bluuebunny/crossref_metadata_2025 huggingface dataset:
XXXIX.—Transformations of Hypergeometric Functions of Two Variables
Authors: Erdélyi A.
Published: April 2015

I. There are several methods for obtaining transformations of hypergeometric functions of two variables.

Firstly, by transformation of the hypergeometric series. When the double series is rewritten as an infinite sum of hypergeometric functions of one variable, the known transformation theory of such functions can be applied to each term. This method is quite simple and, in a limited range, very effective for discovering transformations as well as proving them.

Secondly, by transformation of the systems of partial differential equations satisfied by the hypergeometric functions. This method, though simple in theory, is rather laborious in practice and not very useful for discovering new transformations.
What Instruments Are Available for Polar Studies?
Authors: Brunt Kelly M. , MacGregor Joseph A.
Published: April 2015

Instrumentation for Polar Glaciology and Geophysics Research Workshop; Baltimore, Maryland, 9–10 October 2014
California's 2012–2014 Drought Unusual for Last Millennium
Authors: Kollipara Puneet
Published: April 2015

Soil moisture estimates, inferred from thousands of tree rings spanning the past 12 centuries, highlight the severity of the recent record-breaking drought.
Renewable Energy Trend Could Help with Climate Mitigation
Authors: Showstack Randy
Published: April 2015

Analysts say that a 17% increase in global investment in renewable energy is part of a significant shift in energy trends toward addressing climate change.
Lpr‐induced systemic autoimmunity is unaffected by mast cell deficiency
Authors: van Nieuwenhuijze Annemarie EM , Cauwe Bénédicte , Klatt Denise , Humblet‐Baron Stéphanie , Liston Adrian
Published: April 2015

The function of mast cells in allergic and organ‐specific autoimmune responses is highly controversial. In the current study, we aimed to dissect the role of mast cells in systemic autoimmunity in the B6lpr/lpr mouse, a spontaneous model of systemic lupus erythematosus. B6lpr/lpr mice were interbred with C57Bl/6‐KitW‐sh/W‐sh (Wsh) mice, resulting in mast cell deficiency. The offspring from this cross (Lpr/Wsh mice) developed symptoms of lupus of the same severity as B6lpr/lpr mice. Loss of mast cells on the Lpr background did not alter autoantibody production, proteinuria, the composition of T and B cell populations or autoimmune pathology. Reduced c‐Kit expression did drive expanded splenomegaly and impeded interleukin‐4 production by CD4+ cells, suggesting minor functions for mast cells. In general, we conclude that mast cell deficiency and c‐Kit deficiency do not play a role in the pathogenesis of lupus in B6lpr/lpr mice.
Local–global overlap in diversity informs mechanisms of bacterial biogeography
Authors: Livermore Joshua A , Jones Stuart E
Published: April 2015

Spatial variation in environmental conditions and barriers to organism movement are thought to be important factors for generating endemic species, thus enhancing global diversity. Recent microbial ecology research suggested that the entire diversity of bacteria in the global oceans could be recovered at a single site, thus inferring a lack of bacterial endemism. We argue this is not the case in the global ocean, but might be in other bacterial ecosystems with higher dispersal rates and lower global diversity, like the human gut. We quantified the degree to which local and global bacterial diversity overlap in a diverse set of ecosystems. Upon comparison of observed local–global diversity overlap with predictions from a neutral biogeography model, human-associated microbiomes (gut, skin, mouth) behaved much closer to neutral expectations whereas soil, lake and marine communities deviated strongly from the neutral expectations. This is likely a result of differences in dispersal rate among ‘patches’, global diversity of these systems, and local densities of bacterial cells. It appears that overlap of local and global bacterial diversity is surprisingly large (but likely not one-hundred percent), and most importantly this overlap appears to be predictable based upon traditional biogeographic parameters like community size, global diversity, inter-patch environmental heterogeneity and patch connectivity.
Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe
Authors: Kay Gemma L. , Sergeant Martin J. , Zhou Zhemin , Chan Jacqueline Z.-M. , Millard Andrew , Quick Joshua , Szikossy Ildikó , Pap Ildikó , Spigelman Mark , Loman Nicholas J. , Achtman Mark , Donoghue Helen D. , Pallen Mark J.
Published: April 2015

Tuberculosis (TB) was once a major killer in Europe, but it is unclear how the strains and patterns of infection at ‘peak TB’ relate to what we see today. Here we describe 14 genome sequences of M. tuberculosis, representing 12 distinct genotypes, obtained from human remains from eighteenth-century Hungary using metagenomics. All our historic genotypes belong to M. tuberculosis Lineage 4. Bayesian phylogenetic dating, based on samples with well-documented dates, places the most recent common ancestor of this lineage in the late Roman period. We find that most bodies yielded more than one M. tuberculosis genotype and we document an intimate epidemiological link between infections in two long-dead individuals. Our results suggest that metagenomic approaches usefully inform detection and characterization of historical and contemporary infections.
The positive influence of fullerene derivatives bonded to manganese(iii) porphyrins on water proton relaxation
Authors: Zou Toujun , Zhen Mingming , Chen Daiqin , Li Ruimin , Guan Mirong , Shu Chunying , Han Hongbin , Wang Chunru
Published: April 2015

Manganese-porphyrin compounds as MRI contrast agents have drawn particular attention due to high relaxivities and unique biodistribution.
Generation of cycloheptynes and cyclooctynes via a sulfoxide–magnesium exchange reaction of readily synthesized 2-sulfinylcycloalkenyl triflates
Authors: Yoshida Suguru , Karaki Fumika , Uchida Keisuke , Hosoya Takamitsu
Published: April 2015

Cycloheptynes and cyclooctynes have been efficiently generated via a sulfoxide–magnesium exchange reaction of readily synthesized 2-sulfinylcycloalkenyl triflates.
Simple access to β-trifluoromethyl-substituted ketones via copper-catalyzed ring-opening trifluoromethylation of substituted cyclopropanols
Authors: Kananovich Dzmitry G. , Konik Yulia A. , Zubrytski Dzmitry M. , Järving Ivar , Lopp Margus
Published: April 2015

A variety of β-trifluoromethyl ketones have been easily prepared by CuCl-catalyzed ring-opening trifluoromethylation of cyclopropanols with Togni reagent.
Synthesis of tungsten carbide nanoparticles in biochar matrix as a catalyst for dry reforming of methane to syngas
Authors: Yan Qiangu , Lu Yongwu , To Filip , Li Yebo , Yu Fei
Published: April 2015

Tungsten carbide (WC) nanoparticles were synthesized by carbothermal reduction (CR) of tungsten-promoted biochar.
Facile synthesis and photocatalytic properties of ZnO core/ZnS–CdS solid solution shell nanorods grown vertically on reductive graphene oxide
Authors: Xu Jimeng , Sang Huanxin , Wang Xitao , Wang Kang
Published: April 2015

The synthesis of ZnO core/ZnxCd1−xS shell nanorods grown vertically on RGO sheets and the important role played by ZnxCd1−xS on photocatalytic activity are described.
Colchicine derivatives with potent anticancer activity and reduced P-glycoprotein induction liability
Authors: Singh Baljinder , Kumar Ashok , Joshi Prashant , Guru Santosh K. , Kumar Suresh , Wani Zahoor A. , Mahajan Girish , Hussain Aashiq , Qazi Asif Khurshid , Kumar Ajay , Bharate Sonali S. , Gupta Bishan D. , Sharma Parduman R. , Hamid Abid , Saxena Ajit K. , Mondhe Dilip M. , Bhushan Shashi , Bharate Sandip B. , Vishwakarma Ram A.
Published: April 2015

Colchicine derivatives with reduced P-gp induction liability have been identified.
A facile strategy to fabricate glucose-responsive vesicles via a template of thermo-sensitive micelles
Authors: Yang Hao , Ma Rujiang , Yue Jing , Li Chang , Liu Yong , An Yingli , Shi Linqi
Published: April 2015

Polymer vesicles fabricated based on the complexation between PBA- and GA containing block copolymers exhibited glucose-responsiveness at physiological pH.
In situ Si doping of heteroepitaxially grown c-BN thin films at different temperatures
Authors: Yin H. , Ziemann P.
Published: April 2015

Phase pure cubic boron nitride (c-BN) films have been epitaxially grown on (001) diamond substrates at 420 °C, 600 °C and 900 °C.
Hybrid magnetic–plasmonic nanocomposite: embedding cobalt clusters in gold nanorods
Authors: Emam A. N. , Mohamed M. B. , Girgis E. , Rao K. V.
Published: April 2015

Preparation of Plasmonic–magnetic hybrid nanorods via modified seed mediated method: using cobalt seeds instead of gold to prepare Au–Co NRs.
Cu(i) complex based on 6H-indolo[2,3-b]quinoxaline: structure and electrocatalytic properties for hydrogen evolution reaction from water
Authors: Zhang Pan , Yang Xin , Jiang Penggang , Yin Junli , Gong Yun , Lin Jianhua
Published: April 2015

A Cu(i) complex can act as an electrochemically stable electrocatalyst for the hydrogen evolution reaction, which can improve the exchanging current density with ca. 40 kJ mol−1 of Ea from 30 to 50 °C.
Molecularly imprinted and nanoengineered camphor soot functionalized PAN-nanofibers for effluent treatment
Authors: Sharma Surabhi , Balasubramanian K.
Published: April 2015

A novel platform for the synthesis of ion-imprinted electrospun PAN–camphor soot nanofibers for the speciation and treatment of radioactive metal ions is proposed.
Diketo acids and their amino acid/dipeptidic analogues as promising scaffolds for the development of bacterial methionine aminopeptidase inhibitors
Authors: Masood Mir Mohammad , Pillalamarri Vijay K. , Irfan Mohammad , Aneja Babita , Jairajpuri Mohamad Aman , Zafaryab Md. , Rizvi M. Moshahid A. , Yadava Umesh , Addlagatta Anthony , Abid Mohammad
Published: April 2015

Diketo acids and their peptidic analogues were designed and synthesised as bacterial MetAP inhibitors. In the enzymatic assay, the representative compound5eshowed excellent inhibition of bacterial MetAPs with no cytotoxicity.
A high efficiency biological system for treatment of coal gasification wastewater – a key in-depth technological research
Authors: Ji Qinhong , Tabassum Salma , Yu Guangxin , Chu Chunfeng , Zhang Zhenjia
Published: April 2015

Wastewater treatment technology with a simple processing unit, easy management, low energy consumption, low sludge production and a cost of 0.135 $ per m3.
ESR/UV-Vis-NIR spectroelectrochemical study and electrochromic contrast enhancement of a polythiophene derivative bearing a pendant viologen
Authors: Gadgil Bhushan , Damlin Pia , Dmitrieva Evgenia , Ääritalo Timo , Kvarnström Carita
Published: April 2015

Improved electrochromism of a polythiophene derivative bearing pendant viologen group and its ESR/UV-Vis-NIR spectroelectrochemical characterization.
Green synthesis of a palladium–polyaniline nanocomposite for green Suzuki–Miyaura coupling reactions
Authors: Dutt Sunil , Kumar Raj , Siril Prem Felix
Published: April 2015

One pot synthesis of the pd–polyaniline nanocomposite and its catalytic activity in Suzuki–Miyaura coupling reaction in water.
Combined epitaxial self-assembly of block copolymer lamellae on a hexagonal pre-pattern within microgrooves
Authors: Jung Hyunjung , Woo Sanghoon , Park Sungmin , Lee Sumi , Kang Minhyuk , Choe Youngson , Son Jeong Gon , Ryu Du Yeol , Huh June , Bang Joona
Published: April 2015

We demonstrated a simple and feasible technology for a DSA process by combining graphoepitaxy with “inexpensive” chemoepitaxial assembly to improve the alignment of lamellar microdomains.
Helical alignment inversion of microtubules in accordance with a structural change in their lattice
Authors: Shikinaka Kazuhiro , Mori Saori , Shigehara Kiyotaka , Masunaga Hiroyasu
Published: April 2015

Finely-regulated giant helical alignments of microtubules with centimeter order according to their lattice structure form over a temperature gradient during anisotropic spiral propagation via tubulin dimer addition in a capillary cell.
Synthesis of a calcium-bridged siloxene by a solid state reaction for optical and electrochemical properties
Authors: Imagawa Haruo , Takahashi Naoko , Nonaka Takamasa , Kato Yuichi , Nishikawa Kazutaka , Itahara Hiroshi
Published: April 2015

A Ca-bridged siloxene resulting from the deintercalation of Ca from CaSi2was synthesized, which shows stable Li storage performance.
High rate fabrication of room temperature red photoluminescent SiC nanocrystals
Authors: Cao Tengfei , Cheng Yan , Zhang Haibao , Yan Binhang , Cheng Yi
Published: April 2015

SiC nanocrystals with room temperature red region photoluminescence are fabricated at a high rate in atmospheric pressure thermal plasma using SiCl4 and C2H2 as the silicon source and carbon source, respectively.
Systematically tuning the ΔESTand charge balance property of bipolar hosts for low operating voltage and high power efficiency solution-processed electrophosphorescent devices
Authors: Ban Xinxin , Jiang Wei , Sun Kaiyong , Yang Haiyong , Miao Yanan , Yang Fenghao , Sun Yueming , Huang Bin , Duan Lian
Published: April 2015

Balanced charge transporting behavior appears to be more important than an extremely small ΔESTin solution-processed devices.
Flow topologies and turbulence scales in a jet-in-cross-flow
Authors: Ruiz A. M. , Lacaze G. , Oefelein J. C.
Published: April 2015

This paper presents a detailed analysis of the flow topologies and turbulence scales in the jet-in-cross-flow experiment of Su and Mungal [“Simultaneous measurements of scalar and velocity field evolution in turbulent crossflowing jets,” J. Fluid Mech. 513(1), 1–45 (2004)]. The analysis is performed using the Large Eddy Simulation (LES) technique with a highly resolved grid and time-step and well controlled boundary conditions. This enables quantitative agreement with the first and second moments of turbulence statistics measured in the experiment. LES is used to perform the analysis since experimental measurements of time-resolved 3D fields are still in their infancy and because sampling periods are generally limited with direct numerical simulation. A major focal point is the comprehensive characterization of the turbulence scales and their evolution. Time-resolved probes are used with long sampling periods to obtain maps of the integral scales, Taylor microscales, and turbulent kinetic energy spectra. Scalar-fluctuation scales are also quantified. In the near-field, coherent structures are clearly identified, both in physical and spectral space. Along the jet centerline, turbulence scales grow according to a classical one-third power law. However, the derived maps of turbulence scales reveal strong inhomogeneities in the flow. From the modeling perspective, these insights are useful to design optimized grids and improve numerical predictions in similar configurations.
Simultaneous measurement of temperature and magnetic field based on a long period grating concatenated with multimode fiber
Authors: Miao Yinping , Zhang Hao , Lin Jichao , Song Binbin , Zhang Kailiang , Lin Wei , Liu Bo , Yao Jianquan
Published: April 2015

A dual-parameter measurement scheme based on a long-period fiber grating (LPFG) concatenated with a multimode fiber (MMF) has been proposed and experimentally demonstrated for simultaneous measurement of magnetic field and temperature. Splicing the LPFG with the etched MMF enables the coupling between the core modes and different cladding modes of the LPFG as well as the interferences between higher-order modes in the MMF. Due to different transmission mechanisms of the LPFG and mode interference, the proposed sensor shows transmission dip wavelength sensitivities of 0.02878 nm/Oe and −0.04048 nm/°C for multi-mode interference (MMI) and −0.0024 nm/Oe and 0.03929 nm/°C for the LPFG, respectively. By monitoring the opposite behaviors of resonance wavelength shift corresponding to the LPFG and MMI, the magnetic field and environmental temperature can be simultaneously measured. The spectral characteristics of the proposed sensor that could be tuned through control of both environmental temperature and applied magnetic field, which would provide a promising candidate for dual-channel filtering applications as well as multi-parameter measurement applications.
Addressable multi-nozzle electrohydrodynamic jet printing with high consistency by multi-level voltage method
Authors: Pan Yanqiao , Huang YongAn , Guo Lei , Ding Yajiang , Yin Zhouping
Published: April 2015

It is critical and challenging to achieve the individual jetting ability and high consistency in multi-nozzle electrohydrodynamic jet printing (E-jet printing). We proposed multi-level voltage method (MVM) to implement the addressable E-jet printing using multiple parallel nozzles with high consistency. The fabricated multi-nozzle printhead for MVM consists of three parts: PMMA holder, stainless steel capillaries (27G, outer diameter 400 μm) and FR-4 extractor layer. The key of MVM is to control the maximum meniscus electric field on each nozzle. The individual jetting control can be implemented when the rings under the jetting nozzles are 0 kV and the other rings are 0.5 kV. The onset electric field for each nozzle is ∼3.4 kV/mm by numerical simulation. Furthermore, a series of printing experiments are performed to show the advantage of MVM in printing consistency than the “one-voltage method” and “improved E-jet method”, by combination with finite element analyses. The good dimension consistency (274μm, 276μm, 280μm) and position consistency of the droplet array on the hydrophobic Si substrate verified the enhancements. It shows that MVM is an effective technique to implement the addressable E-jet printing with multiple parallel nozzles in high consistency.
Predicting wildfire occurrence distribution with spatial point process models and its uncertainty assessment: a case study in the Lake Tahoe Basin, USA
Authors: Yang Jian , Weisberg Peter J. , Dilts Thomas E. , Loudermilk E. Louise , Scheller Robert M. , Stanton Alison , Skinner Carl
Published: April 2015

Strategic fire and fuel management planning benefits from detailed understanding of how wildfire occurrences are distributed spatially under current climate, and from predictive models of future wildfire occurrence given climate change scenarios. In this study, we fitted historical wildfire occurrence data from 1986 to 2009 to a suite of spatial point process (SPP) models with a model averaging approach. We then predicted human- and lightning-caused wildfire occurrence over the 2010–2100 period in the Lake Tahoe Basin, a forested watershed in the western US with an extensive wildland–urban interface. The purpose of our research was threefold, including (1) to quantify the influence of biophysical and anthropogenic explanatory variables on spatial patterns of wildfire occurrence, (2) to model current and future spatial distribution of wildfire occurrence under two carbon emission scenarios (A2 and B1), and (3) to assess prediction uncertainty due to model selection. We found that climate variables exerted stronger influences on lightning-caused fires, with climatic water deficit the most important climatic variable for both human- and lightning-caused fires. The recent spatial distribution of wildfire hotspots was mainly constrained by anthropogenic factors because most wildfires were human-caused. The future distribution of hotspots (i.e. places with high fire occurrence density), however, was predicted to shift to higher elevations and ridge tops due to a more rapid increase of lightning-caused fires. Landscape-scale mean fire occurrence density, averaged from our top SPP models with similar empirical support, was predicted to increase by 210% and 70% of the current level under the A2 and B1 scenarios. However, individual top SPP models could lead to substantially different predictions including a small decrease, a moderate increase, and a very large increase, demonstrating the critical need to account for model uncertainty.
High-yield hydrogen production from biomass by in vitro metabolic engineering: Mixed sugars coutilization and kinetic modeling
Authors: Rollin Joseph A. , Martin del Campo Julia , Myung Suwan , Sun Fangfang , You Chun , Bakovic Allison , Castro Roberto , Chandrayan Sanjeev K. , Wu Chang-Hao , Adams Michael W. W. , Senger Ryan S. , Zhang Y.-H. Percival
Published: April 2015

Significance

Hydrogen (H
2
) has great potential to be used to power passenger vehicles. One solution to these problems is to distribute and store renewable carbohydrate instead, converting it to hydrogen as required. In this work more than 10 purified enzymes were combined into artificial enzymatic pathways and a high yield from both glucose and xylose to hydrogen was achieved. Also, gaseous hydrogen can be separated from aqueous substrates easily, greatly decreasing product separation costs, and avoid reconcentrating sugar solutions. This study describes high-yield enzymatic hydrogen production from biomass sugars and an engineered reaction rate increase achieved through the use of kinetic modeling. Distributed hydrogen production based on evenly distributed less-costly biomass could accelerate the implementation of the hydrogen economy.
Information flow between interacting human brains: Identification, validation, and relationship to social expertise
Authors: Bilek Edda , Ruf Matthias , Schäfer Axel , Akdeniz Ceren , Calhoun Vince D. , Schmahl Christian , Demanuele Charmaine , Tost Heike , Kirsch Peter , Meyer-Lindenberg Andreas
Published: April 2015

Significance

Social interaction is the likely driver of human brain evolution, critical for health, and underlies phenomena as varied as childhood development, stock market behavior, and much of what is studied in the humanities. However, appropriate experimental methods to study the underlying brain processes are still developing and technically challenging. Here, we extend previous pioneering approaches in neuroimaging [functional MRI (fMRI) hyperscanning] to provide a method for studying information flow between interacting humans in a two-person approach. A scan environment enabling synchronized data acquisition and interaction-based fMRI tasks is described. We provide a generally applicable analysis method to identify interacting brain systems. Specific social brain systems are identified as drivers of interaction in humans, and we find a link to a measure of social expertise.
Exonuclease TREX1 degrades double-stranded DNA to prevent spontaneous lupus-like inflammatory disease
Authors: Grieves Jessica L. , Fye Jason M. , Harvey Scott , Grayson Jason M. , Hollis Thomas , Perrino Fred W.
Published: April 2015

Significance

The TREX1 enzyme degrades DNA, and mutations in the
TREX1
gene cause autoimmune diseases. The
TREX1
D18N mutation causes a form of lupus called familial chilblain lupus. We solved the structure of TREX1 D18N bound to dsDNA, showing how the enzyme interacts with dsDNA. We also replaced the
TREX1
WT gene in mice with the
TREX1
D18N mutated gene and showed how this mutation causes a lupus-like disease. Together, the TREX1 D18N–dsDNA structure and the spontaneous disease exhibited in the
TREX1
D18N mouse help to define how TREX1 degrades dsDNA to prevent this molecule from acting as an autoantigen in the mouse and, most likely, in humans to promote autoimmune disease.
Telomere dysfunction causes alveolar stem cell failure
Authors: Alder Jonathan K. , Barkauskas Christina E. , Limjunyawong Nathachit , Stanley Susan E. , Kembou Frant , Tuder Rubin M. , Hogan Brigid L. M. , Mitzner Wayne , Armanios Mary
Published: April 2015

Significance

Idiopathic pulmonary fibrosis and emphysema are leading causes of mortality, but there are no effective therapies. Mutations in telomerase are the most common identifiable risk factor for idiopathic pulmonary fibrosis. They also predispose to severe emphysema in smokers, occurring at a frequency similar to α-1 antitrypsin deficiency. The work shown here points to alveolar stem cell senescence as a driver of these pathologies. Epithelial stem cell failure was associated with secondary inflammatory recruitment and exquisite susceptibility to injury from “second hits.” The findings suggest that efforts to reverse the stem cell failure state directly, rather than its secondary consequences, may be an effective therapy approach in telomere-mediated lung disease.
Detection of endogenous and food-derived collagen dipeptide prolylhydroxyproline (Pro-Hyp) in allergic contact dermatitis-affected mouse ear
Authors: Kusubata Masashi , Koyama Yoh-ichi , Tometsuka Chisa , Shigemura Yasutaka , Sato Kenji
Published: April 2015

Generation of collagen dipeptides and deposition of orally administered prolylhydroxyproline (Pro-Hyp) in local inflammatory sites were examined in mice with hapten (2,4-dinitrofluorobenzene)-induced dermatitis in the ear. Pro-Hyp content in the hapten-treated ear was significantly higher in the chronic phase of contact dermatitis than the vehicle control. In contrast, hydroxyprolylglycine contents remained at lower levels in all cases compared to Pro-Hyp. Four hours after the ingestion of [13C5,15N]Pro and [13C5,15N]Pro-Hyp, labeled-Pro-Hyp and Pro, respectively, appeared only in the ear with dermatitis. Thus, Pro-Hyp is generated and degraded as part of the rapid synthesis and degradation of collagen in the ear with dermatitis. In addition to the endogenously generated Pro-Hyp, the orally administered Pro-Hyp was deposited in the ears.
G3BP1 promotes stress-induced RNA granule interactions to preserve polyadenylated mRNA
Authors: Aulas Anaïs , Caron Guillaume , Gkogkas Christos G. , Mohamed Nguyen-Vi , Destroismaisons Laurie , Sonenberg Nahum , Leclerc Nicole , Parker J. Alex , Vande Velde Christine
Published: April 2015

G3BP1, a target of TDP-43, is required for normal stress granule (SG) assembly, but the functional consequences of failed SG assembly remain unknown. Here, using both transformed cell lines and primary neurons, we investigated the functional impact of this disruption in SG dynamics. While stress-induced translational repression and recruitment of key SG proteins was undisturbed, depletion of G3BP1 or its upstream regulator TDP-43 disturbed normal interactions between SGs and processing bodies (PBs). This was concomitant with decreased SG size, reduced SG–PB docking, and impaired preservation of polyadenylated mRNA. Reintroduction of G3BP1 alone was sufficient to rescue all of these phenotypes, indicating that G3BP1 is essential for normal SG–PB interactions and SG function.
Open source software for quantification of cell migration, protrusions, and fluorescence intensities
Authors: Barry David J. , Durkin Charlotte H. , Abella Jasmine V. , Way Michael
Published: April 2015

Cell migration is frequently accompanied by changes in cell morphology (morphodynamics) on a range of spatial and temporal scales. Despite recent advances in imaging techniques, the application of unbiased computational image analysis methods for morphodynamic quantification is rare. For example, manual analysis using kymographs is still commonplace, often caused by lack of access to user-friendly, automated tools. We now describe software designed for the automated quantification of cell migration and morphodynamics. Implemented as a plug-in for the open-source platform, ImageJ, ADAPT is capable of rapid, automated analysis of migration and membrane protrusions, together with associated fluorescently labeled proteins, across multiple cells. We demonstrate the ability of the software by quantifying variations in cell population migration rates on different extracellular matrices. We also show that ADAPT can detect and morphologically profile filopodia. Finally, we have used ADAPT to compile an unbiased description of a “typical” bleb formed at the plasma membrane and quantify the effect of Arp2/3 complex inhibition on bleb retraction.
Regulatory network inferred using expression data of small sample size: application and validation in erythroid system
Authors: Zhu Fan , Shi Lihong , Engel James Douglas , Guan Yuanfang
Published: April 2015

Motivation: Modeling regulatory networks using expression data observed in a differentiation process may help identify context-specific interactions. The outcome of the current algorithms highly depends on the quality and quantity of a single time-course dataset, and the performance may be compromised for datasets with a limited number of samples.

Results: In this work, we report a multi-layer graphical model that is capable of leveraging many publicly available time-course datasets, as well as a cell lineage-specific data with small sample size, to model regulatory networks specific to a differentiation process. First, a collection of network inference methods are used to predict the regulatory relationships in individual public datasets. Then, the inferred directional relationships are weighted and integrated together by evaluating against the cell lineage-specific dataset. To test the accuracy of this algorithm, we collected a time-course RNA-Seq dataset during human erythropoiesis to infer regulatory relationships specific to this differentiation process. The resulting erythroid-specific regulatory network reveals novel regulatory relationships activated in erythropoiesis, which were further validated by genome-wide TR4 binding studies using ChIP-seq. These erythropoiesis-specific regulatory relationships were not identifiable by single dataset-based methods or context-independent integrations. Analysis of the predicted targets reveals that they are all closely associated with hematopoietic lineage differentiation.

Availability and implementation: The predicted erythroid regulatory network is available at http://guanlab.ccmb.med.umich.edu/data/inferenceNetwork/.

Contact:  gyuanfan@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data
Authors: Alon Shahar , Erew Muhammad , Eisenberg Eli
Published: April 2015

Summary: DREAM: detecting RNA editing associated with microRNAs, is a webserver for the identification of mature microRNA editing events using deep sequencing data. Raw microRNA sequencing reads can be provided as input, the reads are aligned against the genome and custom scripts process the data, search for potential editing sites and assess the statistical significance of the findings. The output is a text file with the location and the statistical description of all the putative editing sites detected.

Availability and implementation: DREAM is freely available on the web at http://www.cs.tau.ac.il/∼mirnaed/.

Contact: elieis@post.tau.ac.il
Three minimal sequences found in Ebola virus genomes and absent from human DNA
Authors: Silva Raquel M. , Pratas Diogo , Castro Luísa , Pinho Armando J. , Ferreira Paulo J. S. G.
Published: April 2015

Motivation: Ebola virus causes high mortality hemorrhagic fevers, with more than 25 000 cases and 10 000 deaths in the current outbreak. Only experimental therapies are available, thus, novel diagnosis tools and druggable targets are needed.

Results: Analysis of Ebola virus genomes from the current outbreak reveals the presence of short DNA sequences that appear nowhere in the human genome. We identify the shortest such sequences with lengths between 12 and 14. Only three absent sequences of length 12 exist and they consistently appear at the same location on two of the Ebola virus proteins, in all Ebola virus genomes, but nowhere in the human genome. The alignment-free method used is able to identify pathogen-specific signatures for quick and precise action against infectious agents, of which the current Ebola virus outbreak provides a compelling example.

Availability and Implementation: EAGLE is freely available for non-commercial purposes at http://bioinformatics.ua.pt/software/eagle.

Contact:  raquelsilva@ua.pt; pratas@ua.pt

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Enterococcus faecalislipoteichoic acid suppressesAggregatibacter actinomycetemcomitanslipopolysaccharide-induced IL-8 expression in human periodontal ligament cells
Authors: Im Jintaek , Baik Jung Eun , Kim Kyoung Whun , Kang Seok-Seong , Jeon Jun Ho , Park Ok-Jin , Kim Hyun Young , Kum Kee-Yeon , Yun Cheol-Heui , Han Seung Hyun
Published: April 2015

Periodontitis is caused by multi-bacterial infection and Aggregatibacter actinomycetemcomitans and Enterococcus faecalis are closely associated with inflammatory periodontal diseases. Although lipopolysaccharide (LPS) of A. actinomycetemcomitans (Aa.LPS) and lipoteichoic acid of E. faecalis (Ef.LTA) are considered to be major virulence factors evoking inflammatory responses, their combinatorial effect on the induction of chemokines has not been investigated. In this study, we investigated the interaction between Aa.LPS and Ef.LTA on IL-8 expression in human periodontal ligament (PDL) cells. Aa.LPS, but not Ef.LTA, substantially induced IL-8 expression at the protein and mRNA levels. Interestingly, Ef.LTA suppressed Aa.LPS-induced IL-8 expression without affecting the binding of Aa.LPS to Toll-like receptor (TLR) 4. Ef.LTA reduced Aa.LPS-induced phosphorylation of mitogen-activated protein kinases, including ERK, JNK and p38 kinase. Furthermore, Ef.LTA inhibited the Aa.LPS-induced transcriptional activities of the activating protein 1, CCAAT/enhancer-binding protein and nuclear factor-kappa B transcription factors, all of which are known to regulate IL-8 gene expression. Ef.LTA augmented the expression of IL-1 receptor–associated kinase-M (IRAK-M), a negative regulator of TLR intracellular signaling pathways, in the presence of Aa.LPS at both the mRNA and protein levels. Small interfering RNA silencing IRAK-M reversed the attenuation of Aa.LPS-induced IL-8 expression by Ef.LTA. Collectively, these results suggest that Ef.LTA down-regulates Aa.LPS-induced IL-8 expression in human PDL cells through up-regulation of the negative regulator IRAK-M.
Lack of IL-17 signaling decreases liver fibrosis in murine schistosomiasis japonica
Authors: Zhang Yuxia , Huang Dake , Gao Wenda , Yan Jun , Zhou Wanling , Hou Xin , Liu Miao , Ren Cuiping , Wang Siying , Shen Jijia
Published: April 2015

Accumulating evidence has identified the profibrogenic properties of IL-17A in organ fibrosis. However, the role of IL-17A signal in liver fibrosis induced by Schistosoma japonicum infection remains unclear. In this study, we investigated liver fibrosis in wild-type (WT) and IL-17RA−/− mice upon S. japonicum infection. Hepatic IL-17A, IL-17C, IL-17E (IL-25), IL-17F, IL-17RA, IL-17RB and IL-17RC transcript levels were determined by RT-PCR. IL-17A+ cells were analyzed by flow cytometry and confocal microscopy among granuloma cells. Immunostaining of IL-17R was performed on liver sections. Collagen deposition was assessed by Van Gieson’s staining. IL-17A, IL-17C, IL-17E, IL-17F, IL-17RA and IL-17RC mRNA levels were dramatically increased in fibrotic livers. Among granuloma cells, CD3+ and CD3− lymphocytes, neutrophils and macrophages were found to express IL-17A. Compared to WT, IL-17RA−/− mice displayed attenuated granulomatous inflammation, liver fibrosis, improved liver function and high survival. Meanwhile, α-smooth muscle actin staining and the expression of fibrogenic genes (transforming growth factor β, IL-13 and collagen-I) as well as IL-17A–induced proinflammatory mediators (IL-1β, IL-6, tumor necrosis factor α, CXCL1 and CXCL2) and proteinases (MMP3 and TIMP1) involved in fibrosis were markedly reduced in IL-17RA−/− mice. In addition, Th2 cytokines IL-4 and IL-17E (IL-25) were also decreased in IL-17RA−/− mice. These results indicated that IL-17A signal contributes to the pathogenesis of liver fibrosis in murine schistosomiasis. This effect was induced possibly by activating hepatic stellate cells and stimulating the release of proinflammatory cytokines and chemokines. Furthermore, the Th2 response was also enhanced by IL-17A signals. Our data demonstrate that IL-17A may serve as a promising target for antifibrotic therapy.
Post-Traumatic Stress Disorder
Authors: Brody David L
Published: April 2015

In many contexts, the trauma that caused the concussion can also trigger a strong stress response. Take a focused history from the patient and collateral source for hyperarousal, nightmares, avoidance, emotional numbing, dissociation, and prior diagnosis of post-traumatic stress disorder (PTSD). Assess safety. Severe PTSD can lead to suicide. Refer to a psychologist or counselor with specific expertise in PTSD for prolonged exposure therapy or cognitive behavioral therapy. Optimize sleep. Start an anxiolytic antidepressant. Prescribe prazosin for nightmares. Ideally, use short-acting benzodiazepines only for emergencies. Advise the patient to stop drinking alcohol. Treat chronic pain aggressively if present. Consider a second-line mood stabilizer if necessary. Don’t be afraid to use stimulants if the patient also has impairing attention deficit once the PTSD symptoms are under reasonable control.
Personality Change
Authors: Brody David L
Published: April 2015

Most common concerns include mood instability, depression with loss of interests and pleasures, fatigue, loss of social intelligence, or other changes in interpersonal style. Treat pain aggressively, as uncontrolled pain may be a major factor. Treat any mood instability, depression, fatigue, or loss of social intelligence. For loss of social intelligence, refer to a trained psychologist with expertise in social intelligence and to an occupational performance center if available for rehabilitation of social pragmatics in a group setting. For impairing changes in interpersonal style, refer to a psychologist with expertise in personality disorders. If the personality change is not causing significant problems, it is usually sufficient to educate the patient and family that personality commonly changes after brain injury and do not seem to be a problem at the moment.
Dizziness
Authors: Brody David L
Published: April 2015

Dizziness means many different things to different people: lightheadedness, vertigo, poor balance, mental fogginess, and others concerns. Lightheadedness, meaning a feeling like the patient may pass out, is usually due to low blood pressure, often orthostatic hypotension. Vertigo, meaning a sensation of spinning or movement, can be an inner ear problem or a brain problem: Stop toxic substances; if there is nystagmus, refer to ENT for a full evaluation; perform the Dix-Hallpike maneuver to assess for benign paroxysmal positional vertigo; and refer to physical therapy for repositioning maneuvers if positive; consider vestibular rehabilitation; consider a short course of medication such as scopolamine or meclizine; consider ordering an MRI scan of the brain, as sometimes the concussion unmasks another unrelated problem. Dizziness meaning “mental fogginess” usually turns out to be attention deficit. Dizziness meaning vague and nonspecific malaise usually turns out to be fatigue, depression, or anxiety.
Blurry Vision
Authors: Brody David L
Published: April 2015

Blurry vision after concussion can mean many different things. A loss of acuity in one eye is often due to direct injury to the eye. Intact acuity in each eye, but worse vision with both eyes open is often due to a subtle cranial nerve injury. Subtle 3rd cranial nerve or 4th cranial injuries typically cause vision to be worse looking up or down, whereas 6th nerve injuries are typically worse looking to one side. Visual attention deficit is sometimes described as blurry vision. Migraine auras often cause visual impairment. The chapter suggests modes of treatment for these situations. Paroxysmal changes in vision after concussion should be treated as presumptive migraine, or migraine equivalent even if there is no severe headache. Patients will benefit from best-corrected vision when starting aggressive cognitive rehabilitation even if preexisting visual impairments did not impair them much in everyday life before the concussion.
Smell and Taste Problems
Authors: Brody David L
Published: April 2015

This chapter addresses issues with smell and taste problems after concussion. There are no specific rehabilitative strategies, medications, or surgical procedures available for smell and taste (which is also mostly smell) dysfunction. The most important thing is education for safety, specifically with regard to smoke, natural gas leaks, car malfunctions, and spoiled food. Overeating is also a common consequence, which can be remedied by making food spicier. Phantosmia (smelling things that aren’t really there) is rare but can respond to treatment including trials of medications usually used for neuropathic pain.
Return to Driving
Authors: Brody David L
Published: April 2015

This chapter discusses issues surrounding return to driving after concussion and provides steps to follow in making these decisions. Return to driving decision-making can be challenging, because the risks of driving need to be balanced with the effects on autonomy and financial consequences. Obtain confidential collateral source information, as the patient may not be aware of his or her own deficits. Assess for definite contraindication, including seizures, other cause of intermittent unpredictable loss of consciousness (e.g., sleep attacks, cardiac arrhythmia), performance-impairing medications, visual impairment including peripheral fields, psychosis, severe impulsivity, poor decision-making, and physical impairments. Consider an on-the-road driving assessment performed by occupational therapy or a specialized service.
Medicolegal Aspects of Concussion
Authors: Brody David L
Published: April 2015

To address questions of real disability versus secondary gain, reliable and unbiased collateral source information is critical. The collateral sources should be people who know the patient well before and after the injury but don’t have a financial stake one way or another in the outcome. Often coworkers, neighbors, or community leaders are good choices. No scan or test can “rule in” or “rule out” concussion. Typically, CT scans and MRI scans are normal and there will not be any “objective” evidence for concussion.
Special Topics in Children
Authors: Brody David L
Published: April 2015

This chapter discusses special rules for children under 12 with concussion: (1) Take the history twice: once from the child and once from the parents or guardians. Young children can reliably report headache, nausea, balance problems, problems concentrating, and irritability. Other concerns as well as preinjury problems should be assessed from the parents or guardians. (2) Use age-appropriate language and simplified assessments of severity. (3) Carefully assess for secondary gain factors. A child may either overreport or underreport symptoms to please the parents or guardians. (4) With regard to return to school, sports, and daily life, help the parents or guardians find the “middle way”: not too protective and not too lax. (5) In complex concussion, assess for attention deficit and atypical presentations of migraine, depression, and anxiety. (6) Consider treatment with glucose.
Special Topics in Military Personnel
Authors: Brody David L
Published: April 2015

The best collateral source may be another service member with whom the patient has served in addition to a family member. Evaluate explicitly post-traumatic stress disorder (PTSD), chronic pain, sleep disorders, balance, and hearing loss, as these are common in military personnel with concussion, especially blast-related injuries. Maintain confidentiality. If the patient has been using drugs and/or alcohol, it may be wise to refer them for rehabilitation discretely, since active duty military personnel do not have the same privacy protections that civilians have, and this can jeopardize their future careers. Return-to-duty decision-making is best done in collaboration with military physicians and occupational therapists. Refer to community resources specifically dedicated to wounded warriors.
Common Problems, Realistic Solutions
Authors: Saint Sanjay
Published: April 2015

A hospital-wide intervention is rolled out. There are changes in the team leadership and many operational adjustments: supplies ordered, procedures redesigned, nursing assignments altered. Three major types of troublemakers are described: the active resisters, the organizational constipators, and the timeservers. Motivations range from opposition to any kind of change to a personal animus toward the project champions to a determination to do as little extra work as possible. Requests by patients and their families may be used to try to get around bladder bundle items or a member of the project team may approach nurses with a patronizing attitude. The team cheers short-term progress to encourage staff compliance, solicits concrete criticism as a path to improvement, and adjusts the implementation process to allow for special circumstances. Efforts to use the electronic medical record to game the system must be squelched.
Taking on C. Difficile
Authors: Saint Sanjay
Published: April 2015

The adaptive approach used in the previous chapters to prevent CAUTI is applied to an initiative to prevent Clostridium difficile infection. These two initiatives differ in terms of their scope, the members of their teams, and the elements of their bundles. For preventing C. difficile, for example, the most important bundle item is antimicrobial stewardship, since the use of broad-spectrum antibiotics vastly increases a person’s risk of becoming infected. Infectious disease physicians or clinical pharmacists examine the circumstances of antimicrobial prescriptions they have filled to see whether they meet infection prevention standards; if not, the prescribing physician will receive prompt feedback. Differences aside, the basic elements of the CAUTI framework apply, from the C-suite’s decision to go ahead with the initiative to the tactics used to sell the C. difficile bundle to the hospital staff.
The Future of Infection Prevention
Authors: Saint Sanjay
Published: April 2015

The technical advances described in this chapter could markedly aid the struggle to prevent HAIs. They range from nanomedicine to oral doses of probiotics and IBM’s Watson computer as diagnostician. The adaptive possibilities include further empowerment of the patient, on the one hand, and new approaches to bring hard-pressed clinicians emotional relief and improve their interactions with patients. Studies have shown that large numbers of physicians have suffered burnout. Many doctors and nurses are not fully attentive in their encounters with patients. Growing numbers of clinicians have begun practicing mindfulness, and the authors have designed a model to show how a mindful focus can help clinicians in implementing infection prevention initiatives.
Smoothed particle hydrodynamics with smoothed pseudo-density
Authors: Yamamoto Satoko , Saitoh Takayuki R. , Makino Junichiro
Published: April 2015

In this paper, we present a new formulation of smoothed particle hydrodynamics (SPH), which, unlike the standard SPH (SSPH), is well behaved at the contact discontinuity. The SSPH scheme cannot handle discontinuities in density (e.g., the contact discontinuity and the free surface), because it requires that the density of fluid is positive and continuous everywhere. Thus there is inconsistency in the formulation of the SSPH scheme at discontinuities of the fluid density. To solve this problem, we introduce a new quantity associated with particles and the “density” of that quantity. This “density” evolves through the usual continuity equation with an additional artificial diffusion term, in order to guarantee the continuity of the “density.” We use this “density,” or pseudo-density, instead of the mass density, to formulate our SPH scheme. We call our new method SPH with smoothed pseudo-density, and we show that it is physically consistent and can handle discontinuities quite well.