bluuebunny/crossref_metadata_2025 huggingface dataset:
The LabTube – a novel microfluidic platform for assay automation in laboratory centrifuges
Authors: Kloke A. , Fiebach A. R. , Zhang S. , Drechsel L. , Niekrawietz S. , Hoehl M. M. , Kneusel R. , Panthel K. , Steigert J. , von Stetten F. , Zengerle R. , Paust N.
Published: February 2014

Based on a centrifugally-controlled ballpen-mechanism, the LabTube enables cost-efficient assay automation at even low sample throughput using standard centrifuges.
Computational analyses reveal a prognostic impact of TULP3 as a transcriptional master regulator in pancreatic ductal adenocarcinoma
Authors: Sartor I. T. S. , Zeidán-Chuliá F. , Albanus R. D. , Dalmolin R. J. S. , Moreira J. C. F.
Published: February 2014

Computational analyses identifiedTULP3as a master regulator of transcription in PDAC expression data and moreover its regulated genes, givingTULP3prognostic value.
Self-assembly, photophysical and electrochemical properties and activation of the TiO2 photocatalyst by perylene bisimide
Authors: Senthilraja Adhimoolam , Krishnakumar Balu , Swaminathan Meenakshisundaram , Nagarajan Samuthira
Published: February 2014

DPBI exists as highly fluorescent molecular wires and DPBI loaded TiO2 is more efficient in RO4 photodegradation.
Selective removal of mercury ions using thymine-grafted electrospun polymer nanofibers
Authors: Huang Yunpeng , Hu Dengmai , Wen Shihui , Shen Mingwu , Zhu Meifang , Shi Xiangyang
Published: February 2014

Thymine-grafted poly(vinyl alcohol)–polyethyleneimine nanofibers can be formed for high-efficiency and high-specificity removal of mercury ions from aqueous solution.
Spin density waves in periodically strained graphene nanoribbons
Authors: Al-Aqtash Nabil M. , Sabirianov Renat F.
Published: February 2014

Local magnetic moments (LMMs) along the edges of sinusoidally strained ZGNRs and spin density waves along the axis of ZGNRs.
Targeted delivery of pharmacological chaperones for Gaucher disease to macrophages by a mannosylated cyclodextrin carrier
Authors: Rodríguez-Lavado Julio , de la Mata Mario , Jiménez-Blanco José L. , García-Moreno M. Isabel , Benito Juan M. , Díaz-Quintana Antonio , Sánchez-Alcázar José A. , Higaki Katsumi , Nanba Eiji , Ohno Kousaku , Suzuki Yoshiyuki , Ortiz Mellet Carmen , García Fernández José M.
Published: February 2014

Efficient delivery of pharmacological chaperones for Gaucher disease to macrophages has been achieved.
Catalyst-free tandem Michael addition/decarboxylation of (thio)coumarin-3-carboxylic acids with indoles: facile synthesis of indole-3-substituted 3,4-dihydro(thio)coumarins
Authors: Shao Zhuzhou , Xu Lubin , Wang Liang , Wei Hongtao , Xiao Jian
Published: February 2014

The tandem Michael addition/decarboxylation of (thio)-coumarin-3-carboxylic acids with indoles gives biologically important indole-3-substituted dihydrocoumarins in good to excellent yields under catalyst-free conditions.
Silicon nanocrystals and nanodiamonds in live cells: photoluminescence characteristics, cytotoxicity and interaction with cell cytoskeleton
Authors: Fucikova A. , Valenta J. , Pelant I. , Kalbacova M. Hubalek , Broz A. , Rezek B. , Kromka A. , Bakaeva Z.
Published: February 2014

Our study on biological interaction of silicon nanocrystals (a) and nanodiamonds (b) with cells encourages their use in human medicine.
Structure–function study of tertiary amines as switchable polarity solvents
Authors: Wilson Aaron D. , Stewart Frederick F.
Published: February 2014

A series of tertiary amines have been screened for their function as switchable polarity solvents (SPS). The relative ratios of tertiary amine and carbonate species as well as maximum possible concentration were determined. A new form of SPS with an amine : carbonate ratio significantly greater than unity has been identified. The N,N-dimethyl-n-alkylamine structure has been identified as important to the function of an SPS.
Utilizing thiol–ene coupling kinetics in the design of renewable thermoset resins based on d-limonene and polyfunctional thiols
Authors: Claudino Mauro , Jonsson Mats , Johansson Mats
Published: February 2014

Off-stoichiometric manipulations on the initial thiol–terpene composition strongly favor the formation of di-addition product (a) over mono-additions (b + c) when the reaction system contains an equimolar or relative excess of thiol.
Ultrathin and highly-ordered CoO nanosheet arrays for lithium-ion batteries with high cycle stability and rate capability
Authors: Li Dongdong , Ding Liang-Xin , Wang Suqing , Cai Dandan , Wang Haihui
Published: February 2014

Ultrathin and highly-ordered 2D CoO nanosheet arrays exhibit superior electrochemical performance as an attractive anode material for LIBs.
Gas-phase anion exchange towards ZnO/ZnSe heterostructures with intensive visible light emission
Authors: Wang Yan , Liu Meng-Xia , Ling Tao , Tang Cheng-Chun , Zhi Chun-Yi , Du Xi-Wen
Published: February 2014

Gas-phase anion exchange was employed to convert ZnO nanorods into a ZnO/ZnSe heterostructure or pure ZnSe nanorods. The product showed intensive visible light emission, which was attributed to the VZn-related defect complexes in the ZnO core.
Development of a one-step microwave-assisted extraction procedure for highly efficient extraction of multiclass fungicides in soils
Authors: Merdassa Yared , Liu Jing-fu , Megersa Negussie
Published: February 2014

A one-step microwave-assisted extraction procedure for highly efficient multiresidue extraction of seven fungicides in soil was developed.
Quantitative-nanoliter immunoassay in capillary immune microreactor adopted inkjet technology
Authors: Yang Jianmin , Zeng Hulie , Xue Shuhua , Chen Fengming , Nakajima Hizuru , Uchiyama Katsumi
Published: February 2014

A quantitatively controlled immunoassay based on inkjet technology to perform nanoliter immunoassay in a capillary microreactor was presented.
A second-generation ligand for the enantioselective rhodium-catalyzed addition of arylboronic acids to alkenylazaarenes
Authors: Roy Iain D. , Burns Alan R. , Pattison Graham , Michel Boris , Parker Alexandra J. , Lam Hon Wai
Published: February 2014

A 2,4,6-trialkylanilide-containing chiral diene has been identified as a superior ligand for the enantioselective rhodium-catalyzed arylation of alkenylazaarenes with arylboronic acids.
Large-scale synthesis and formation mechanism study of basic aluminium sulfate microcubic crystals
Authors: Xia Yuguo , Chen Bo , Jiao Xiuling , Chen Dairong
Published: February 2014

Al3+ derived from the (100) plane of γ-AlOOH at a relatively high H+ concentration can form well-defined basic aluminium sulfate microcrystals through a hydrothermal process.
Anomalous low-temperature proton conductivity enhancement in a novel protonic nanocomposite
Authors: Clark D. , Tong J. , Morrissey A. , Almansoori A. , Reimanis I. , O'Hayre R.
Published: February 2014

A novel protonic ceramic composite is synthesized that comprises nanoscale nickel metal films at the grain boundaries of the proton-conducting ceramic, BaCe0.7Zr0.1Y0.1Yb0.1O3−δ. Low-temperature proton conductivity improvements of up to 46× are observed.
Hydrocarbon and hydrogen-rich syngas production by biomass catalytic pyrolysis and bio-oil upgrading over biochar catalysts
Authors: Ren Shoujie , Lei Hanwu , Wang Lu , Bu Quan , Chen Shulin , Wu Joan
Published: February 2014

A renewable biochar catalyst was developed with high porosity, high surface area, high minerals and surface functional groups. It enhanced hydrogen (27.02 vol% in syngas) and hydrocarbons (42.56 area% in upgraded bio-oil) production in biomass catalytic pyrolysis and bio-oil upgrading. The biochar catalysts had good thermal stability and durability with less coking according to the thermal gravimetric (TG) analysis.
Molecular iodine mediated synthesis of polysubstituted oxazoles by oxidative domino cyclization in water
Authors: Naresh Gunaganti , Narender Tadigoppula
Published: February 2014

A simple and efficient iodine-mediated domino protocol has been developed to construct polysubstituted oxazoles through the C-heteroatom bond formation in water from readily available β-ketoesters and primary amines in high yields.
Mesoporous lithium vanadium oxide as a thin film electrode for lithium-ion batteries: comparison between direct synthesis of LiV2O5 and electrochemical lithium intercalation in V2O5
Authors: Caes S. , Arrebola J. C. , Krins N. , Eloy P. , Gaigneaux E. M. , Henrist C. , Cloots R. , Vertruyen B.
Published: February 2014

γ-LiV2O5 and α-V2O5 mesoporous thin films are prepared by a soft-templating route to compare the electrochemical performances of as-synthesized LiV2O5 with the in situ electrochemical intercalation of lithium ions in α-V2O5.
Magnetic-field-assisted aerosol pyrolysis synthesis of iron pyrite sponge-like nanochain networks as cost-efficient counter electrodes in dye-sensitized solar cells
Authors: Wei Zhanhua , Qiu Yongcai , Chen Haining , Yan Keyou , Zhu Zonglong , Kuang Qin , Yang Shihe
Published: February 2014

Aerosol pyrolysis of Fe(CO)5 in an atmosphere of sulfur vapor under a magnetic field is shown to controllably produce iron pyrite (FeS2) three-dimensional nanochain networks.
Chemical trends of Mn4+emission in solids
Authors: Du M. H.
Published: February 2014

Calculated Mn4+emission energies for various oxides as functions of Mn–O bond length. The experimental values are shown (in red) wherever available. There are three groups of materials: the ones with small O–Mn–O bond angle distortion (black squares), the ones with large O–Mn–O bond angle distortion (blue circles), and phosphates (green triangles). Weak Mn4+-ligand hybridization as a result of long Mn–O bond lengths and/or large O–Mn–O bond angle distortion generally leads to higher emission energies.
Integrin-linked kinase: a new member of the kinases involved in hypertensive end-organ damage?
Authors: Obama Takashi , Eguchi Satoru
Published: February 2014

Integrin-linked kinase predominantly localizes at focal adhesions to regulate actin cytoskeletal dynamics, including cell migration and matrix remodelling. Although recent studies have suggested both physiological and pathophysiological roles of integrin-linked kinase in the cardiovascular and renal system, its involvement in hypertensive organ dysfunctions, such as those that occur in kidney, has not been investigated. In the present issue of Clinical Science, Alique and co-workers have demonstrated that angiotensin II-induced renal inflammatory responses were attenuated in mice with conditional deficiency of integrin-linked kinase, which were associated with suppression of nuclear factor κB activation and reactive oxygen species generation but not hypertension. The significance, potential mechanisms and future direction are presented and discussed in this Commentary.
Three‐user interference channel with common information: a rate splitting‐based achievability scheme
Authors: Ardalani Nahid , Mirmohseni Mahtab , Reza Aref Mohammad
Published: February 2014

In this study, the three‐user interference channel (IFC) with common information is considered, where each receiver decode not only the private message from the intended transmitter but also the common messages from the non‐intended transmitters by applying a simultaneous decoding scheme. An achievable rate region is presented using rate splitting and superposition encoding at the transmitters and simultaneous joint decoding at the receivers in which the transmitters cooperatively send the split messages which allows the interference cancellation at the receivers. The implicit form of the achievable rate region is also extended to K‐user IFC with common information. Finally the inner bound derived for the three‐user discrete memoryless IFC with common information is generalised to the Gaussian case and is evaluated in a numerical example.
Capacity maximisation of the secondary link in cognitive radio networks with hybrid spectrum access strategy
Authors: Tan Xiaobo , Zhang Hang , Hu Jian
Published: February 2014

A hybrid spectrum access strategy which is different from traditional underlay or overlay strategy is proposed. In this strategy, the secondary users cooperatively sense the states of the primary users in the sharing spectrum band. Based on the sensing results and an additional requirement on the bit error rate, the secondary transmitter adapts its transmit power and modulation level. Specifically, if the primary user is detected to be inactive, the secondary transmitter allocates its power subject to a peak transmit power constraint. Else if the primary user is active, the average interference power constraint would also be imposed to protect the primary transmission. To demonstrate the superiority of the hybrid strategy, capacity of the secondary link with this strategy over Rayleigh fading channel is studied. It has been assumed that diversity combing technique is available at the secondary receiver. Perfect and imperfect estimations of the channel power gain from secondary transmitter to primary receiver are also considered. Then the expression of capacity of the secondary link is derived by using Lagrange dual decomposition method. Simulation results demonstrate that the capacity of the secondary link with hybrid strategy is significantly improved when compared with the traditional ones.
Conditions for stability of linear continuous Markovian switching singular systems
Authors: Xiao Xiaoqing , Zhou Lei , Ho Daniel W.C. , Lu Guoping
Published: February 2014

This study addresses the stability problem for linear continuous‐time Markovian switching singular systems. Based on a refined description for jumps of the system states at the switching instants, sufficient conditions for exponential stability in the mean‐square sense of the Markovian switching singular system are obtained by means of multiple Lyapunov function method. The obtained results present a new analysis of the impact for switching law‐induced state jump on the stability property of the considered system. Numerical examples are presented to illustrate the effectiveness of the proposed approach.
Fast hardware architecture for grey‐level image morphology with flat structuring elements
Authors: Torres‐Huitzil Cesar
Published: February 2014

Mathematical morphology operators, applied in many vision‐based applications, are characterised by repetitive operations on large amounts of data. Thus, novel design strategies for efficient hardware implementations are necessary. This study presents and evaluates a real‐time hardware architecture for grey‐level image erosion and dilation that processes data in streams for an efficient utilisation of memory bandwidth and low on‐chip memory requirements. A low‐complexity and highly modular architecture is proposed based on a sequence of pipeline stages, and parallel processing in order to minimise computational times. The design is intended to be used as a hardware accelerator in real‐time embedded image processing applications requiring moderate‐size and non‐rectangular flat structuring elements on high‐resolution images. The architecture is prototyped on a field programmable gate array device operating at a clock frequency of 260 MHz on a Virtex‐6 device which compares favourably to the well‐known delay‐line‐based hardware architectures in terms of complexity, memory requirements and execution time. A 7 × 7 dilation/erosion operator on 1280 × 1024 grey‐level image can be performed at a rate of 95 frames per second, but the architecture can be scaled up if required.
Single switch three‐phase ac to dc converter with reduced voltage stress and current total harmonic distortion
Authors: Juan Yu Lin
Published: February 2014

A three‐phase ac/dc converter with low‐voltage stress and current total harmonic distortion (THD) for micro‐scale wind turbines is proposed in this study. A coupled inductor and buffering capacitors are integrated in the proposed converter to reduce the voltage stresses on the main switch and diodes. Moreover, the discontinuous conduction mode power factor correction technique is adopted to reduce the generator current THD. Corresponding operation principles of the proposed converter are also analysed and illustrated. A prototype with rated output power 200 W was constructed for evaluating the validity and performance of the proposed converter. From the experimental results, it can be seen that the voltage stress of all the active switches and diodes is reduced to half of the output voltage. Owing to the reduced voltage stress, the generator current THD and converter efficiency are both improved with respect to the conventional three‐phase single switch ac/dc converter. The efficiency is improved to about 92% which is 10% higher than the conventional single switch rectifier and the current THD is reduced by 2–6%.
High‐efficiency bidirectional single‐input multiple‐output power converter
Authors: Wai Rong‐Jong , Hong Lian‐Sheng , Liaw Jun‐Jie
Published: February 2014

This study investigates the design of a high‐efficiency bidirectional single‐input multiple‐output (BSIMO) power converter. According to the power management, the proposed BSIMO converter can operate at a step‐up state (energy release) and a step‐down state (energy storage). At the step‐up state, it can boost the voltage of a low‐voltage input power source to a controllable high‐voltage dc bus and middle‐voltage output terminals. If there is redundant energy in the high‐voltage dc bus, one can reversely transmit the energy. The high‐voltage dc bus can take as the main power, and middle‐voltage output terminals can supply powers for individual middle‐voltage dc loads or to charge auxiliary power sources (e.g. battery modules). In this study, a coupled‐inductor‐based BSIMO converter utilises only three power switches to accomplish the bidirectional power control with the properties of voltage clamping and soft switching, and the corresponding device specifications are adequately designed. As a result, the objectives of high‐efficiency power conversion, bidirectional energy transmission, high step‐up/step‐down ratios and various output voltages with different levels can be obtained. The effectiveness of the proposed BSIMO power converter is verified by experimental results of a kW‐level prototype in practical applications.
Low-grade waste heat driven desalination technology
Authors: Christ Alexander , Wang Xiaolin , Regenauer-Lieb Klaus , Chua Hui Tong
Published: February 2014

Low-grade heat driven multi-effect distillation (MED) desalination is a very promising environmentally friendly, low emission technology. Many countries, such as Australia, are water short and conventional desalination technology is energy intensive. If a primary fossil fuel source is used, then desalination will significantly contribute to carbon dioxide emission. Low-grade waste heat from process plants and power plants generate minimal additional carbon dioxide. This source of energy is typically abundant at a temperature around 65–90 °C, which dovetails with MED technology. In this paper, we report on a new MED technology that couples perfectly with low grade waste heat to give at least a 25% freshwater yield improvement compared with conventional MED design. Typical applications and their expected improvement will also be reported.
The capacitated plant location problem with customer and supplier matching and interval demands uncertainty
Authors: Mehdi Kaveh , Salahi Maziar , Jamalian Ali
Published: February 2014

The capacitated plant location problem with customer and supplier matching can be modeled as a mixed integer linear program, where the product distribution from plants to customers and the material supply from suppliers to plants are considered together. In order to save allocation cost, distribution trip and a supply trip is merged into one triangular trip. Moreover, vehicles from plants visit a customer and a supplier for each trip. In this paper, we assume interval uncertainties in the demands of costumers. We show that the robust counterpart of the original model with interval uncertainty is equivalent to a larger mixed integer linear program. Finally, the original and robust models are compared on several randomly generated examples showing the impact of uncertainty.
Large airtanker use and outcomes in suppressing wildland fires in the United States
Authors: Calkin David E. , Stonesifer Crystal S. , Thompson Matthew P. , McHugh Charles W.
Published: February 2014

Wildfire activity in the United States incurs substantial costs and losses, and presents challenges to federal, state, tribal and local agencies that have responsibility for wildfire management. Beyond the potential socioeconomic and ecological losses, and the monetary costs to taxpayers due to suppression, wildfire management is a dangerous occupation. Aviation resources, in particular large airtankers, currently play a critical role in wildfire management, and account for a relatively large share of both suppression expenditure and firefighting fatalities. A recent airtanker modernisation strategy released by the US Department of Agriculture Forest Service and the US Department of Interior highlighted cost effectiveness as the fundamental tenet of both the replacement strategy and the use of aerial firefighting resources. However, determining the cost effectiveness of alternative airtanker fleets is challenging due to limited data and substantial uncertainty regarding aerial firefighting effectiveness. In this paper, we significantly expand on current airtanker usage and effectiveness knowledge, by incorporating spatially explicit drop location data linked to firefighting resource orders to better identify the period in the fire history when drops occurred, and through characterisation of the resulting outcomes of fires that received drops during initial attack. Our results confirm earlier work suggesting extensive use of large airtankers on extended attack, despite policy suggesting priority use in initial attack. Further, results suggest that containment rates for fires receiving large airtanker use during initial attack are quite low. We explore possible causes for these results, address potential limitations with our methods and data, and offer recommendations for improvements in data collection and aviation management.
Mapping day-of-burning with coarse-resolution satellite fire-detection data
Authors: Parks Sean A.
Published: February 2014

Evaluating the influence of observed daily weather on observed fire-related effects (e.g. smoke production, carbon emissions and burn severity) often involves knowing exactly what day any given area has burned. As such, several studies have used fire progression maps – in which the perimeter of an actively burning fire is mapped at a fairly high temporal resolution – or MODIS satellite data to determine the day-of-burning, thereby allowing an evaluation of the influence of daily weather. However, fire progression maps have many caveats, the most substantial being that they are rarely mapped on a daily basis and may not be available in remote locations. Although MODIS fire detection data provide an alternative due to its global coverage and high temporal resolution, its coarse spatial resolution (1km2) often requires that it be downscaled. An objective evaluation of how to best downscale, or interpolate, MODIS fire detection data is necessary. I evaluated 10 spatial interpolation techniques on 21 fires by comparing the day-of-burning as estimated with spatial interpolation of MODIS fire detection data to the day-of-burning that was recorded in fire progression maps. The day-of-burning maps generated with the best performing interpolation technique showed reasonably high quantitative and qualitative agreement with fire progression maps. Consequently, the methods described in this paper provide a viable option for producing day-of-burning data where fire progression maps are of poor quality or unavailable.
A G protein–coupled receptor and the intracellular synthase of its agonist functionally cooperate
Authors: Binda Chantal , Génier Samuel , Cartier Andréane , Larrivée Jean-François , Stankova Jana , Young Jason C. , Parent Jean-Luc
Published: February 2014

Export of newly synthesized G protein–coupled receptors (GPCRs) remains poorly characterized. We show in this paper that lipocalin-type prostaglandin D2 (PGD2) synthase (L-PGDS) interacts intracellularly with the GPCR DP1 in an agonist-independent manner. L-PGDS promotes cell surface expression of DP1, but not of other GPCRs, in HEK293 and HeLa cells, independent of L-PGDS enzyme activity. In addition, formation of a DP1–Hsp90 complex necessary for DP1 export to the cell surface is dependent on the interaction between L-PGDS and the C-terminal MEEVD residues of Hsp90. Surprisingly, PGD2 synthesis by L-PGDS is promoted by coexpression of DP1, suggesting a possible intracrine/autocrine signaling mechanism. In this regard, L-PGDS increases the formation of a DP1–ERK1/2 complex and increases DP1-mediated ERK1/2 signaling. Our findings define a novel cooperative mechanism in which a GPCR (DP1) promotes the activity of the enzyme (L-PGDS) that produces its agonist (PGD2) and in which this enzyme in turn acts as a cofactor (of Hsp90) to promote export and agonist-dependent activity of the receptor.
CellGeo: A computational platform for the analysis of shape changes in cells with complex geometries
Authors: Tsygankov Denis , Bilancia Colleen G. , Vitriol Eric A. , Hahn Klaus M. , Peifer Mark , Elston Timothy C.
Published: February 2014

Cell biologists increasingly rely on computer-aided image analysis, allowing them to collect precise, unbiased quantitative results. However, despite great progress in image processing and computer vision, current computational approaches fail to address many key aspects of cell behavior, including the cell protrusions that guide cell migration and drive morphogenesis. We developed the open source MATLAB application CellGeo, a user-friendly computational platform to allow simultaneous, automated tracking and analysis of dynamic changes in cell shape, including protrusions ranging from filopodia to lamellipodia. Our method maps an arbitrary cell shape onto a tree graph that, unlike traditional skeletonization algorithms, preserves complex boundary features. CellGeo allows rigorous but flexible definition and accurate automated detection and tracking of geometric features of interest. We demonstrate CellGeo’s utility by deriving new insights into (a) the roles of Diaphanous, Enabled, and Capping protein in regulating filopodia and lamellipodia dynamics in Drosophila melanogaster cells and (b) the dynamic properties of growth cones in catecholaminergic a–differentiated neuroblastoma cells.
PP2ARts1 is a master regulator of pathways that control cell size
Authors: Zapata Jessica , Dephoure Noah , MacDonough Tracy , Yu Yaxin , Parnell Emily J. , Mooring Meghan , Gygi Steven P. , Stillman David J. , Kellogg Douglas R.
Published: February 2014

Cell size checkpoints ensure that passage through G1 and mitosis occurs only when sufficient growth has occurred. The mechanisms by which these checkpoints work are largely unknown. PP2A associated with the Rts1 regulatory subunit (PP2ARts1) is required for cell size control in budding yeast, but the relevant targets are unknown. In this paper, we used quantitative proteome-wide mass spectrometry to identify proteins controlled by PP2ARts1. This revealed that PP2ARts1 controls the two key checkpoint pathways thought to regulate the cell cycle in response to cell growth. To investigate the role of PP2ARts1 in these pathways, we focused on the Ace2 transcription factor, which is thought to delay cell cycle entry by repressing transcription of the G1 cyclin CLN3. Diverse experiments suggest that PP2ARts1 promotes cell cycle entry by inhibiting the repressor functions of Ace2. We hypothesize that control of Ace2 by PP2ARts1 plays a role in mechanisms that link G1 cyclin accumulation to cell growth.
Hop-on hop-off: Polysomes take a tour of the cell on endosomes
Authors: Palacios Isabel M.
Published: February 2014

After export from the nucleus, ribosomes need to be distributed throughout the entire cell so that protein synthesis can occur even at distant sites. In the elongated hyphal cell of the fungus Ustilago maydis, Higuchi et al. (2014. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201307164) now demonstrate that polysomes associate with early endosomes that undergo kinesin 3– and dynein-dependent long-range motility. The bidirectional movement of early endosomes randomly distributes polysomes, which may ensure the even distribution of the translation machinery across the entire cell.
Ottoline Leyser: The beauty of plant genetics
Authors: Sedwick Caitlin
Published: February 2014

Leyser studies how plant hormones shape body plan in Arabidopsis.
Ventilator-Associated Pneumonia: Overdiagnosis and Treatment Are Common in Medical and Surgical Intensive Care Units
Authors: Nussenblatt Veronique , Avdic Edina , Berenholtz Sean , Daugherty Elizabeth , Hadhazy Eric , Lipsett Pamela A. , Maragakis Lisa L. , Perl Trish M. , Speck Kathleen , Swoboda Sandra M. , Ziai Wendy , Cosgrove Sara E.
Published: February 2014

Objective.

Diagnosing ventilator-associated pneumonia (VAP) is difficult, and misdiagnosis can lead to unnecessary and prolonged antibiotic treatment. We sought to quantify and characterize unjustified antimicrobial use for VAP and identify risk factors for continuation of antibiotics in patients without VAP after 3 days.

Methods.

Patients suspected of having VAP were identified in 6 adult intensive care units (ICUs) over 1 year. A multidisciplinary adjudication committee determined whether the ICU team's VAP diagnosis and therapy were justified, using clinical, microbiologic, and radiographic data at diagnosis and on day 3. Outcomes included the proportion of VAP events misdiagnosed as and treated for VAP on days 1 and 3 and risk factors for the continuation of antibiotics in patients without VAP after day 3.

Results.

Two hundred thirty-one events were identified as possible VAP by the ICUs. On day 1, 135 (58.4%) of them were determined to not have VAP by the committee. Antibiotics were continued for 120 (76%) of 158 events without VAP on day 3. After adjusting for acute physiology and chronic health evaluation II score and requiring vasopressors on day 1, sputum culture collection on day 3 was significantly associated with antibiotic continuation in patients without VAP. Patients without VAP or other infection received 1,183 excess days of antibiotics during the study.

Conclusions.

Overdiagnosis and treatment of VAP was common in this study and led to 1,183 excess days of antibiotics in patients with no indication for antibiotics. Clinical differences between non-VAP patients who had antibiotics continued or discontinued were minimal, suggesting that clinician preferences and behaviors contribute to unnecessary prescribing.
Contact Precautions More Is Not Necessarily Better
Authors: Dhar Sorabh , Marchaim Dror , Tansek Ryan , Chopra Teena , Yousuf Adnan , Bhargava Ashish , Martin Emily T. , Talbot Thomas R. , Johnson Laura E. , Hingwe Ameet , Zuckerman Jerry M. , Bono Bartholomew R. , Shuman Emily K. , Poblete Jose , Tran MaryAnn , Kulhanek Grace , Thyagarajan Rama , Nagappan Vijayalakshmi , Herzke Carrie , Perl Trish M. , Kaye Keith S.
Published: February 2014

Objective.

To determine whether increases in contact isolation precautions are associated with decreased adherence to isolation practices among healthcare workers (HCWs).

Design.

Prospective cohort study from February 2009 to October 2009.

Setting.

Eleven teaching hospitals.

Participants.

HCWs.

Methods.

One thousand thirteen observations conducted on HCWs. Additional data included the number of persons in isolation, types of HCWs, and hospital-specific contact precaution practices. Main outcome measures included compliance with individual components of contact isolation precautions (hand hygiene before and after patient encounter, donning of gown and glove upon entering a patient room, and doffing upon exiting) and overall compliance (all 5 measures together) during varying burdens of isolation.

Results.

Compliance with hand hygiene was as follows: prior to donning gowns/gloves, 37.2%; gowning, 74.3%; gloving, 80.1%; doffing of gowns/gloves, 80.1%; after gown/glove removal, 61%. Compliance with all components was 28.9%. As the burden of isolation increased (20% or less to greater than 60%), a decrease in compliance with hand hygiene (43.6%—4.9%) and with all 5 components (31.5%—6.5%) was observed. In multivariable analysis, there was an increase in noncompliance with all 5 components of the contact isolation precautions bundle (odds ratio [OR], 6.6 [95% confidence interval (CI), 1.15-37.44];P= .03) and in noncompliance with hand hygiene prior to donning gowns and gloves (OR, 10.1 [95% CI, 1.84—55.54];P= .008) associated with increasing burden of isolation.

Conclusions.

As the proportion of patients in contact isolation increases, compliance with contact isolation precautions decreases. Placing 40% of patients under contact precautions represents a tipping point for noncompliance with contact isolation precautions measures.
Preclinical Toxicity Screening of Intrathecal Oxytocin in Rats and Dogs
Authors: Yaksh Tony L. , Hobo Shotaro , Peters Christopher , Osborn Kent G. , Richter Philip J. , Rossi Steven S. , Grafe Marjorie R. , Eisenach James C.
Published: February 2014

Background

Anatomic, physiologic, and behavioral studies in animals suggest that spinally released oxytocin should produce analgesia in humans and may also protect from chronic pain after injury. In this article, the authors report preclinical toxicity screening of oxytocin for intrathecal delivery.

Methods

Intrathecal oxytocin, 11 μg (6 U) or vehicle, was injected intrathecally in 24 rats, followed by frequent behavioral assessment and histologic examination of spinal contents 2 or 14 days after injection. In three dogs, a range of intrathecal oxytocin doses (18 to 550 μg in 0.5 ml) was injected followed by physiologic, biochemical, and behavioral assessments. Ten dogs were then randomized to receive five daily injections of intrathecal oxytocin, 550 μg in 0.5 ml, or vehicle with similar assessments and, necropsy and histologic analysis were conducted 2 days later.

Results

In rats, intrathecal oxytocin resulted in transient scratching and itching behaviors, without other differences from vehicle. There was no behavioral, gross anatomic, or histologic evidence of neurotoxicity. Dose ranging in dogs suggested mild effects on motor tone, blood pressure, and heart rate at the 550 μg dose. Repeated boluses in dogs did not produce behavioral, biochemical, neurological, gross anatomic, or histologic evidence of neurotoxicity.

Conclusions

Substances, including natural neurotransmitters, may be toxic when administered in pharmacologic doses in the spinal cord. This preclinical toxicity screen in two species suggests that bolus injections of oxytocin in concentrations up to 1,100 μg/ml are unlikely to cause neurotoxicity. The authors also support cautious clinical application of intrathecal oxytocin under regulatory supervision.
Loss of Drosophila Ataxin-7, a SAGA subunit, reduces H2B ubiquitination and leads to neural and retinal degeneration
Authors: Mohan Ryan D. , Dialynas George , Weake Vikki M. , Liu Jianqi , Martin-Brown Skylar , Florens Laurence , Washburn Michael P. , Workman Jerry L. , Abmayr Susan M.
Published: February 2014

The Spt–Ada–Gcn5–acetyltransferase (SAGA) chromatin-modifying complex possesses acetyltransferase and deubiquitinase activities. Within this modular complex, Ataxin-7 anchors the deubiquitinase activity to the larger complex. Here we identified and characterized Drosophila Ataxin-7 and found that reduction of Ataxin-7 protein results in loss of components from the SAGA complex. In contrast to yeast, where loss of Ataxin-7 inactivates the deubiquitinase and results in increased H2B ubiquitination, loss of Ataxin-7 results in decreased H2B ubiquitination and H3K9 acetylation without affecting other histone marks. Interestingly, the effect on ubiquitination was conserved in human cells, suggesting a novel mechanism regulating histone deubiquitination in higher organisms. Consistent with this mechanism in vivo, we found that a recombinant deubiquitinase module is active in the absence of Ataxin-7 in vitro. When we examined the consequences of reduced Ataxin-7 in vivo, we found that flies exhibited pronounced neural and retinal degeneration, impaired movement, and early lethality.
lncRNA recruits RNAi and the exosome to dynamically regulate pho1 expression in response to phosphate levels in fission yeast
Authors: Shah Sneha , Wittmann Sina , Kilchert Cornelia , Vasiljeva Lidia
Published: February 2014

Numerous noncoding transcripts of unknown function have recently been identified. In this study, we report a novel mechanism that relies on transcription of noncoding RNA prt (pho1-repressing transcript) regulating expression of the pho1 gene. A product of this gene, Pho1, is a major secreted phosphatase needed for uptake of extracellular phosphate in fission yeast. prt is produced from the promoter located upstream of the pho1 gene in response to phosphate, and its transcription leads to deposition of RNAi-dependent H3K9me2 across the pho1 locus. In contrast, phosphate starvation leads to loss of H3K9me2 and pho1 induction. Strikingly, deletion of Clr4, a H3K9 methyltransferase, results in faster pho1 induction in response to phosphate starvation. We propose a new role for noncoding transcription in establishing transient heterochromatin to mediate an effective transcriptional response to environmental stimuli. RNAi recruitment to prt depends on the RNA-binding protein Mmi1. Importantly, we found that the exosome complex and Mmi1 are required for transcription termination and the subsequent degradation of prt but not pho1 mRNA. Moreover, in mitotic cells, transcription termination of meiotic RNAs also relies on this mechanism. We propose that exosome-dependent termination constitutes a specialized system that primes transcripts for degradation to ensure their efficient elimination.
The molecular topography of silenced chromatin in Saccharomyces cerevisiae
Authors: Thurtle Deborah M. , Rine Jasper
Published: February 2014

Heterochromatin imparts regional, promoter-independent repression of genes and is epigenetically heritable. Understanding how silencing achieves this regional repression is a fundamental problem in genetics and development. Current models of yeast silencing posit that Sir proteins, recruited by transcription factors bound to the silencers, spread throughout the silenced region. To test this model directly at high resolution, we probed the silenced chromatin architecture by chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-seq) of Sir proteins, histones, and a key histone modification, H4K16-acetyl. These analyses revealed that Sir proteins are strikingly concentrated at and immediately adjacent to the silencers, with lower levels of enrichment over the promoters at HML and HMR, the critical targets for transcriptional repression. The telomeres also showed discrete peaks of Sir enrichment yet a continuous domain of hypoacetylated histone H4K16. Surprisingly, ChIP-seq of cross-linked chromatin revealed a distribution of nucleosomes at silenced loci that was similar to Sir proteins, whereas native nucleosome maps showed a regular distribution throughout silenced loci, indicating that cross-linking captured a specialized chromatin organization imposed by Sir proteins. This specialized chromatin architecture observed in yeast informs the importance of a steric contribution to regional repression in other organisms.
Pharmacological rescue of Ras signaling, GluA1-dependent synaptic plasticity, and learning deficits in a fragile X model
Authors: Lim Chae-Seok , Hoang Elizabeth T. , Viar Kenneth E. , Stornetta Ruth L. , Scott Michael M. , Zhu J. Julius
Published: February 2014

Fragile X syndrome, caused by the loss of Fmr1 gene function, is the most common form of inherited mental retardation, with no effective treatment. Using a tractable animal model, we investigated mechanisms of action of a few FDA-approved psychoactive drugs that modestly benefit the cognitive performance in fragile X patients. Here we report that compounds activating serotonin (5HT) subtype 2B receptors (5HT2B-Rs) or dopamine (DA) subtype 1-like receptors (D1-Rs) and/or those inhibiting 5HT2A-Rs or D2-Rs moderately enhance Ras–PI3K/PKB signaling input, GluA1-dependent synaptic plasticity, and learning in Fmr1 knockout mice. Unexpectedly, combinations of these 5HT and DA compounds at low doses synergistically stimulate Ras–PI3K/PKB signal transduction and GluA1-dependent synaptic plasticity and remarkably restore normal learning in Fmr1 knockout mice without causing anxiety-related side effects. These findings suggest that properly dosed and combined FDA-approved psychoactive drugs may effectively treat the cognitive impairment associated with fragile X syndrome.
Driving nucleolar assembly
Authors: McCann Kathleen L. , Baserga Susan J.
Published: February 2014

In this issue of Genes & Development, Grob and colleagues (pp. 220–230) identify the minimal molecular requirements to assemble a fully functional nucleolus in human cells and demonstrate the importance of the nucleolar transcription factor upstream binding factor (UBF) as a mitotic bookmark at the ribosomal DNA (rDNA).
Epigenetic modification and inheritance in sexual reversal of fish
Authors: Shao Changwei , Li Qiye , Chen Songlin , Zhang Pei , Lian Jinmin , Hu Qiaomu , Sun Bing , Jin Lijun , Liu Shanshan , Wang Zongji , Zhao Hongmei , Jin Zonghui , Liang Zhuo , Li Yangzhen , Zheng Qiumei , Zhang Yong , Wang Jun , Zhang Guojie
Published: February 2014

Environmental sex determination (ESD) occurs in divergent, phylogenetically unrelated taxa, and in some species, co-occurs with genetic sex determination (GSD) mechanisms. Although epigenetic regulation in response to environmental effects has long been proposed to be associated with ESD, a systemic analysis on epigenetic regulation of ESD is still lacking. Using half-smooth tongue sole (Cynoglossus semilaevis) as a model—a marine fish that has both ZW chromosomal GSD and temperature-dependent ESD—we investigated the role of DNA methylation in transition from GSD to ESD. Comparative analysis of the gonadal DNA methylomes of pseudomale, female, and normal male fish revealed that genes in the sex determination pathways are the major targets of substantial methylation modification during sexual reversal. Methylation modification in pseudomales is globally inherited in their ZW offspring, which can naturally develop into pseudomales without temperature incubation. Transcriptome analysis revealed that dosage compensation occurs in a restricted, methylated cytosine enriched Z chromosomal region in pseudomale testes, achieving equal expression level in normal male testes. In contrast, female-specific W chromosomal genes are suppressed in pseudomales by methylation regulation. We conclude that epigenetic regulation plays multiple crucial roles in sexual reversal of tongue sole fish. We also offer the first clues on the mechanisms behind gene dosage balancing in an organism that undergoes sexual reversal. Finally, we suggest a causal link between the bias sex chromosome assortment in the offspring of a pseudomale family and the transgenerational epigenetic inheritance of sexual reversal in tongue sole fish.
Mitochondrial Na+/Ca2+ Exchange Assays
Authors: Palty Raz , Shoshan-Barmatz Varda
Published: February 2014

Here, we describe two complementary assays designed to analyze mitochondrial Na+/Ca2+ exchange activity. In both procedures, the counter ion transport of sodium and calcium ions across the inner membrane of mitochondria is assayed in permeabilized cells preloaded with a mitochondria-selective Na+ probe, CoroNa-Red, or with a mitochondria-targeted calcium sensor, ratiometric-pericam, respectively. These methods, therefore, do not require a mitochondrial preisolation step, with the native cellular mitochondrial architecture being maintained. Importantly, these methods equilibrate the cytosol with the extracellular milieu to allow control over the extra-mitochondrial ionic environment, while eliminating any possible interference by plasma membrane transporters.
Generation of Drug-Resistant Tumors Using Intermittent Dosing of Tyrosine Kinase Inhibitors in Mouse
Authors: Pirazzoli Valentina , Politi Katerina
Published: February 2014

Resistance to targeted therapies has emerged as a major hurdle for the successful use of drugs in the clinic. Therefore, understanding the underlying molecular mechanisms of drug resistance is crucial for the identification of strategies to prevent and overcome it. Given the defined nature of the oncogenic lesions present in genetically engineered mouse models (GEMMs) and the relative ease of sample collection and analysis, they are ideal systems in which to recapitulate the response and subsequent emergence of resistance to targeted therapies. When agents that are very effective at eradicating tumors are used in GEMMs, obtaining drug-resistant tumors can be a challenge. One approach to generating such tumors is the use of a suboptimal intermittent dosing strategy to treat the animals, which allows for periods of tumor growth and progression in the absence of drug. This intermittent dosing strategy has been used successfully to study resistance to the tyrosine kinase erlotinib in lung cancer models and is described here. Although this protocol is specific for this experimental system, the concepts and general design can be adapted for use with GEMMs of other cancers.
Cre-Dependent Adeno-Associated Virus Preparation and Delivery for Labeling Neurons in the Mouse Brain
Authors: Huang Z. Josh , Taniguchi Hiroki , He Miao , Kuhlman Sandra
Published: February 2014

Virus-mediated gene delivery is a powerful strategy for labeling and manipulating neurons in mammalian brains. A major drawback of this gene delivery method has been the lack of cell-type specificity. However, methods that combine Cre-knockin mice and Cre-activated adeno-associated virus (AAV) have now been developed to achieve high-level, stable, and cell-type-specific gene expression. Here, we describe a protocol for the design, production, and delivery of Cre-dependent AAVs. This method is simple and highly efficient, and allows chronic live imaging of defined classes of synapses in the mouse brain.
Tracking Receptors Using Individual Fluorescent and Nonfluorescent Nanolabels
Authors: Cognet Laurent , Lounis Brahim , Choquet Daniel
Published: February 2014

The plasma membrane is a fluid–mosaic structure in which some molecules seem to be randomly distributed and others show a precise compartmentalization that is related to their functional properties. These membrane domains are submicrometer in size and therefore are close to or below the optical diffraction limit. This makes their study difficult by conventional microscopy. Moreover, these compartments are usually dynamic in size and composition as their component molecules can continuously enter and exit by diffusion. Real-time, high-resolution, live-imaging methods rather than static imaging are thus required to reflect the real behavior of membrane molecules. Single-molecule techniques fulfill these requirements, as they provide information about the dynamics of molecules, together with nanometer resolution to study their distribution. Here we describe imaging and tracking techniques using nanometer-sized optical labels for the study of the movement of individual or small assemblies of membrane proteins. These labels include fluorescent dyes, luminescent nanocrystals, and absorbing metallic nanoparticles. Single-molecule tracking (SMT), with the use of organic dyes and semiconductor quantum dots (QDs), and single-particle tracking (SPT), with the use of gold nanoparticles, allow one to study the diffusion of individual molecules, their compartmentalization, and their interactions with other molecules. This protocol describes three methods for imaging and tracking membrane proteins: SMT using an organic dye, quantum dot tracking (QDT), and single-nanoparticle photothermal tracking (SNaPT) using gold nanoparticles. Organic dyes and QDs are tracked by single-molecule epifluorescence microscopy. Gold nanoparticles are detected by photothermal heterodyne imaging (PHI) and tracked using a triangulation scheme.