bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bidirectional optical transcutaneous telemetric link for brain machine interface
Authors: Liu T. , Anders J. , Ortmanns M. 
Published: October 2015

A wavelength division multiplexing‐based bidirectional optical transcutaneous telemetric data link for brain machine interfaces is reported. By converting the digitised electronic signals to a stream of infrared and visible optical pulses, the optical telemetry wirelessly transmits data between the implanted neural recorder/stimulator and the external control devices. A red visible vertical cavity surface emitting laser (VCSEL) with a peak wavelength of 680 nm is used in the downlink to transmit data from the external base unit to the implant. A near infrared VCSEL with a peak wavelength of 850 nm is utilised in the uplink for data transmission from the implants to the external device. An optical filter is applied to minimise the interference between the two channels. In‐vitro experiments show that the uplink is capable of transmitting data at 100 Mbps through 2 mm of porcine skin while the downlink is simultaneously working at a rate of 1 Mbps. The power consumption of the implant part of the telemetry, including the transmitter for the uplink and the receiver for the downlink are 3.2 mW and 290 μW, corresponding to a transmission power efficiencies of 32 and 290 pJ/bit, respectively, which are among the best reported and unseen for bidirectional high‐speed transcutaneous communication.
Impulse radio UWB receiver analysis of non‐coherently detected orthogonal signal
Authors: Niemelä V. , Kumpuniemi T. , Hämäläinen M. , Iinatti J. 
Published: October 2015

In this Letter, performance analysis of an impulse radio (IR) ultra wideband (UWB) correlation based receiver utilising non‐coherent detection of orthogonal signalling is provided. The receiver's performance is presented through analysis and simulations in the additive white Gaussian noise (AWGN) channel. Results which show that in non‐coherent detection of binary orthogonal signalling there is a difference between the traditional narrowband and IR approaches are provided. In the narrowband communication, there is a well‐known, approximately 1 dB, difference between coherent and non‐coherent orthogonal signal detection in AWGN. It is demonstrated here that in the binary orthogonal signalling of IR receiver the difference between coherent and non‐coherent detection is insignificant, only tenths of decibels. This can be significant piece of information while considering different receiver structures for wireless sensor networks.
High performance LPF Structure with sharp roll‐off and low VSWR
Authors: Mousavi S.M.H. , Makki S.V.A. , Hooshangi Sh. , Alirezaee Sh. , Siahkamari H. , Ahmadi M. 
Published: October 2015

A symmetrical compact microstrip lowpass filter (LPF) with ultra‐wide rejection band and low voltage standing wave ratio (VSWR) using a novel structure of stepped impedance and butterfly‐shaped resonators is presented and fabricated. The LPF has a 3 dB cut‐off frequency at 1.513 GHz. The series structure of the butterfly‐shaped resonators result in a high roll‐off rate of 187.8 dB/GHz. By generating multiple transmission zeros, a wide stopband (with 35 dB rejection degree) is achieved. To reach a small circuit, the bended transmission line is properly utilised. Moreover, 171% relative stopband bandwidth and dimensions of 0.087λg × 0.157λg (λg is the guided wavelength at 1.513 GHz) are other specifications of this LPF. In addition, an acceptable match is obtained between the simulated and measured responses. In the end, the LPF achieves a high figure‐of‐merit of 82288.
5 GHz all‐digital delay‐locked loop for future memory systems beyond double data rate 4 synchronous dynamic random access memory
Authors: Lee Dongyeol , Kim Jongsun 
Published: October 2015

A new low‐power, fast‐locking, all‐digital delay‐locked loop (DLL) that uses a disposable time‐to‐digital converter (TDC) is presented for future memory systems beyond double data rate 4. To achieve fast locking and high‐frequency operation, the proposed DLL utilises a new hybrid (TDC + binary + sequential) search algorithm that results in a fast locking time of 11 clock cycles without the false lock and harmonic lock problems. By minimising the intrinsic delay of the digital delay line, the proposed DLL achieves an operating frequency range of 1.5–5.0 GHz which is higher than that of the current state‐of‐the‐art all‐digital DLLs. The DLL is fabricated in a 65 nm CMOS process and it achieves a peak‐to‐peak (p–p) output clock jitter of 14 ps (with a p–p input clock jitter of 8 ps) at 5 GHz. The DLL consumes 6.9 mW at 1 V and occupies an active area of 0.025 mm2.
Simple sampling clock synchronisation scheme for reduced‐guard‐interval coherent optical OFDM systems
Authors: Omomukuyo O. , Chang D. , Dobre O.A. , Venkatesan R. , Ngatched T.M.N. 
Published: October 2015

A simple data‐aided scheme for sampling clock synchronisation in reduced‐guard‐interval coherent optical OFDM (RGI‐CO‐OFDM) systems is proposed. In the proposed scheme, the sampling clock offset (SCO) is estimated by using the training symbols reserved for channel estimation, thus avoiding extra training overhead. The SCO is then compensated by resampling, using a time‐domain interpolation filter. The feasibility of the proposed scheme is demonstrated by means of numerical simulations in a 32 Gbaud 16‐QAM dual‐polarisation RGI‐CO‐OFDM system.
MMR: a tool for read multi-mapper resolution
Authors: Kahles André , Behr Jonas , Rätsch Gunnar 
Published: October 2015

Abstract
Motivation: Mapping high-throughput sequencing data to a reference genome is an essential step for most analysis pipelines aiming at the computational analysis of genome and transcriptome sequencing data. Breaking ties between equally well mapping locations poses a severe problem not only during the alignment phase but also has significant impact on the results of downstream analyses. We present the multi-mapper resolution (MMR) tool that infers optimal mapping locations from the coverage density of other mapped reads.
Results: Filtering alignments with MMR can significantly improve the performance of downstream analyses like transcript quantitation and differential testing. We illustrate that the accuracy (Spearman correlation) of transcript quantification increases by 15% when using reads of length 51. In addition, MMR decreases the alignment file sizes by more than 50%, and this leads to a reduced running time of the quantification tool. Our efficient implementation of the MMR algorithm is easily applicable as a post-processing step to existing alignment files in BAM format. Its complexity scales linearly with the number of alignments and requires no further inputs.
Availability and implementation: Open source code and documentation are available for download at http://github.com/ratschlab/mmr. Comprehensive testing results and further information can be found at http://bioweb.me/mmr.
Contact: andre.kahles@ratschlab.org or gunnar.ratsch@ratschlab.org
Supplementary information: Supplementary data are available at Bioinformatics online.
CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules
Authors: Cestarelli Valerio , Fiscon Giulia , Felici Giovanni , Bertolazzi Paola , Weitschek Emanuel 
Published: October 2015

AbstractMotivation: Nowadays, knowledge extraction methods from Next Generation Sequencing data are highly requested. In this work, we focus on RNA-seq gene expression analysis and specifically on case–control studies with rule-based supervised classification algorithms that build a model able to discriminate cases from controls. State of the art algorithms compute a single classification model that contains few features (genes). On the contrary, our goal is to elicit a higher amount of knowledge by computing many classification models, and therefore to identify most of the genes related to the predicted class.Results: We propose CAMUR, a new method that extracts multiple and equivalent classification models. CAMUR iteratively computes a rule-based classification model, calculates the power set of the genes present in the rules, iteratively eliminates those combinations from the data set, and performs again the classification procedure until a stopping criterion is verified. CAMUR includes an ad-hoc knowledge repository (database) and a querying tool.We analyze three different types of RNA-seq data sets (Breast, Head and Neck, and Stomach Cancer) from The Cancer Genome Atlas (TCGA) and we validate CAMUR and its models also on non-TCGA data. Our experimental results show the efficacy of CAMUR: we obtain several reliable equivalent classification models, from which the most frequent genes, their relationships, and the relation with a particular cancer are deduced.Availability and implementation: dmb.iasi.cnr.it/camur.phpContact: emanuel@iasi.cnr.itSupplementary information: Supplementary data are available at Bioinformatics online.
Fit3D: a web application for highly accurate screening of spatial residue patterns in protein structure data
Authors: Kaiser Florian , Eisold Alexander , Bittrich Sebastian , Labudde Dirk 
Published: October 2015

Abstract
Summary: The clarification of linkage between protein structure and function is still a demanding process and can be supported by comparison of spatial residue patterns, so-called structural motifs. However, versatile up-to-date resources to search for local structure similarities are rare. We present Fit3D, an easily accessible web application for highly accurate screening of structural motifs in 3D protein data.
Availability and implementation: The web application is accessible at https://biosciences.hs-mittweida.de/fit3d and program sources of the command line version were released under the terms of GNU GPLv3. Platform-independent binaries and documentations for offline usage are available at https://bitbucket.org/fkaiser/fit3d.
Contact: florian.kaiser@hs-mittweida.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Riboswitch Scanner: an efficient pHMM-based web-server to detect riboswitches in genomic sequences
Authors: Mukherjee Sumit , Sengupta Supratim 
Published: October 2015

Abstract
Summary: Riboswitches are non-coding RNA located in the 5′ untranslated regions where they bind a target metabolite used to specify the riboswitch class and control the expression of associated genes. Accurate identification of riboswitches is the first step towards understanding their regulatory and functional roles in the cell. In this article, we describe a new web application named Riboswitch Scanner which provides an automated pipeline for pHMM-based detection of riboswitches in partial as well as complete genomic sequences rapidly, with high sensitivity and specificity.
Availability and implementation: Riboswitch Scanner can be freely accessed on the web at http://service.iiserkol.ac.in/∼riboscan/.
Contact: mukherjee.sumit89@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
The Dynamic Relationship Between Clinical Symptomatology and Viral Shedding in Naturally Acquired Seasonal and Pandemic Influenza Virus Infections
Authors: Ip Dennis K. M. , Lau Lincoln L. H. , Chan Kwok-Hung , Fang Vicky J. , Leung Gabriel M. , Peiris Malik J. S. , Cowling Benjamin J. 
Published: October 2015

Abstract
Background.  Although the pattern of viral shedding over time has been documented in volunteer challenge studies, understanding of the relationship between clinical symptomatology and viral shedding in naturally acquired influenza infections in humans remains limited.
Methods.  In a community-based study in Hong Kong from 2008 to 2014, we followed up initially healthy individuals and identified 224 secondary cases of natural influenza virus infection in the household setting. We examined the dynamic relationship between patterns of clinical symptomatology and viral shedding as quantified using reverse transcription polymerase chain reaction and viral culture in 127 cases with a clinical picture of acute respiratory infection.
Results.  Viral shedding in influenza A virus infections peaked on the first 1–2 days of clinical illness, and decreased gradually to undetectable levels by day 6–7, matching closely with the dynamics of clinical illness. Viral shedding in influenza B virus infections rose up to 2 days prior to symptom onset and persisted for 6–7 days after onset with a bimodal pattern.
Conclusions.  Our results suggest that while clinical illness profiles may serve as a proxy for clinical infectiousness in influenza A virus infections, patients may potentially be infectious even before symptom onset or after clinical improvement in influenza B virus infections.
Flash-ionization of pre-existing circumstellar material around Nova Oph 2015
Authors: Munari U. , Walter F. M. 
Published: October 2015

Abstract
We have obtained daily high-resolution Echelle spectroscopy of Nova Oph 2015 during its initial evolution. It reveals the presence of pre-existing circumstellar material around the nova, which can be interpreted as the wind of an evolved companion. On earliest observations, the emission line profiles of Nova Oph 2015 displayed a very narrow emission component (full width at half-maximum [FWHM] ∼ 60 km s−1), recombining over a time-scale of 5 days and showing constant low velocity (RV⊙ = −4.5 km s−1), that we interpret as coming from the wind of the secondary recombining after the ionization from the initial UV-flash of the nova. The underlying broad component underwent a marked reduction in both FWHM and width at zero intensity (the latter declining from 4000 to 2000 km s−1 in 10 days) while increasing by six times in flux, that we believe is the result of the high-velocity ejecta of the nova being slowed down while trying to expand within the surrounding wind of the companion. Nova Oph 2015 is possibly unique among novae with evolved companions in having displayed a long rise to maximum brightness and a slow decline from it, an Fe ii-type classification, and a probable sub-giant luminosity class for the secondary.
Genetic counseling and tumor predisposition in neuro-oncology
practice
Authors: Dunbar Erin M. , Eppolito Amanda , Henson John W. 
Published: October 2015

Abstract
Tumor predisposition syndromes may be under-recognized in neuro-oncology practice. Identifying patients with a hereditary tumor predisposition permits appropriate tumor management as well as surveillance and risk-reduction measures for patients and their families. The American College of Medical Genetics and Genomics and the National Society of Genetic Counselors recently published referral guidelines for tumor predisposition assessment, providing an impetus to review the use of genetic counseling in neuro-oncology and to describe features of the less stereotypic conditions from the perspective of neuro-oncology practice. This review also provides a framework for the identification and management of these conditions, as well as references to guidelines and resources for providers and patients.
Evidence for a 36 ks phase modulation in the hard X-ray pulses from the magnetar 1E 1547.0−5408
Authors: Makishima Kazuo , Enoto Teruaki , Murakami Hiroaki , Furuta Yoshihiro , Nakano Toshio , Sasano Makoto , Nakazawa Kazuhiro 
Published: October 2015

Abstract
The Suzaku data for the highly variable magnetar 1E 1547.0−5408, obtained during the 2009 January activity, were reanalyzed. The 2.07 s pulsation, detected in the 15–40 keV HXD data, was found to exhibit phase modulation, which can be modeled by a sinusoid with a period of $36.0^{+4.5}_{-2.5}\:$ks and an amplitude of 0.52 ± 0.14 s. While the effect is also seen in the 10–14 keV XIS data, the modulation amplitude decreased towards lower energies, becoming consistent with 0 below 4 keV. After the case of 4U 0142+61, this makes the second example of this kind of behavior detected from magnetars. The effect can be interpreted as a manifestation of torque-free precession of this magnetar, which is suggested to be prolately deformed under the presence of a strong toroidal field of ∼1016 G.
Radiation mechanisms and physical properties of the γ-ray narrow-line Seyfert 1 galaxies
Authors: Yang Jianping , Zhou Bin 
Published: October 2015

Abstract
We investigate the physical properties and radiation mechanisms of 11 states of five narrow-line Seyfert 1 (NLS1) galaxies detected by the Large Area Telescope on board Fermi through modeling the quasi-simultaneous multi-band observations. We obtain the best-fitting model parameters and their uncertainties for each state with the χ2-minimization procedure and discuss their implications on the characteristics of jet. Similar to blazars, their spectral energy distributions (SEDs) have a two-humped structure and their non-thermal emission can be modelled with the single-zone synchrotron + inverse Compton (IC) model. For all states, the GeV γ-rays may be contributed by the external Compton (EC) emission components. The observations of Fermi are mostly located at the declining stage of the EC humps. Text &lt; 0.5 eV in all cases (Text is the characteristic temperature of external soft photons), suggesting that their radiation zones may be usually located outside of the broad line region (BLR) and the soft photons of Compton scattering mainly come from the dust torus. Compared with the bright Fermi blazars studied by Ghisellini et al. (2014, Nature, 515, 376), the Pjet (the power of the jets) of NLS1 galaxies detected by Fermi is similar to that of the flat spectrum radio quasars (FSRQs) but a little larger than that of the BL Lac objects (BL Lacs). However, a comparison of Pr (the powers of radiations) with the FSRQs and BL Lac objects shows that NLS1 galaxies’ Pr has values comparable to BL Lac objects but lower than FSRQs in spite of having similar Pjet values and the same energy carrier (the cold protons) as the FSRQs. Observations indicate that γ-NLS1 galaxies might have lower η (efficiency of gravitational energy release) values than GeV blazars.
Rotation curve decomposition for size–mass relations of bulge, disk, and dark halo components in spiral galaxies
Authors: Sofue Yoshiaki 
Published: October 2015

Abstract
Rotation curves of more than 100 spiral galaxies were compiled from the literature, and deconvolved into bulge, disk, and dark halo components using χ2 fitting in order to determine their scale radii and masses. Correlation analyses were obtained of the fitting parameters for galaxies that satisfied selection and accuracy criteria. Size–mass relations indicate that the sizes and masses are positively correlated among different components in such a way that the larger or more massive the dark halo, the larger or more massive the disk and bulge. Empirical size–mass relations were obtained for bulge, disk and dark halo by least-squares fitting. The disk-to-halo mass ratio was found to be systematically greater by a factor of three than that predicted by cosmological simulations combined with photometry. A preliminary mass function for the dark halo was obtained, which is represented by the Schechter function followed by a power law.
A Unified Theory of Firm Selection and Growth
*
Authors: Arkolakis Costas 
Published: October 2015

Abstract
This article develops an analytical framework to study firm and exporter growth and provides a dynamic foundation for a standard general equilibrium trade model. Firm-level growth is the result of idiosyncratic productivity improvements with a continuous arrival of new potential producers. A firm enters a market if it is profitable to incur the marginal cost to reach the first consumer and pays an increasing marketing cost to reach additional consumers. I calibrate the model using data on the cross section of firm sales and bilateral trade, as well as the rate of incumbent firm exit. The calibrated model predicts that a firm’s growth is inversely related to its initial size, and that the distribution of growth rates of small firms is heavily skewed to the right. These predictions are confirmed by looking at the growth of sales of U.S. firms and Brazilian exporters to the United States. I use this model to study the impact of cross-firm reallocations on economic activity and measured productivity.
Guided Growth Implant Failure is a Result of Cyclic Fatigue: Explant Analysis With Scanning Electron Microscopy
Authors: Clement Anna E.B. , Vanderby Ray , Halanski Matthew A. , Noonan Kenneth J. 
Published: October 2015

Background:
Guided growth is often used to correct limb deformity and yet implant screw failure in modular systems has been reported. There have been no reports of plate failure and we do not know the exact mode of failure when screws do break.

Methods:
We report the first published case of a fractured plate in a modular plate and screw construct that was used to correct Blount disease in a child through guided growth. The implants were removed and analyzed for method of failure using scanning electron microscopy.

Results:
Scanning electron microscopy of the explant confirms that the mode of failure was not a result of static tension from growth. Rather, analysis confirms cyclic fatigue that led to crack propagation across the anterior side of the plate until overload caused complete plate failure.

Conclusions:
This analysis confirms an in vivo cyclic compression-relaxation of the growth plate presumably to weight-bearing, and that when excessive may lead to implant failure as seen here in this case.

Level of Evidence:
Level V.
Pediatric Orthopaedic Workforce in 2014: Current Workforce and Projections for the Future
Authors: Sawyer Jeffrey R. , Jones Kerwyn C. , Copley Lawson A. , Chambers Stephanie 
Published: October 2015

Background:
The changing nature of the United States (US) health care system has prompted debate concerning the physician supply. The basic questions are: do we have an adequate number of surgeons to meet current demands and are we training the correct number of surgeons to meet future demands? The purpose of this analysis was to characterize the current pediatric orthopaedic workforce in terms of supply and demand, both present and future.

Methods:
Databases were searched (POSNA, SF Match, KID, MGMA) to determine the current pediatric orthopaedic workforce and workforce distribution, as well as pediatric orthopaedic demand.

Results:
The number of active Pediatric Orthopaedic Society of North America (POSNA) members increased over the past 20 years, from 410 in 1993 to 653 in 2014 (155% increase); however, the density of POSNA members is not equally distributed, but correlates to population density. The number of estimated pediatric discharges, orthopaedic and nonorthopaedic, has remained relatively stable from 6,348,537 in 1997 to 5,850,184 in 2012. Between 2003 and 2013, the number of pediatric orthopaedic fellows graduating from Accreditation Council for Graduate Medical Education and non-Accreditation Council for Graduate Medical Education programs increased from 39 to 50 (29%), with a peak of 67 fellows (71%) in 2009.

Discussion:
Although predicting the exact need for pediatric orthopaedic surgeons (POS) is impossible because of the complex interplay among macroeconomic, governmental, insurance, and local factors, some trends were identified: the supply of POS has increased, which may offset the expected numbers of experienced surgeons who will be leaving the workforce in the next 10 to 15 years; macroeconomic factors influencing demand for physician services, driven by gross domestic product and population growth, are expected to be stable in the near future; expansion of the scope of practice for POS is expected to continue; and further similar assessments are warranted.

Level of Evidence:
Level II—economic and decision analysis.