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https://www.readbyqxmd.com/read/28645204/when-homoplasy-is-not-homoplasy-dissecting-trait-evolution-by-contrasting-composite-and-reductive-coding
#1
Alejandro Torres-Montúfar, Thomas Borsch, Helga Ochoterena
The conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs reductive). Up to now, there is no common agreement to either code characters as complex or simple...
June 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28645168/genomic-reconstruction-of-the-history-of-native-sheep-reveals-the-peopling-patterns-of-nomads-and-the-expansion-of-early-pastoralism-in-east-asia
#2
Yong-Xin Zhao, Ji Yang, Feng-Hua Lv, Xiao-Ju Hu, Xing-Long Xie, Min Zhang, Wen-Rong Li, Ming-Jun Liu, Yu-Tao Wang, Jin-Quan Li, Yong-Gang Liu, Yan-Ling Ren, Feng Wang, EEr Hehua, Juha Kantanen, Johannes Arjen Lenstra, Jian-Lin Han, Meng-Hua Li
China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in more than 1,000 modern samples. Population genomic analyses combined with archaeological records and historical ethnic demographics data revealed genetic signatures of their origins, secondary expansions and admixtures, thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia...
June 22, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28645158/the-potential-for-co-evolution-of-co2-concentrating-mechanisms-and-rubisco-in-diatoms
#3
Jodi N Young, Brian M Hopkinson
Diatoms are a diverse group of unicellular algae that contribute significantly to global photosynthetic carbon fixation and export in the modern ocean, and are an important source of microfossils for paleoclimate reconstructions. Because of their importance in the environment, diatoms have been a focus of study on the physiology and ecophysiology of carbon fixation, in particular their CO2-concentrating mechanisms (CCMs) and Rubisco characteristics. While carbon fixation in diatoms is not as well understood as in certain model aquatic photoautotrophs, a greater number of species have been examined in diatoms...
June 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28644945/complications-and-cost-of-syndactyly-reconstruction-in-the-united-states-analysis-of-the-pediatric-health-information-system
#4
Maria F Canizares, Lanna Feldman, Patricia E Miller, Peter M Waters, Donald S Bae
BACKGROUND: Syndactyly is one of the most common congenital differences of the upper extremity and offers an exceptional opportunity to evaluate value-based care in pediatric orthopedic surgery. We designed a study to characterize complications and cost associated to syndactyly surgery among US pediatric hospitals. METHODS: A total of 2047 patients were identified for syndactyly surgery at 38 pediatric hospitals from 2009 to 2012 using the Pediatric Health Information System (PHIS) database...
July 2017: Hand: Official Journal of the American Association for Hand Surgery
https://www.readbyqxmd.com/read/28644943/failure-of-wrist-hemiarthroplasty
#5
Eric G Huish, Zachary Lum, H Brent Bamberger, Marc A Trzeciak
BACKGROUND: Wrist hemiarthroplasty has emerged as a motion-sparing option for severe wrist arthritis. It is technically easy with advantages of limited bone resection and no risk of nonunion. Given the relative infancy of the procedure in clinical practice, there are limited data on patient outcomes. METHODS: Eleven patients were treated with wrist reconstructive hemiarthroplasty. Indications included 1 patient with scaphoid nonunion advanced collapse, 9 patients with scapholunate advanced collapse, and 1 patient with capitolunate arthritis...
July 2017: Hand: Official Journal of the American Association for Hand Surgery
https://www.readbyqxmd.com/read/28644917/an-oxygen-isotope-chronometer-for-cellulose-deposition-the-successive-leaves-formed-by-tillers-of-a-c4-perennial-grass
#6
Hai Tao Liu, Fang Yang, Xiao Ying Gong, Rudi Schäufele, Hans Schnyder
Multiannual time series of (palaeo)hydrological information can be reconstructed from the oxygen isotope composition of cellulose (δ(18) OCel ) in biological archives, e.g. tree-rings, but our ability to temporally resolve information at subannual scale is limited. We capitalized on the short and predictable leaf appearance interval (2.4 d) of a perennial C4 grass (Cleistogenes squarrosa), to assess its potential for providing highly time-resolved δ(18) OCel records of vapor pressure deficit (VPD). Plants grown at low (0...
June 23, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28644809/structured-kernel-dictionary-learning-with-correlation-constraint-for-object-recognition
#7
Zhengjue Wang, Yinghua Wang, Hongwei Liu, Hao Zhang
In this paper, we propose a new discriminative non-linear dictionary learning approach, called correlation constrained structured kernel KSVD, for object recognition. The objective function for dictionary learning contains a reconstructive term and a discriminative term. In the reconstructive term, signals are implicitly non-linearly mapped into a space, where a structured kernel dictionary, each sub-dictionary of which lies in the span of the mapped signals from the corresponding class, is established. In the discriminative term, by analyzing the classification mechanism, the correlation constraint is proposed in kernel form, constraining the correlations between different discriminative codes, and restricting the coefficient vectors to be transformed into a feature space, where the features are highly correlated inner-class and nearly independent between-classes...
June 21, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28644802/fully-non-linear-sp3-approximation-based-fluorescence-optical-tomography
#8
Naren Naik, Nishigandha Patil, Yamini Yadav, Jerry Eriksson, Asima Pradhan
In fluorescence optical tomography, many works in literature focus on the linear reconstruction problem to obtain the fluorescent yield or the linearized reconstruction problem to obtain the absorption coefficient. The nonlinear reconstruction problem, to reconstruct the fluorophore absorption coefficient, is of interest in imaging studies as it presents the possibility of better reconstructions owing to a more appropriate model. Accurate and computationally efficient forward models are also critical in the reconstruction process...
June 21, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28644800/online-combination-of-epid-cherenkov-imaging-for-3d-dosimetry-in-a-liquid-phantom
#9
Petr Bruza, Jacqueline M Andreozzi, David J Gladstone, Lesley A Jarvis, Joerg Rottmann, Brian W Pogue
Online acquisition of Cherenkov and portal imaging data was combined with a reconstruction scheme called EC3D, providing a full 3D dosimetry of megavoltage X-ray beams in a water tank. The methodology was demonstrated and quantified in a single static beam. Furthermore, the dynamics and visualization of the 3D dose reconstruction were demonstrated with a volumetric modulated arc therapy (VMAT) plan for TG-119 C-Shape geometry. The developed algorithm combines depth dose information, provided by Cherenkov images, with the lateral dose distribution, provided by the electronic portal imaging device (EPID)...
June 20, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28644799/hybrid-cs-dmri-periodic-time-variant-subsampling-and-omnidirectional-total-variation-based-reconstruction
#10
Yipeng Liu, Shan Wu, Xiaolin Huang, Bing Chen, Ce Zhu
Compressive sensing (CS) has been used to accelerate dynamic magnetic resonance imaging (DMRI). Currently, the online CS-DMRI is faster, whereas the offline CS-DMRI provides higher accuracy for image reconstruction. To achieve good image reconstruction performance in terms of both speed and accuracy, we propose a hybrid CS-DMRI method using periodic timevariant subsampling for different frames. In each period, there is one reference frame that is sampled at a higher subsampling ratio. The two nearby reference frames with good reconstruction quality can be used to provide rough predictions of the other frames between them...
June 20, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28644798/joint-alignment-of-multiple-point-sets-with-batch-and-incremental-expectation-maximization
#11
Dimitrios Georgios Evangelidis, Radu Horaud
This paper addresses the problem of registering multiple point sets. Solutions to this problem are often approximated by repeatedly solving for pairwise registration, which results in an uneven treatment of the sets forming a pair: a model set and a data set. The main drawback of this strategy is that the model set may contain noise and outliers, which negatively affects the estimation of the registration parameters. In contrast, the proposed formulation treats all the point sets on an equal footing. Indeed, all the points are drawn from a central Gaussian mixture, hence the registration is cast into a clustering problem...
June 21, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28644677/young-athletes-after-anterior-cruciate-ligament-reconstruction-with-single-leg-landing-asymmetries-at-the-time-of-return-to-sport-demonstrate-decreased-knee-function-2-years-later
#12
Matthew P Ithurburn, Mark V Paterno, Kevin R Ford, Timothy E Hewett, Laura C Schmitt
BACKGROUND: Previous work shows that young athletes after anterior cruciate ligament reconstruction (ACLR) demonstrate single-leg (SL) landing movement asymmetries at the time of return to sport (RTS); however, the effect of movement asymmetries on longitudinal knee-related function after ACLR has not been examined. Hypothesis/Purpose: The purpose of this study was to examine the effect of SL drop-landing movement symmetry at the time of RTS on knee-related function 2 years later in young athletes after ACLR...
June 1, 2017: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/28644631/demonstration-of-monogamy-relations-for-einstein-podolsky-rosen-steering-in-gaussian-cluster-states
#13
Xiaowei Deng, Yu Xiang, Caixing Tian, Gerardo Adesso, Qiongyi He, Qihuang Gong, Xiaolong Su, Changde Xie, Kunchi Peng
Understanding how quantum resources can be quantified and distributed over many parties has profound applications in quantum communication. As one of the most intriguing features of quantum mechanics, Einstein-Podolsky-Rosen (EPR) steering is a useful resource for secure quantum networks. By reconstructing the covariance matrix of a continuous variable four-mode square Gaussian cluster state subject to asymmetric loss, we quantify the amount of bipartite steering with a variable number of modes per party, and verify recently introduced monogamy relations for Gaussian steerability, which establish quantitative constraints on the security of information shared among different parties...
June 9, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28644617/dynamic-covalent-chemistry-of-carbon-dioxide-opportunities-to-address-environmental-issues
#14
Jean Septavaux, Geoffroy Germain, Julien Leclaire
Extraction and purification of basic chemicals from complex mixtures has been a persistent issue throughout the development of the chemical sciences. The chemical industry and academic research have grown over the centuries by following a deconstruction-reconstruction approach, reminiscent of the metabolism process. Chemists have designed and optimized extraction, purification, and transformation processes of molecules from natural deposits (fossil fuels, biomass, ores), in order to reassemble them into complex adducts...
June 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28644444/energy-and-carbon-metabolisms-in-a-deep-terrestrial-subsurface-fluid-microbial-community
#15
Lily Momper, Sean P Jungbluth, Michael D Lee, Jan P Amend
The terrestrial deep subsurface is a huge repository of microbial biomass, but in relation to its size and physical heterogeneity, few sites have been investigated in detail. Here, we applied a culture-independent metagenomic approach to characterize the microbial community composition in deep (1500 meters below surface) terrestrial fluids. Samples were collected from a former gold mine in Lead, South Dakota, USA, now Sanford Underground Research Facility (SURF). We reconstructed 74 genomes from metagenomes (MAGs), enabling the identification of common metabolic pathways...
June 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28644152/incorporating-hypr-de-noising-within-iterative-pet-reconstruction-hypr-osem
#16
Ju-Chieh Kevin Cheng, Julian C Matthews, Vesna Sossi, Jose Anton-Rodriguez, Andre Salomon, Ronald Boellaard
HighlY constrained back-PRojection (HYPR) is a post-processing de-noising technique originally developed for time-resolved Magnetic Resonance Imaging. It has been recently applied to dynamic imaging for Positron Emission Tomography (PET) and shown promising results. In this work, we have developed an iterative reconstruction algorithm (HYPR-OSEM) which improves the signal-to-noise ratio (SNR) in static imaging (i.e. single frame reconstruction) by incorporating HYPR de-noising directly within the ordered subsets expectation maximization (OSEM) algorithm...
June 23, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28644151/ecg-based-4d-dose-reconstruction-of-cardiac-arrhythmia-ablation-with-carbon-ion-beams-application-in-a-porcine-model
#17
Daniel Richter, H Immo Lehmann, Anna Eichhorn, Anna M Constantinescu, Robert Kaderka, Matthias Prall, Patrick Lugenbiel, Mitsuru Takami, Dierk Thomas, Christoph Bert, Marco Durante, Douglas L Packer, Christian Graeff
Noninvasive ablation of cardiac arrhythmia by scanned particle radiotherapy is highly promising, but especially challenging due to cardiac and respiratory motion. Irradiations for catheter-free ablation in intact pigs were carried out at the GSI Helmholtz Center in Darmstadt using scanned carbon ions. Here, we present real-time electrocardiogram (ECG) data to estimate time-resolved (4D) delivered dose. For 11 animals, surface ECGs and temporal structure of beam delivery were acquired during irradiation. R waves were automatically detected from surface ECGs...
June 23, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28643891/direct-comparison-of-high-temporal-resolution-cine-mri-with-doppler-ultrasound-for-assessment-of-diastolic-dysfunction-in-mice
#18
Thomas A Roberts, Anthony N Price, Laurence H Jackson, Valerie Taylor, Anna L David, Mark F Lythgoe, Daniel J Stuckey
Diastolic dysfunction is a sensitive early indicator of heart failure and can provide additional data to conventional measures of systolic function. Transmitral Doppler ultrasound, which measures the one-dimensional flow of blood through the mitral valve, is currently the preferred method for the measurement of diastolic function, but the measurement of the left ventricular volume changes using high-temporal-resolution cinematic magnetic resonance imaging (CINE MRI) is an alternative approach which is emerging as a potentially more robust and user-independent technique...
June 23, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/28643789/tidal-dynamics-and-mangrove-carbon-sequestration-during-the-oligo-miocene-in-the-south-china-sea
#19
Daniel S Collins, Alexandros Avdis, Peter A Allison, Howard D Johnson, Jon Hill, Matthew D Piggott, Meor H Amir Hassan, Abdul Razak Damit
Modern mangroves are among the most carbon-rich biomes on Earth, but their long-term (≥10(6) years) impact on the global carbon cycle is unknown. The extent, productivity and preservation of mangroves are controlled by the interplay of tectonics, global sea level and sedimentation, including tide, wave and fluvial processes. The impact of these processes on mangrove-bearing successions in the Oligo-Miocene of the South China Sea (SCS) is evaluated herein. Palaeogeographic reconstructions, palaeotidal modelling and facies analysis suggest that elevated tidal range and bed shear stress optimized mangrove development along tide-influenced tropical coastlines...
June 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28643694/simultaneous-maximum-a-i-posteriori-i-longitudinal-pet-image-reconstruction
#20
Sam Ellis, Andrew J Reader
Positron emission tomography (PET) is frequently used to monitor functional changes that occur over extended time scales, for example in longitudinal oncology PET protocols that include routine clinical follow-up scans to assess the efficacy of a course of treatment. In these contexts PET datasets are currently reconstructed into images using single-dataset reconstruction methods. Inspired by recently proposed joint PET-MR reconstruction methods, we propose to reconstruct longitudinal datasets simultaneously by using a joint penalty term in order to exploit the high degree of similarity between longitudinal images...
June 23, 2017: Physics in Medicine and Biology
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