bluuebunny/crossref_metadata_2025_split huggingface dataset:
Late Pleistocene and early Holocene change in the Weddell Sea: a new climate record from the Patriot Hills, Ellsworth Mountains, West Antarctica
Authors: TURNEY CHRIS , FOGWILL CHRIS , VAN OMMEN TAS D. , MOY ANDREW D. , ETHERIDGE DAVID , RUBINO MAURO , CURRAN MARK A. J. , RIVERA ANDRÉS 
Published: October 2013

ABSTRACTThe transition from the late Pleistocene to the Holocene (30 000–5000 years ago) was a period of considerable climate variability, which has been associated with changes in deep water formation and the intensity of the Meridional Overturning Circulation. Although numerous records exist across the North Atlantic region, few Antarctic ice core records have been obtained from the south. Here we exploit the potential of upwelling ancient ice – so‐called blue ice areas (BIAs) – from the Patriot Hills in the Ellsworth Mountains to derive the first deuterium isotope record (δD) from continental Antarctica south of the Weddell Sea. Gas analysis and glaciological considerations provide a first relative chronology. Inferred temperature trends from the Patriot Hills BIA and snow pit suggest changing climate influences during the transition between the last glacial period and Holocene. Under modern conditions, the interplay between the Antarctic high‐pressure system and the Southern Annular Mode appears to play a significant role in controlling katabatic wind flow over the site while the BIA record suggests that greater sea ice extent during the last glacial period was a major control. Our results demonstrate the considerable potential of the Patriot Hills site for reconstructing past climate change in the south Atlantic region.
Virtual reality and motor imagery: Promising tools for assessment and therapy in Parkinson's disease
Authors: Mirelman Anat , Maidan Inbal , Deutsch Judith E. 
Published: October 2013

AbstractMotor imagery (MI) and virtual reality (VR) are two evolving therapeutic approaches that make use of cognitive function to study and enhance movement, in particular, balance and mobility of people with Parkinson's disease (PD). This review examines the literature on the use of VR and MI in the assessment of mobility and as a therapeutic intervention to improve balance and gait in patients with PD. A study was eligible for inclusion if MI or VR were used to assess motor or cognitive function to improve gait, balance, or mobility in patients with PD. Data were extracted on the following categories: participants; study design; intervention (type, duration, and frequency); and outcomes. Intervention studies were evaluated for quality using the Physiotherapy Evidence Database scale. Sixteen studies were identified; 4 articles used MI and 12 used VR for assessment and treatment of gait impairments in PD. The studies included small samples and were diverse in terms of methodology. Quality of the intervention trials varied from fair for VR to good for MI. The benefits of using MI and VR for assessment and treatment were noted. Encouraging findings on the potential benefits of using MI and VR in PD were found, although further good‐quality research is still needed. Questions remain on the optimal use, content of interventions, and generalizability of findings across the different stages of the disease. The possible mechanisms underlying MI and VR and recommendations for future research and therapy are also presented. © 2013 International Parkinson and Movement Disorder Society
Classification of gait disturbances: Distinguishing between continuous and episodic changes
Authors: Giladi Nir , Horak Fay B. , Hausdorff Jeffrey M. 
Published: October 2013

ABSTRACTThe increased awareness of the importance of gait and postural control to quality of life and functional independence has led many research groups to study the pathophysiology, epidemiology, clinical, and therapeutic aspects of these motor functions. In recognition of the increased awareness of the significance of this topic, the Movement Disorders journal is devoting this entire issue to gait and postural control. Leading research groups provide critical reviews of the current knowledge and propose future directions for this evolving field.The intensive work in this area throughout the world has created an urgent need for a unified language. Because gait and postural disturbances are so common, the clinical classification should be clear, straightforward, and simple to use. As an introduction to this special issue, we propose a new clinically based classification scheme that is organized according to the dominant observed disturbance, while taking into account the results of a basic neurological exam. The proposed classification differentiates between continuous and episodic gait disturbances because this subdivision has important ramifications from the functional, prognostic, and mechanistic perspectives.We anticipate that research into gait and postural control will continue to flourish over the next decade as the search for new ways of promoting mobility and independence aims to keep up with the exponentially growing population of aging older adults. Hopefully, this new classification scheme and the articles focusing on gait and postural control in this special issue of the Movement Disorders journal will help to facilitate future investigations in this exciting, rapidly growing area. © 2013 International Parkinson and Movement Disorder Society
Social communication mediates the relationship between emotion perception and externalizing behaviors in young adult survivors of pediatric traumatic brain injury (TBI)
Authors: Ryan Nicholas P. , Anderson Vicki , Godfrey Celia , Eren Senem , Rosema Stefanie , Taylor Kaitlyn , Catroppa Cathy 
Published: October 2013

AbstractTraumatic brain injury (TBI) is a common cause of childhood disability, and is associated with elevated risk for long‐term social impairment. Though social (pragmatic) communication deficits may be among the most debilitating consequences of childhood TBI, few studies have examined very long‐term communication outcomes as children with TBI make the transition to young adulthood. In addition, the extent to which reduced social function contributes to externalizing behaviors in survivors of childhood TBI remains poorly understood. The present study aimed to evaluate the extent of social communication difficulty among young adult survivors of childhood TBI (n = 34, injury age: 1.0–7.0 years; M time since injury: 16.55 years) and examine relations among aspects of social function including emotion perception, social communication and externalizing behaviors rated by close‐other proxies. Compared to controls the TBI group had significantly greater social communication difficulty, which was associated with more frequent externalizing behaviors and poorer emotion perception. Analyses demonstrated that reduced social communication mediated the association between poorer emotion perception and more frequent externalizing behaviors. Our findings indicate that socio‐cognitive impairments may indirectly increase the risk for externalizing behaviors among young adult survivors of childhood TBI, and underscore the need for targeted social skills interventions delivered soon after injury, and into the very long‐term.
A role for p38 MAPK in head and neck cancer cell growth and tumor‐induced angiogenesis and lymphangiogenesis
Authors: Leelahavanichkul Kantima , Amornphimoltham Panomwat , Molinolo Alfredo A. , Basile John R. , Koontongkaew Sittichai , Gutkind J. Silvio 
Published: October 2013

We have recently gained a remarkable understanding of the mutational landscape of head and neck squamous cell carcinoma (HNSCC). However, the nature of the dysregulated signaling networks contributing to HNSCC progression is still poorly defined. Here, we have focused on the role of the family of mitogen activated kinases (MAPKs), extracellular regulated kinase (ERK), c‐Jun terminal kinase (JNK) and p38 MAPK in HNSCC. Immunohistochemical analysis of a large collection of human HNSCC tissues revealed that the levels of the phosphorylated active form of ERK1/2 and JNK were elevated in less than 33% and 16% of the cases, respectively. Strikingly, however, high levels of active phospho‐p38 were observed in most (79%) of hundreds of tissues analyzed. We explored the biological role of p38 in HNSCC cell lines using three independent approaches: treatment with a specific p38 inhibitor, SB203580; a retro‐inhibition strategy consisting in the use of SB203580 combined with the expression of an inhibitor‐insensitive mutant form of p38α; and short‐hairpin RNAs (shRNAs) targeting p38α. We found that specific blockade of p38 signaling significantly inhibited the proliferation of HNSCC cells both in vitro and in vivo. Indeed, we observed that p38 inhibition in HNSCC cancer cells reduces cancer growth in tumor xenografts and a remarkable decrease in intratumoral blood and lymphatic vessels. We conclude that p38α functions as a positive regulator of HNSCC in the context of the tumor microenvironment, controlling cancer cell growth as well as tumor‐induced angiogenesis and lymphangiogenesis.
The elastocapillary Landau–Levich problem
Authors: Dixit Harish N. , Homsy G. M. 
Published: October 2013

AbstractWe study the classical Landau–Levich dip-coating problem for the case in which the interface possesses both elasticity and surface tension. The aim of the study is to develop a complete asymptotic theory of the elastocapillary Landau–Levich problem in the limit of small flow speeds. As such, the paper also extends our previous study on purely elastic Landau–Levich flow (Dixit & Homsy J. Fluid Mech., vol. 732, 2013, pp. 5–28) to include the effect of surface tension. The elasticity of the interface is described by the Helfrich model and surface tension is modelled in the usual way. We define an elastocapillary number, $\epsilon $, which represents the relative strength of elasticity to surface tension. Based on the size of $\epsilon $, we can define three different regimes of interest. In each of these regimes, we carry out asymptotic expansions in the small capillary (or elasticity) numbers, which represents the balance of viscous forces to surface tension (or elasticity).In the weak elasticity regime, the film thickness is a small correction to the classical Landau–Levich law and can be written as $$\begin{eqnarray*}{\tilde {h} }_{\infty , c} = (0. 9458- 0. 0839~\mathscr{E}){l}_{c} C{a}^{2/ 3} , \quad \epsilon \ll 1,\end{eqnarray*}$$ where ${l}_{c} $ is the capillary length, $Ca$ is the capillary number and $\mathscr{E}= \epsilon / C{a}^{2/ 3} $. In the elastocapillary regime, the film thickness is a function of $\epsilon $ through the power-law relationship $$\begin{eqnarray*}{\tilde {h} }_{\infty , ec} = {\bar {h} }_{\infty , e} L\hspace{0.167em} f(\epsilon )C{a}^{4/ 7} , \quad \epsilon \sim O(1),\end{eqnarray*}$$ where ${\bar {h} }_{\infty , e} $ is a numerical coefficient obtained in our previous study, $L$ is the elastocapillary length, and $f(\epsilon )$ represents the functional dependence of film thickness on the elastocapillary parameter.
Damn You, Little h! (Or, Real-World Applications of the Hubble Constant Using Observed and Simulated Data)
Authors: Croton Darren J. 
Published: October 2013

AbstractThe Hubble constant, H0, or its dimensionless equivalent, “little h”, is a fundamental cosmological property that is now known to an accuracy better than a few per cent. Despite its cosmological nature, little h commonly appears in the measured properties of individual galaxies. This can pose unique challenges for users of such data, particularly with survey data. In this paper we show how little h arises in the measurement of galaxies, how to compare like-properties from different datasets that have assumed different little h cosmologies, and how to fairly compare theoretical data with observed data, where little h can manifest in vastly different ways. This last point is particularly important when observations are used to calibrate galaxy formation models, as calibrating with the wrong (or no) little h can lead to disastrous results when the model is later converted to the correct h cosmology. We argue that in this modern age little h is an anachronism, being one of least uncertain parameters in astrophysics, and we propose that observers and theorists instead treat this uncertainty like any other. We conclude with a ‘cheat sheet’ of nine points that should be followed when dealing with little h in data analysis.
Boron ion beam generation using a self-sputtering planar magnetron
Authors: Vizir Aleksey , Nikolaev Aleksey , Oks Efim , Savkin Konstantin , Shandrikov Maxim , Yushkov Georgy 
Published: October 2013

A boron ion source based on planar magnetron discharge with solid boron target has been developed. To obtain a sufficient conductivity of the boron target for high current discharge ignition, the target was heated to the temperature more than 350 °C. To reach this temperature, thermally isolated target was heated by low-current high-voltage magnetron DC discharge. Applying a high-current pulse (100 μs range) provides a self-sputtering mode of the discharge, which generates the boron plasma. Boron ion beam with current more than 150 mA was extracted from the plasma by applying an accelerating voltage of 20 kV. The boron ion fraction in the beam reached 95%, averaged over the pulse length, and the rest ions were working gas (Kr+). It was shown that “keeping alive” DC discharge completely eliminates a time delay of pulsed discharge current onset, and reduces the pulsed discharge minimal working pressure.
SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads
Authors: Wu Jikun , Zhang Wenqian , Huang Songbo , He Zengquan , Cheng Yanbing , Wang Jun , Lam Tak-Wah , Peng Zhiyu , Yiu Siu-Ming 
Published: October 2013

Abstract
Motivation: RNA-Seq provides a powerful approach to carry out ab initio investigation of fusion transcripts representing critical translocation and post-transcriptional events that recode hereditary information. Most of the existing computational fusion detection tools are challenged by the issues of accuracy and how to handle multiple mappings.
Results: We present a novel tool SOAPfusion for fusion discovery with paired-end RNA-Seq reads. SOAPfusion is accurate and efficient for fusion discovery with high sensitivity (≥93%), low false-positive rate (≤1.36%), even the coverage is as low as 10×, highlighting its ability to detect fusions efficiently at low sequencing cost. From real data of Universal Human Reference RNA (UHRR) samples, SOAPfusion detected 7 novel fusion genes, more than other existing tools and all genes have been validated through reverse transcription-polymerase chain reaction followed by Sanger sequencing. SOAPfusion thus proves to be an effective method with precise applicability in search of fusion transcripts, which is advantageous to accelerate pathological and therapeutic cancer studies.
Availability: http://soap.genomics.org.cn/SOAPfusion.html
Contact: smyiu@cs.hku.hk
Supplementary information: Supplementary data are available at Bioinformatics online.
PLIDA: cross-platform gene expression normalization using perturbed topic models
Authors: Deshwar Amit G. , Morris Quaid 
Published: October 2013

Abstract
Motivation: Gene expression data are currently collected on a wide range of platforms. Differences between platforms make it challenging to combine and compare data collected on different platforms. We propose a new method of cross-platform normalization that uses topic models to summarize the expression patterns in each dataset before normalizing the topics learned from each dataset using per-gene multiplicative weights.
Results: This method allows for cross-platform normalization even when samples profiled on different platforms have systematic differences, allows the simultaneous normalization of data from an arbitrary number of platforms and, after suitable training, allows for online normalization of expression data collected individually or in small batches. In addition, our method outperforms existing state-of-the-art platform normalization tools.
Availability and implementation: MATLAB code is available at http://morrislab.med.utoronto.ca/plida/.
Contact: Amit.Deshwar@utoronto.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
GIIRA—RNA-Seq driven gene finding incorporating ambiguous reads
Authors: Zickmann Franziska , Lindner Martin S. , Renard Bernhard Y. 
Published: October 2013

Abstract
Motivation: The reliable identification of genes is a major challenge in genome research, as further analysis depends on the correctness of this initial step. With high-throughput RNA-Seq data reflecting currently expressed genes, a particularly meaningful source of information has become commonly available for gene finding. However, practical application in automated gene identification is still not the standard case. A particular challenge in including RNA-Seq data is the difficult handling of ambiguously mapped reads.
Results: We present GIIRA (Gene Identification Incorporating RNA-Seq data and Ambiguous reads), a novel prokaryotic and eukaryotic gene finder that is exclusively based on a RNA-Seq mapping and inherently includes ambiguously mapped reads. GIIRA extracts candidate regions supported by a sufficient number of mappings and reassigns ambiguous reads to their most likely origin using a maximum-flow approach. This avoids the exclusion of genes that are predominantly supported by ambiguous mappings. Evaluation on simulated and real data and comparison with existing methods incorporating RNA-Seq information highlight the accuracy of GIIRA in identifying the expressed genes.
Availability and implementation: GIIRA is implemented in Java and is available from https://sourceforge.net/projects/giira/.
Contact: renardB@rki.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Two novel pathway analysis methods based on a hierarchical model
Authors: Evangelou Marina , Dudbridge Frank , Wernisch Lorenz 
Published: October 2013

AbstractMotivation: Over the past few years several pathway analysis methods have been proposed for exploring and enhancing the analysis of genome-wide association data. Hierarchical models have been advocated as a way to integrate SNP and pathway effects in the same model, but their computational complexity has prevented them being applied on a genome-wide scale to date.Methods: We present two novel methods for identifying associated pathways. In the proposed hierarchical model, the SNP effects are analytically integrated out of the analysis, allowing computationally tractable model fitting to genome-wide data. The first method uses Bayes factors for calculating the effect of the pathways, whereas the second method uses a machine learning algorithm and adaptive lasso for finding a sparse solution of associated pathways.Results: The performance of the proposed methods was explored on both simulated and real data. The results of the simulation study showed that the methods outperformed some well-established association methods: the commonly used Fisher’s method for combining P-values and also the recently published BGSA. The methods were applied to two genome-wide association study datasets that aimed to find the genetic structure of platelet function and body mass index, respectively. The results of the analyses replicated the results of previously published pathway analysis of these phenotypes but also identified novel pathways that are potentially involved.Availability: An R package is under preparation. In the meantime, the scripts of the methods are available on request from the authors.Contact: marina.evangelou@cimr.cam.ac.ukSupplementary Information: Supplementary data are available at Bioinformatics online.
Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets
Authors: Rodriguez-R Luis M. , Konstantinidis Konstantinos T. 
Published: October 2013

Abstract
Motivation: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Owing to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed.
Results: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, operational taxonomic unit calling or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that ∼200 Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed.
Availability and implementation: Nonpareil is available at https://github.com/lmrodriguezr/nonpareil/ under the Artistic License 2.0.
Contact: kostas@ce.gatech.edu.
Supplementary information: Supplementary data are available at Bioinformatics online.
De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads
Authors: Hernandez David , Tewhey Ryan , Veyrieras Jean-Baptiste , Farinelli Laurent , Østerås Magne , François Patrice , Schrenzel Jacques 
Published: October 2013

Abstract
Motivation: Paired-end sequencing allows circumventing the shortness of the reads produced by second generation sequencers and is essential for de novo assembly of genomes. However, obtaining a finished genome from short reads is still an open challenge. We present an algorithm that exploits the pairing information issued from inserts of potentially any length. The method determines paths through an overlaps graph by using a constrained search tree. We also present a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization. Finally, we introduce an interactive mode that allows querying an assembly at targeted regions.
Results: We assess our methods by assembling two Staphylococcus aureus strains that were sequenced on the Illumina platform. Using 100 bp paired-end reads and minimal manual curation, we produce a finished genome sequence for the previously undescribed isolate SGH-10-168.
Availability and implementation: The presented algorithms are implemented in the standalone Edena software, freely available under the General Public License (GPLv3) at www.genomic.ch/edena.php.
Contact: david.hernandez@genomic.ch
Supplementary Information: Supplementary data are available at Bioinformatics online.
A Two-Hybrid-Receptor Assay Demonstrates Heteromer Formation as Switch-On for Plant Immune Receptors
Authors: Albert Markus , Jehle Anna Kristina , Fürst Ursula , Chinchilla Delphine , Boller Thomas , Felix Georg 
Published: October 2013

AbstractReceptor kinases sense extracellular signals and trigger intracellular signaling and physiological responses. However, how does signal binding to the extracellular domain activate the cytoplasmic kinase domain? Activation of the plant immunoreceptor Flagellin sensing2 (FLS2) by its bacterial ligand flagellin or the peptide-epitope flg22 coincides with rapid complex formation with a second receptor kinase termed brassinosteroid receptor1 associated kinase1 (BAK1). Here, we show that the receptor pair of FLS2 and BAK1 is also functional when the roles of the complex partners are reversed by swapping their cytosolic domains. This reciprocal constellation prevents interference by redundant partners that can partially substitute for BAK1 and demonstrates that formation of the heteromeric complex is the molecular switch for transmembrane signaling. A similar approach with swaps between the Elongation factor-Tu receptor and BAK1 also resulted in a functional receptor/coreceptor pair, suggesting that a “two-hybrid-receptor assay” is of more general use for studying heteromeric receptor complexes.