bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single Shot Polarization Characterization of XUV FEL Pulses from Crossed Polarized Undulators
Authors: Ferrari E. , Allaria E. , Buck J. , De Ninno G. , Diviacco B. , Gauthier D. , Giannessi L. , Glaser L. , Huang Z. , Ilchen M. , Lambert G. , Lutman A. A. , Mahieu B. , Penco G. , Spezzani C. , Viefhaus J. 
Published: August 2015

AbstractPolarization control is a key feature of light generated by short-wavelength free-electron lasers. In this work, we report the first experimental characterization of the polarization properties of an extreme ultraviolet high gain free-electron laser operated with crossed polarized undulators. We investigate the average degree of polarization and the shot-to-shot stability and we analyze aspects such as existing possibilities for controlling and switching the polarization state of the emitted light. The results are in agreement with predictions based on Gaussian beams propagation.
Real-time terahertz digital holography with a quantum cascade laser
Authors: Locatelli Massimiliano , Ravaro Marco , Bartalini Saverio , Consolino Luigi , Vitiello Miriam S. , Cicchi Riccardo , Pavone Francesco , De Natale Paolo 
Published: August 2015

AbstractCoherent imaging in the THz range promises to exploit the peculiar capabilities of these wavelengths to penetrate common materials like plastics, ceramics, paper or clothes with potential breakthroughs in non-destructive inspection and quality control, homeland security and biomedical applications. Up to now, however, THz coherent imaging has been limited by time-consuming raster scanning, point-like detection schemes and by the lack of adequate coherent sources. Here, we demonstrate real-time digital holography (DH) at THz frequencies exploiting the high spectral purity and the mW output power of a quantum cascade laser combined with the high sensitivity and resolution of a microbolometric array. We show that, in a one-shot exposure, phase and amplitude information of whole samples, either in reflection or in transmission, can be recorded. Furthermore, a 200 times reduced sensitivity to mechanical vibrations and a significantly enlarged field of view are observed, as compared to DH in the visible range. These properties of THz DH enable unprecedented holographic recording of real world dynamic scenes.
Enhancing Tabletop X-Ray Phase Contrast Imaging with Nano-Fabrication
Authors: Miao Houxun , Gomella Andrew A. , Harmon Katherine J. , Bennett Eric E. , Chedid Nicholas , Znati Sami , Panna Alireza , Foster Barbara A. , Bhandarkar Priya , Wen Han 
Published: August 2015

AbstractX-ray phase-contrast imaging is a promising approach for improving soft-tissue contrast and lowering radiation dose in biomedical applications. While current tabletop imaging systems adapt to common x-ray tubes and large-area detectors by employing absorptive elements such as absorption gratings or monolithic crystals to filter the beam, we developed nanometric phase gratings which enable tabletop x-ray far-field interferometry with only phase-shifting elements, leading to a substantial enhancement in the performance of phase contrast imaging. In a general sense the method transfers the demands on the spatial coherence of the x-ray source and the detector resolution to the feature size of x-ray phase masks. We demonstrate its capabilities in hard x-ray imaging experiments at a fraction of clinical dose levels and present comparisons with the existing Talbot-Lau interferometer and with conventional digital radiography.
Mathematical Modelling and Prediction of the Effect of Chemotherapy on Cancer Cells
Authors: Namazi Hamidreza , Kulish Vladimir V. , Wong Albert 
Published: August 2015

AbstractCancer is a class of diseases characterized by out-of-control cells’ growth which affect DNAs and make them damaged. Many treatment options for cancer exist, with the primary ones including surgery, chemotherapy, radiation therapy, hormonal therapy, targeted therapy and palliative care. Which treatments are used depends on the type, location and grade of the cancer as well as the person’s health and wishes. Chemotherapy is the use of medication (chemicals) to treat disease. More specifically, chemotherapy typically refers to the destruction of cancer cells. Considering the diffusion of drugs in cancer cells and fractality of DNA walks, in this research we worked on modelling and prediction of the effect of chemotherapy on cancer cells using Fractional Diffusion Equation (FDE). The employed methodology is useful not only for analysis of the effect of special drug and cancer considered in this research but can be expanded in case of different drugs and cancers.
Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization
Authors: Benoit Isabelle , Zhou Miaomiao , Vivas Duarte Alexandra , Downes Damien J. , Todd Richard B. , Kloezen Wendy , Post Harm , Heck Albert J. R. , Maarten Altelaar A. F. , de Vries Ronald P. 
Published: August 2015

AbstractDegradation of plant biomass to fermentable sugars is of critical importance for the use of plant materials for biofuels. Filamentous fungi are ubiquitous organisms and major plant biomass degraders. Single colonies of some fungal species can colonize massive areas as large as five soccer stadia. During growth, the mycelium encounters heterogeneous carbon sources. Here we assessed whether substrate heterogeneity is a major determinant of spatial gene expression in colonies ofAspergillus niger. We analyzed whole-genome gene expression in five concentric zones of 5-day-old colonies utilizing sugar beet pulp as a complex carbon source. Growth, protein production and secretion occurred throughout the colony. Genes involved in carbon catabolism were expressed uniformly from the centre to the periphery whereas genes encoding plant biomass degrading enzymes and nitrate utilization were expressed differentially across the colony. A combined adaptive response of carbon-catabolism and enzyme production to locally available monosaccharides was observed. Finally, our results demonstrate thatA. nigeremploys different enzymatic tools to adapt its metabolism as it colonizes complex environments.
Electromagnetically Induced Entanglement
Authors: Yang Xihua , Xiao Min 
Published: August 2015

AbstractQuantum entanglement provides an essential resource for quantum computation, quantum communication and quantum network. How to conveniently and efficiently produce entanglement between bright light beams presents a challenging task to build realistic quantum information processing networks. Here, we present an efficient and convenient way to realize a novel quantum phenomenon, named electromagnetically induced entanglement, in the conventional Λ-type three-level atomic system driven by a strong pump field and a relatively weak probe field. Nearly perfect entanglement between the two fields can be achieved with a low coherence decay rate between the two lower levels, high pump-field intensity and large optical depth of the atomic ensemble. The physical origin is quantum coherence between the lower doublet produced by the pump and probe fields, similar to the well-known electromagnetically induced transparency. This method would greatly facilitate the generation of nondegenerate narrow-band continuous-variable entanglement between bright light beams by using only coherent laser fields and may find potential and broad applications in realistic quantum information processing.
Do Shale Pore Throats Have a Threshold Diameter for Oil Storage?
Authors: Zou Caineng , Jin Xu , Zhu Rukai , Gong Guangming , Sun Liang , Dai Jinxing , Meng Depeng , Wang Xiaoqi , Li Jianming , Wu Songtao , Liu Xiaodan , Wu Juntao , Jiang Lei 
Published: August 2015

AbstractIn this work, a nanoporous template with a controllable channel diameter was used to simulate the oil storage ability of shale pore throats. On the basis of the wetting behaviours at the nanoscale solid-liquid interfaces, the seepage of oil in nano-channels of different diameters was examined to accurately and systematically determine the effect of the pore diameter on the oil storage capacity. The results indicated that the lower threshold for oil storage was a pore throat of 20 nm, under certain conditions. This proposed pore size threshold provides novel, evidence-based criteria for estimating the geological reserves, recoverable reserves and economically recoverable reserves of shale oil. This new understanding of shale oil processes could revolutionize the related industries.
Internet and Audiology: A Review of the First International Meeting
Authors: Andersson Gerhard , Lunner Thomas , Laplante-Lévesque Ariane , Preminger Jill E. 
Published: August 2015

Purpose
The purpose of this research forum article is to describe the impetus for holding the First International Meeting on Internet and Audiology (October 2014) and to introduce the special research forum that arose from the meeting.

Method
The rationale for the First International Meeting on Internet and Audiology is described. This is followed by a short description of the research sections and articles appearing in the special issue. Six articles consider the process of health care delivery over the Internet; this includes health care specific to hearing, tinnitus, and balance. Four articles discuss the development of effective Internet-based treatment programs. Six articles describe and evaluate Internet-based interventions specific to adult hearing aid users.

Conclusion
The fledgling field of Internet and audiology is remarkably broad. The Second International Meeting on Internet and Audiology ocurred in September 2015.
Research Verification of Production Practices Using Intensive Aeration at a Hybrid Catfish Operation
Authors: Bott Lisa B , Roy Luke A , Hanson Terrill R , Chappell Jesse , Whitis Gregory N 
Published: August 2015

Abstract
Aquaculture research verification programs are designed to demonstrate and test research-based practices recommended by extension services on commercial-scale operations. From 2010 to 2013, in western Alabama, three management protocols were followed over three crop cycles on a farm producing hybrid catfish (female Channel Catfish Ictalurus punctatus × male Blue Catfish I. furcatus) using high levels of aeration. The protocols were an owner-defined, multiple-batch treatment and single-batch and multiple-batch treatments defined by the Alabama Cooperative Extension System (ACES). Results from nine production cycles were analyzed to calculate yields, feed conversion ratios (FCRs), cost of production, and net returns. Over three production cycles the owner-defined, multiple-batch treatment outperformed the two ACES-recommended treatments in terms of yield, survival, FCR, and net returns. The owner-defined treatment could vary, and the producer chose to feed above the recommended daily maximum and observed no low dissolved oxygen levels. High losses owing to disease in the ACES multiple-batch treatment led to poor results. The owner-defined multiple-batch system completed three crops in 2.8 years compared with 3.6–3.7 years for the other two treatments. Thus, this study highlights the importance of research-based recommendations being verified under commercial catfish production conditions and the value of research verification programs.
Searching for a counterexample to Kurepa’s conjecture
Authors: Andrejić Vladica , Tatarevic Milos 
Published: August 2015

Kurepa’s conjecture states that there is no odd prime

p
p

that divides

!
p
=
0
!
+
1
!
+
⋯
+
(
p
−
1
)
!

!p=0!+1!+\cdots +(p-1)!

. We search for a counterexample to this conjecture for all

p
>

2

34

p>2^{34}

. We introduce new optimization techniques and perform the computation using graphics processing units. Additionally, we consider the generalized Kurepa’s left factorial given by

!

k

n
=
(
0
!

)
k

+
(
1
!

)
k

+
⋯
+
(
(
n
−
1
)
!

)

k

!^{k}n=(0!)^k +(1!)^k +\cdots +((n-1)!)^{k}

, and show that for all integers

1
>
k
>
100

1>k>100

there exists an odd prime

p
p

such that

p
∣

!
k

p

p\mid !^k p

.
Identification of hierarchical chromatin domains
Authors: Weinreb Caleb , Raphael Benjamin J. 
Published: August 2015

Abstract
Motivation: The three-dimensional structure of the genome is an important regulator of many cellular processes including differentiation and gene regulation. Recently, technologies such as Hi-C that combine proximity ligation with high-throughput sequencing have revealed domains of self-interacting chromatin, called topologically associating domains (TADs), in many organisms. Current methods for identifying TADs using Hi-C data assume that TADs are non-overlapping, despite evidence for a nested structure in which TADs and sub-TADs form a complex hierarchy.
Results: We introduce a model for decomposition of contact frequencies into a hierarchy of nested TADs. This model is based on empirical distributions of contact frequencies within TADs, where positions that are far apart have a greater enrichment of contacts than positions that are close together. We find that the increase in contact enrichment with distance is stronger for the inner TAD than for the outer TAD in a TAD/sub-TAD pair. Using this model, we develop the TADtree algorithm for detecting hierarchies of nested TADs. TADtree compares favorably with previous methods, finding TADs with a greater enrichment of chromatin marks such as CTCF at their boundaries.
Availability and implementation: A python implementation of TADtree is available at http://compbio.cs.brown.edu/software/
Contact: braphael@cs.brown.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
EPGA2: memory-efficient de novo assembler
Authors: Luo Junwei , Wang Jianxin , Li Weilong , Zhang Zhen , Wu Fang-Xiang , Li Min , Pan Yi 
Published: August 2015

Abstract
Motivation: In genome assembly, as coverage of sequencing and genome size growing, most current softwares require a large memory for handling a great deal of sequence data. However, most researchers usually cannot meet the requirements of computing resources which prevent most current softwares from practical applications.
Results: In this article, we present an update algorithm called EPGA2, which applies some new modules and can bring about improved assembly results in small memory. For reducing peak memory in genome assembly, EPGA2 adopts memory-efficient DSK to count K-mers and revised BCALM to construct De Bruijn Graph. Moreover, EPGA2 parallels the step of Contigs Merging and adds Errors Correction in its pipeline. Our experiments demonstrate that all these changes in EPGA2 are more useful for genome assembly.
Availability and implementation: EPGA2 is publicly available for download at https://github.com/bioinfomaticsCSU/EPGA2.
Contact: jxwang@csu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
HiXCorr: a portable high-speed XCorr engine for high-resolution tandem mass spectrometry
Authors: Kim Hyunwoo , Jo Hosung , Park Heejin , Paek Eunok 
Published: August 2015

Abstract
Summary: Peptide identification is an important problem in proteomics. One of the most popular scoring schemes for peptide identification is XCorr (cross-correlation). Since calculating XCorr is computationally intensive, a lot of efforts have been made to develop fast XCorr engines. However, the existing XCorr engines are not suitable for high-resolution MS/MS spectrometry because they are either slow or require a specific type of CPU. We present a portable high-speed XCorr engine for high-resolution tandem mass spectrometry by developing a novel algorithm for calculating XCorr. The algorithm enables XCorr calculation 1.25–49 times faster than previous algorithms for 0.01 Da fragment tolerance. Furthermore, our engine is easily portable to any machine with different types of CPU because it is developed in C language. Hence, our XCorr engine will expedite peptide identification by high-resolution tandem mass spectrometry.
Availability and implementation: Available at http://isa.hanyang.ac.kr/HiXCorr/HiXCorr.html.
Contact: hjpark@hanyang.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations
Authors: Pybus Marc , Luisi Pierre , Dall'Olio Giovanni Marco , Uzkudun Manu , Laayouni Hafid , Bertranpetit Jaume , Engelken Johannes 
Published: August 2015

Abstract
Motivation: Detecting positive selection in genomic regions is a recurrent topic in natural population genetic studies. However, there is little consistency among the regions detected in several genome-wide scans using different tests and/or populations. Furthermore, few methods address the challenge of classifying selective events according to specific features such as age, intensity or state (completeness).
Results: We have developed a machine-learning classification framework that exploits the combined ability of some selection tests to uncover different polymorphism features expected under the hard sweep model, while controlling for population-specific demography. As a result, we achieve high sensitivity toward hard selective sweeps while adding insights about their completeness (whether a selected variant is fixed or not) and age of onset. Our method also determines the relevance of the individual methods implemented so far to detect positive selection under specific selective scenarios. We calibrated and applied the method to three reference human populations from The 1000 Genome Project to generate a genome-wide classification map of hard selective sweeps. This study improves detection of selective sweep by overcoming the classical selection versus no-selection classification strategy, and offers an explanation to the lack of consistency observed among selection tests when applied to real data. Very few signals were observed in the African population studied, while our method presents higher sensitivity in this population demography.
Availability and implementation: The genome-wide results for three human populations from The 1000 Genomes Project and an R-package implementing the ‘Hierarchical Boosting’ framework are available at http://hsb.upf.edu/.
Contact: jaume.bertranpetit@upf.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
msa: an R package for multiple sequence alignment
Authors: Bodenhofer Ulrich , Bonatesta Enrico , Horejš-Kainrath Christoph , Hochreiter Sepp 
Published: August 2015

Abstract
Summary: Although the R platform and the add-on packages of the Bioconductor project are widely used in bioinformatics, the standard task of multiple sequence alignment has been neglected so far. The msa package, for the first time, provides a unified R interface to the popular multiple sequence alignment algorithms ClustalW, ClustalOmega and MUSCLE. The package requires no additional software and runs on all major platforms. Moreover, the msa package provides an R interface to the powerful package shade which allows for flexible and customizable plotting of multiple sequence alignments.
Availability and implementation: msa is available via the Bioconductor project: http://bioconductor.org/packages/release/bioc/html/msa.html. Further information and the R code of the example presented in this paper are available at http://www.bioinf.jku.at/software/msa/.
Contact: bodenhofer@bioinf.jku.at or msa@bioinf.jku.at
Magnetar activity via the density–shear instability in Hall-MHD
Authors: Gourgouliatos Konstantinos N. , Kondić Todor , Lyutikov Maxim , Hollerbach Rainer 
Published: August 2015

Abstract
We investigate the density–shear instability in Hall-magnetohydrodynamics (Hall-MHD) via numerical simulation of the full non-linear problem in the context of magnetar activity. We confirm the development of the instability of a plane-parallel magnetic field with an appropriate intensity and electron density profile, in accordance with analytic theory. We find that the instability also appears for a monotonically decreasing electron number density and magnetic field, a plane-parallel analogue of an azimuthal or meridional magnetic field in the crust of a magnetar. The growth rate of the instability depends on the Hall properties of the field (magnetic field intensity, electron number density and the corresponding scaleheights), while being insensitive to weak resistivity. Since the Hall effect is the driving process for the evolution of the crustal magnetic field of magnetars, we argue that this instability is critical for systems containing strong meridional or azimuthal fields. We find that this process mediates the formation of localized structures with much stronger magnetic field than the average, which can lead to magnetar activity and accelerate the dissipation of the field and consequently the production of Ohmic heating. Assuming a 5 × 1014 G magnetic field at the base of crust, we anticipate that magnetic field as strong as 1015 G will easily develop in regions of typical size of a few hundred metres, containing magnetic energy of 1043 erg, sufficient to power magnetar bursts. These active regions are more likely to appear in the magnetic equator where the tangential magnetic field is stronger.
Mass ratio of the 2 pc binary brown dwarf LUH 16 and limits on planetary companions from astrometry
Authors: Sahlmann J. , Lazorenko P. F. 
Published: August 2015

Abstract
We analyse FORS2/VLT I-band imaging data to monitor the motions of both components in the nearest known binary brown dwarf WISE J104915.57-531906.1AB (LUH 16) over one year. The astrometry is dominated by parallax and proper motion, but with a precision of ∼0.2 mas per epoch we accurately measure the relative position change caused by the orbital motion of the pair. This allows us to directly measure a mass ratio of q = 0.78 ± 0.10 for this system. We also search for the signature of a planetary-mass companion around either of the A and B component and exclude at 3σ the presence of planets with masses larger than 2 MJ and orbital periods of 20–300 d. We update the parallax of LUH 16 to 500.51 ± 0.11 mas, i.e. just within 2 pc. This study yields the first direct constraint on the mass ratio of LUH 16 and shows that the system does not harbour any close-in giant planets.
The genie in the learning organisation? The experience of using multi-level action learning at the Leadership Foundation
Authors: Clifton Louise , Gentle Paul 
Published: August 2015

Purpose
– The purpose of this paper is to examine the working practices and outcomes of an action research project in a specialist organisation engaged in the field of leadership development. The intention of the project was to enable the company involved to become a stronger learning organisation at a time when it was developing a future strategy.

Design/methodology/approach
– The paper uses a case study approach to describe and analyse a three-stage process involving the use of a focus group, organisational climate survey and voluntary action learning sets. Interviews with participants are analysed thematically in order to assess the impact of the action research project on the organisation’s culture.

Findings
– Participation by the majority of the Leadership Foundation’s staff in action learning and related opportunities for feedback within the organisation helped move its culture towards wider participation in strategy development and a whole organisation approach to working. Other organisations wishing to build collaborative working cultures can learn from the implications of the project, particularly those concerning the need to attend to the intended outcomes of action learning and the role of skilled, critical facilitators in action learning processes.

Originality/value
– The paper is innovative in that it explores practitioner-led action research work in a setting of leadership and organisational development. It will interest leaders and managers who seek to build learning organisations, as well as organisational developers with an interest in enhancing the impact of action learning.