 1.55 [1.14–2.11] for 1 more HCW). Global network measurements did not capture associations between contacts and carriage.CONCLUSIONSElectronically recorded CPIs inform on the risk of MRSA carriage, warranting more study of in-hospital contact networks to design targeted intervention strategies.Infect. Control Hosp. Epidemiol.2015;36(8):922–929
Rational combination treatment with histone deacetylase inhibitors and immunomodulatory drugs in multiple myeloma
Authors: Hideshima T , Cottini F , Ohguchi H , Jakubikova J , Gorgun G , Mimura N , Tai Y-T , Munshi N C , Richardson P G , Anderson K C 
Published: May 2015

AbstractImmunomodulatory drugs (IMiDs) thalidomide, lenalidomide (Len) and pomalidomide trigger anti-tumor activities in multiple myeloma (MM) by targetting cereblon and thereby impacting IZF1/3, c-Myc and IRF4. Histone deacetylase inhibitors (HDACi) also downregulate c-Myc. We therefore determined whether IMiDs with HDACi trigger significant MM cell growth inhibition by inhibiting or downregulating c-Myc. Combination treatment of Len with non-selective HDACi suberoylanilide hydroxamic acid or class-I HDAC-selective inhibitor MS275 induces synergic cytotoxicity, associated with downregulation of c-Myc. Unexpectedly, we observed that decreased levels of cereblon (CRBN), a primary target protein of IMiDs, was triggered by these agents. Indeed, sequential treatment of MM cells with MS275 followed by Len shows less efficacy than simultaneous treatment with this combination. Importantly ACY1215, an HDAC6 inhibitor with minimal effects on class-I HDACs, together with Len induces synergistic MM cytotoxicity without alteration of CRBN expression. Our results showed that only modest class-I HDAC inhibition is able to induce synergistic MM cytotoxicity in combination with Len. These studies may provide the framework for utilizing HDACi in combination with Len to both avoid CRBN downregulation and enhance anti-MM activities.
High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures
Authors: Sosa Oscar A , Gifford Scott M , Repeta Daniel J , DeLong Edward F 
Published: May 2015

Abstract
The role of bacterioplankton in the cycling of marine dissolved organic matter (DOM) is central to the carbon and energy balance in the ocean, yet there are few model organisms available to investigate the genes, metabolic pathways, and biochemical mechanisms involved in the degradation of this globally important carbon pool. To obtain microbial isolates capable of degrading semi-labile DOM for growth, we conducted dilution to extinction cultivation experiments using seawater enriched with high molecular weight (HMW) DOM. In total, 93 isolates were obtained. Amendments using HMW DOM to increase the dissolved organic carbon concentration 4x (280 μm) or 10x (700 μm) the ocean surface water concentrations yielded positive growth in 4–6% of replicate dilutions, whereas &lt;1% scored positive for growth in non-DOM-amended controls. The majority (71%) of isolates displayed a distinct increase in cell yields when grown in increasing concentrations of HMW DOM. Whole-genome sequencing was used to screen the culture collection for purity and to determine the phylogenetic identity of the isolates. Eleven percent of the isolates belonged to the gammaproteobacteria including Alteromonadales (the SAR92 clade) and Vibrio. Surprisingly, 85% of isolates belonged to the methylotrophic OM43 clade of betaproteobacteria, bacteria thought to metabolically specialize in degrading C1 compounds. Growth of these isolates on methanol confirmed their methylotrophic phenotype. Our results indicate that dilution to extinction cultivation enriched with natural sources of organic substrates has a potential to reveal the previously unsuspected relationships between naturally occurring organic nutrients and the microorganisms that consume them.
Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon
Authors: Sorokin Dimitry Y , Kublanov Ilya V , Gavrilov Sergei N , Rojo David , Roman Pawel , Golyshin Peter N , Slepak Vladlen Z , Smedile Francesco , Ferrer Manuel , Messina Enzo , La Cono Violetta , Yakimov Michail M 
Published: May 2015

Abstract
Archaea domain is comprised of many versatile taxa that often colonize extreme habitats. Here, we report the discovery of strictly anaerobic extremely halophilic euryarchaeon, capable of obtaining energy by dissimilatory reduction of elemental sulfur using acetate as the only electron donor and forming sulfide and CO2 as the only products. This type of respiration has never been observed in hypersaline anoxic habitats and is the first example of such metabolic capability in the entire Archaea domain. We isolated and cultivated these unusual organisms, selecting one representative strain, HSR2, for detailed characterization. Our studies including physiological tests, genome sequencing, gene expression, metabolomics and [14C]-bicarbonate assimilation assays revealed that HSR2 oxidized acetate completely via the tricarboxylic acid cycle. Anabolic assimilation of acetate occurred via activated glyoxylate bypass and anaplerotic carboxylation. HSR2 possessed sulfurtransferase and an array of membrane-bound polysulfide reductase genes, all of which were expressed during the growth. Our findings suggest the biogeochemical contribution of haloarchaea in hypersaline anoxic environments must be reconsidered.
RNA structure determination by solid-state NMR spectroscopy
Authors: Marchanka Alexander , Simon Bernd , Althoff-Ospelt Gerhard , Carlomagno Teresa 
Published: May 2015

AbstractKnowledge of the RNA three-dimensional structure, either in isolation or as part of RNP complexes, is fundamental to understand the mechanism of numerous cellular processes. Because of its flexibility, RNA represents a challenge for crystallization, while the large size of cellular complexes brings solution-state NMR to its limits. Here, we demonstrate an alternative approach on the basis of solid-state NMR spectroscopy. We develop a suite of experiments and RNA labeling schemes and demonstrate for the first time that ssNMR can yield a RNA structure at high-resolution. This methodology allows structural analysis of segmentally labelled RNA stretches in high-molecular weight cellular machines—independent of their ability to crystallize— and opens the way to mechanistic studies of currently difficult-to-access RNA-protein assemblies.
Wave energy budget analysis in the Earth’s radiation belts uncovers a missing energy
Authors: Artemyev A.V. , Agapitov O.V. , Mourenas D. , Krasnoselskikh V.V. , Mozer F.S. 
Published: May 2015

AbstractWhistler-mode emissions are important electromagnetic waves pervasive in the Earth’s magnetosphere, where they continuously remove or energize electrons trapped by the geomagnetic field, controlling radiation hazards to satellites and astronauts and the upper-atmosphere ionization or chemical composition. Here, we report an analysis of 10-year Cluster data, statistically evaluating the full wave energy budget in the Earth’s magnetosphere, revealing that a significant fraction of the energy corresponds to hitherto generally neglected very oblique waves. Such waves, with 10 times smaller magnetic power than parallel waves, typically have similar total energy. Moreover, they carry up to 80% of the wave energy involved in wave–particle resonant interactions. It implies that electron heating and precipitation into the atmosphere may have been significantly under/over-valued in past studies considering only conventional quasi-parallel waves. Very oblique waves may turn out to be a crucial agent of energy redistribution in the Earth’s radiation belts, controlled by solar activity.
Atomistic design of microbial opsin-based blue-shifted optogenetics tools
Authors: Kato Hideaki E. , Kamiya Motoshi , Sugo Seiya , Ito Jumpei , Taniguchi Reiya , Orito Ayaka , Hirata Kunio , Inutsuka Ayumu , Yamanaka Akihiro , Maturana Andrés D. , Ishitani Ryuichiro , Sudo Yuki , Hayashi Shigehiko , Nureki Osamu 
Published: May 2015

AbstractMicrobial opsins with a bound chromophore function as photosensitive ion transporters and have been employed in optogenetics for the optical control of neuronal activity. Molecular engineering has been utilized to create colour variants for the functional augmentation of optogenetics tools, but was limited by the complexity of the protein–chromophore interactions. Here we report the development of blue-shifted colour variants by rational design at atomic resolution, achieved through accurate hybrid molecular simulations, electrophysiology and X-ray crystallography. The molecular simulation models and the crystal structure reveal the precisely designed conformational changes of the chromophore induced by combinatory mutations that shrink its π-conjugated system which, together with electrostatic tuning, produce large blue shifts of the absorption spectra by maximally 100 nm, while maintaining photosensitive ion transport activities. The design principle we elaborate is applicable to other microbial opsins, and clarifies the underlying molecular mechanism of the blue-shifted action spectra of microbial opsins recently isolated from natural sources.
Notes on stochastic (bio)-logic gates: computing with allosteric cooperativity
Authors: Agliari Elena , Altavilla Matteo , Barra Adriano , Dello Schiavo Lorenzo , Katz Evgeny 
Published: May 2015

AbstractRecent experimental breakthroughs have finally allowed to implement in-vitro reaction kinetics (the so calledenzyme based logic) which code for two-inputs logic gates and mimic the stochastic AND (and NAND) as well as the stochastic OR (and NOR). This accomplishment, together with the already-known single-input gates (performing as YES and NOT), provides a logic base and paves the way to the development of powerful biotechnological devices. However, as biochemical systems are always affected by the presence of noise (e.g. thermal), standard logic is not the correct theoretical reference framework, rather we show that statistical mechanics can work for this scope: here we formulate a complete statistical mechanical description of the Monod-Wyman-Changeaux allosteric model for both single and double ligand systems, with the purpose of exploring their practical capabilities to express noisy logical operators and/or perform stochastic logical operations. Mixing statistical mechanics with logics and testing quantitatively the resulting findings on the available biochemical data, we successfully revise the concept of cooperativity (and anti-cooperativity) for allosteric systems, with particular emphasis on its computational capabilities, the related ranges and scaling of the involved parameters and its differences with classical cooperativity (and anti-cooperativity).
Genome-wide transcriptome profiling provides insights into floral bud development of summer-flowering Camellia azalea
Authors: Fan Zhengqi , Li Jiyuan , Li Xinlei , Wu Bin , Wang Jiangying , Liu Zhongchi , Yin Hengfu 
Published: May 2015

AbstractThe transition from vegetative to reproductive growth in woody perennials involves pathways controlling flowering timing, bud dormancy and outgrowth in responses to seasonal cues. However little is known about the mechanism governing the adaptation of signaling pathways to environmental conditions in trees. Camellia azalea is a rare species in this genus flowering during summer, which provides a unique resource for floral timing breeding. Here we reported a comprehensive transcriptomics study to capture the global gene profiles during floral bud development in C. azalea. We examined the genome-wide gene expression between three developmental stages including floral bud initiation, floral organ differentiation and bud outgrowth and identified nine co-expression clusters with distinctive patterns. Further, we identified the differential expressed genes (DEGs) during development and characterized the functional properties of DEGs by Gene Ontology analysis. We showed that transition from floral bud initiation to floral organ differentiation required changes of genes in flowering timing regulation, while transition to floral bud outgrowth was regulated by various pathways such as cold and light signaling, phytohormone pathways and plant metabolisms. Further analyses of dormancy associated MADS-box genes revealed that SVP- and AGL24- like genes displayed distinct expression patterns suggesting divergent roles during floral bud development.
Interfacing low-energy SAW nebulization with Liquid Chromatography-Mass Spectrometry for the analysis of biological samples
Authors: Tveen-Jensen Karina , Gesellchen Frank , Wilson Rab , Spickett Corinne M. , Cooper Jonathan M. , Pitt Andrew R. 
Published: May 2015

AbstractSoft ionization methods for the introduction of labile biomolecules into a mass spectrometer are of fundamental importance to biomolecular analysis. Previously, electrospray ionization (ESI) and matrix assisted laser desorption-ionization (MALDI) have been the main ionization methods used. Surface acoustic wave nebulization (SAWN) is a new technique that has been demonstrated to deposit less energy into ions upon ion formation and transfer for detection than other methods for sample introduction into a mass spectrometer (MS). Here we report the optimization and use of SAWN as a nebulization technique for the introduction of samples from a low flow of liquid and the interfacing of SAWN with liquid chromatographic separation (LC) for the analysis of a protein digest. This demonstrates that SAWN can be a viable, low-energy alternative to ESI for the LC-MS analysis of proteomic samples.
Realization of a micrometre-scale spin-wave interferometer
Authors: Rousseau O. , Rana B. , Anami R. , Yamada M. , Miura K. , Ogawa S. , Otani Y. 
Published: May 2015

AbstractThe recent development of spin dynamics opens perspectives for various applications based on spin waves, including logic devices. The first important step in the realization of spin-wave-based logics is the manipulation of spin-wave interference. Here, we present the experimental realization of a micrometre-scale spin-wave interferometer consisting of two parallel spin-wave waveguides. The spin waves propagate through the waveguides and the superposition or interference of the electrical signals corresponding to the spin waves is measured. A direct current flowing through a metal wire underneath one of the spin-wave waveguides affects the propagation properties of the corresponding spin wave. The signal of constructive or destructive interference depends on the magnitude and direction of the applied direct current. Thus, the present work demonstrates a unique manipulation of spin-wave interference.
Prediction of Prostate Cancer Recurrence Using Quantitative Phase Imaging
Authors: Sridharan Shamira , Macias Virgilia , Tangella Krishnarao , Kajdacsy-Balla André , Popescu Gabriel 
Published: May 2015

AbstractThe risk of biochemical recurrence of prostate cancer among individuals who undergo radical prostatectomy for treatment is around 25%. Current clinical methods often fail at successfully predicting recurrence among patients at intermediate risk for recurrence. We used a label-free method, spatial light interference microscopy, to perform localized measurements of light scattering in prostatectomy tissue microarrays. We show, for the first time to our knowledge, that anisotropy of light scattering in the stroma immediately adjoining cancerous glands can be used to identify patients at higher risk for recurrence. The data show that lower value of anisotropy corresponds to a higher risk for recurrence, meaning that the stroma adjoining the glands of recurrent patients is more fractionated than in non-recurrent patients. Our method outperformed the widely accepted clinical tool CAPRA-S in the cases we interrogated irrespective of Gleason grade, prostate-specific antigen (PSA) levels and pathological tumor-node-metastasis (pTNM) stage. These results suggest that QPI shows promise in assisting pathologists to improve prediction of prostate cancer recurrence.
Adult-Onset Leukoencephalopathy with Axonal Spheroids and Pigmented Glia Caused by a Novel R782G Mutation in CSF1R
Authors: Foulds Nicola , Pengelly Reuben J. , Hammans Simon R. , Nicoll James A. R. , Ellison David W. , Ditchfield Adam , Beck Sarah , Ennis Sarah 
Published: May 2015

AbstractWe report a new family with autosomal dominant inheritance of a late onset rapidly progressive leukodystrophy in which exome sequencing has revealed a novel mutation p.R782G in the Colony-Stimulating Factor 1 Receptor gene (CSF1R). Neuropathology of two affected family members showed cerebral white matter degeneration with axonal swellings and pigmented macrophages. The few recently reported families with CSF1R mutations had been previously labelled “hereditary diffuse leukencephalopathy with axonal spheroids” (HDLS) and “pigmentary orthochromatic leukodystrophy” (POLD), disorders which now appear to form a disease continuum. The term “adult-onset leukoencephalopathy with axonal spheroids and pigmented glia” (ALSP) has been proposed to encompass this spectrum. As CSF1R regulates microglia this mutation implies that dysregulation of microglia is the primary cause of the disease.
Retinoic acid homeostasis through aldh1a2 and cyp26a1 mediates meiotic entry in Nile tilapia (Oreochromis niloticus)
Authors: Feng Ruijuan , Fang Lingling , Cheng Yunying , He Xue , Jiang Wentao , Dong Ranran , Shi Hongjuan , Jiang Dongneng , Sun Lina , Wang Deshou 
Published: May 2015

AbstractMeiosis is a process unique to the differentiation of germ cells. Retinoic acid (RA) is the key factor controlling the sex-specific timing of meiotic initiation in tetrapods; however, the role of RA in meiotic initiation in teleosts has remained unclear. In this study, the genes encoding RA synthase aldh1a2 and catabolic enzyme cyp26a1 were isolated from Nile tilapia (Oreochromis niloticus), a species without stra8. The expression of aldh1a2 was up-regulated and expression of cyp26a1 was down-regulated before the meiotic initiation in ovaries and in testes. Treatment with RA synthase inhibitor or disruption of Aldh1a2 by CRISPR/Cas9 resulted in delayed meiotic initiation, with simultaneous down-regulation of cyp26a1 and up-regulation of sycp3. By contrast, treatment with an inhibitor of RA catabolic enzyme and disruption of cyp26a1 resulted in earlier meiotic initiation, with increased expression of aldh1a2 and sycp3. Additionally, treatment of XY fish with estrogen (E2) and XX fish with fadrozole led to sex reversal and reversion of meiotic initiation. These results indicate that RA is indispensable for meiotic initiation in teleosts via a stra8 independent signaling pathway where both aldh1a2 and cyp26a1 are critical. In contrast to mammals, E2 is a major regulator of sex determination and meiotic initiation in teleosts.
Quantitative investigation of the poly-adenine DNA dissociation from the surface of gold nanoparticles
Authors: Lu Weiwen , Wang Lihua , Li Jiang , Zhao Yun , Zhou Ziang , Shi Jiye , Zuo Xiaolei , Pan Dun 
Published: May 2015

AbstractIn recent years, poly adenine (polyA) DNA functionalized gold nanoparticles (AuNPs) free of modifications was fabricated with high density of DNA attachment and high hybridization ability similar to those of its thiolated counterpart. This nanoconjugate utilized poly adenine as an anchoring block for binding with the AuNPs surface thereby facilitated the appended recognition block a better upright conformation for hybridization, demonstrating its great potential to be a tunable plasmonic biosensor. It’s one of the key points for any of the practical applications to maintaining stable conjugation between DNA oligonucleotides and gold nanoparticles under various experimental treatments. Thus, in this research, we designed a simple but sensitive fluorescence turn-on strategy to systematically investigate and quantified the dissociation of polyA DNA on gold nanoparticles in diverse experimental conditions. DNA desorbed spontaneously as a function of elevated temperature, ion strength, buffer pH, organic solvents and keeping time. What’s more, evaluating this conjugate stability as affected by the length of its polyA anchor was another crucial aspect in our study. With the improved understanding from these results, we were able to control some of our experimental conditions to maintain a good stability of this kind of polyA DNA−AuNPs nanoconjugates.