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https://www.readbyqxmd.com/read/28796784/beastling-a-software-tool-for-linguistic-phylogenetics-using-beast-2
#1
Luke Maurits, Robert Forkel, Gereon A Kaiping, Quentin D Atkinson
We present a new open source software tool called BEASTling, designed to simplify the preparation of Bayesian phylogenetic analyses of linguistic data using the BEAST 2 platform. BEASTling transforms comparatively short and human-readable configuration files into the XML files used by BEAST to specify analyses. By taking advantage of Creative Commons-licensed data from the Glottolog language catalog, BEASTling allows the user to conveniently filter datasets using names for recognised language families, to impose monophyly constraints so that inferred language trees are backward compatible with Glottolog classifications, or to assign geographic location data to languages for phylogeographic analyses...
2017: PloS One
https://www.readbyqxmd.com/read/28783645/fast-kronecker-product-kernel-methods-via-generalized-vec-trick
#2
Antti Airola, Tapio Pahikkala
Kronecker product kernel provides the standard approach in the kernel methods' literature for learning from graph data, where edges are labeled and both start and end vertices have their own feature representations. The methods allow generalization to such new edges, whose start and end vertices do not appear in the training data, a setting known as zero-shot or zero-data learning. Such a setting occurs in numerous applications, including drug-target interaction prediction, collaborative filtering, and information retrieval...
August 1, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28774439/a-hybrid-algorithm-for-speckle-noise-reduction-of-ultrasound-images
#3
Karamjeet Singh, Sukhjeet Kaur Ranade, Chandan Singh
BACKGROUND AND OBJECTIVE: Medical images are contaminated by multiplicative speckle noise which significantly reduce the contrast of ultrasound images and creates a negative effect on various image interpretation tasks. In this paper, we proposed a hybrid denoising approach which collaborate the both local and nonlocal information in an efficient manner. The proposed hybrid algorithm consist of three stages in which at first stage the use of local statistics in the form of guided filter is used to reduce the effect of speckle noise initially...
September 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28771495/social-and-content-aware-one-class-recommendation-of-papers-in-scientific-social-networks
#4
Gang Wang, XiRan He, Carolyne Isigi Ishuga
With the rapid development of information technology, scientific social networks (SSNs) have become the fastest and most convenient way for researchers to communicate with each other. Many published papers are shared via SSNs every day, resulting in the problem of information overload. How to appropriately recommend personalized and highly valuable papers for researchers is becoming more urgent. However, when recommending papers in SSNs, only a small amount of positive instances are available, leaving a vast amount of unlabelled data, in which negative instances and potential unseen positive instances are mixed together, which naturally belongs to One-Class Collaborative Filtering (OCCF) problem...
2017: PloS One
https://www.readbyqxmd.com/read/28762295/a-constant-conversation-tuning-into-and-harmonizing-the-needs-and-priorities-of-the-body-and-mind
#5
Annie T Chen, Samantha J Kaplan, Rachel Carriere
PURPOSE: Individuals rely upon many types of information to manage an illness, including information provided by their own bodies. This study investigated how people tune into and manage the flow of information from their bodies to manage their health. METHOD: We developed a platform for participants to share and collaboratively reflect on how they engaged in this dialogic process, in which participants contributed to a discussion on topics relating to body listening and body awareness...
December 2017: International Journal of Qualitative Studies on Health and Well-being
https://www.readbyqxmd.com/read/28692697/-formula-see-text-oblivious-similarity-based-searching-for-encrypted-data-outsourced-to-an-untrusted-domain
#6
Zeeshan Pervez, Mahmood Ahmad, Asad Masood Khattak, Naeem Ramzan, Wajahat Ali Khan
Public cloud storage services are becoming prevalent and myriad data sharing, archiving and collaborative services have emerged which harness the pay-as-you-go business model of public cloud. To ensure privacy and confidentiality often encrypted data is outsourced to such services, which further complicates the process of accessing relevant data by using search queries. Search over encrypted data schemes solve this problem by exploiting cryptographic primitives and secure indexing to identify outsourced data that satisfy the search criteria...
2017: PloS One
https://www.readbyqxmd.com/read/28656740/tailoring-reablement-a-grounded-theory-study-of-establishing-reablement-in-a-community-setting-in-norway
#7
Cathrine Moe, Berit Støre Brinchmann
Reablement is an interprofessional, home-based rehabilitation service that aims to enable senior residents to cope with everyday life and to prevent functional impairments. Systematic accounts of what practitioners actually do when establishing reablement are lacking. This study aims to generate a grounded theory of practitioners' patterns of action when establishing reablement. The study is located in Norway, and grounded theory is the methodological approach. Data were collected from January 2014 to August 2016 through participant observations, focus group interviews and individual interviews...
June 27, 2017: Health & Social Care in the Community
https://www.readbyqxmd.com/read/28503105/neurobiological-evidence-for-the-primacy-of-mania-hypothesis
#8
REVIEW
Georgios D Kotzalidis, Chiara Rapinesi, Valeria Savoja, Ilaria Cuomo, Alessio Simonetti, Elisa Ambrosi, Isabella Panaccione, Silvia Gubbini, Pietro De Rossi, Lavinia De Chiara, Delfina Janiri, Gabriele Sani, Alexia E Koukopoulos, Giovanni Manfredi, Flavia Napoletano, Matteo Caloro, Lucia Pancheri, Antonella Puzella, Gemma Callovini, Gloria Angeletti, Antonio Del Casale
BACKGROUND: Athanasios Koukopoulos proposed the primacy of mania hypothesis (PoM) in a 2006 book chapter and later, in two peer-reviewed papers with Nassir Ghaemi and other collaborators. This hypothesis supports that in bipolar disorder, mania leads to depression, while depression does not lead to mania. OBJECTIVE: To identify evidence in literature that supports or falsifies this hypothesis. METHOD: We searched the medical literature (PubMed, Embase, PsycINFO, and the Cochrane Library) for peer-reviewed papers on the primacy of mania, the default mode function of the brain in normal people and in bipolar disorder patients, and on illusion superiority until 6 June, 2016...
April 2017: Current Neuropharmacology
https://www.readbyqxmd.com/read/28493466/-it-s-fast-it-s-quick-it-stops-me-being-sick-how-to-influence-preparation-of-opioid-tablets-for-injection
#9
Lise Lafferty, Carla Treloar, Nick van Breda, Maureen Steele, Sarah Hiley, Ian Flaherty, Allison Salmon
INTRODUCTION AND AIMS: Injection of pharmaceutical opioids (PO) among people who inject drugs has increased in many countries. The common method for preparing PO tablets for injection uses heat, resulting in greater particulate matter and therefore increased risk of local infection risk and damage to veins and organs. A cold preparation process has fewer risks, but this preparation method is not commonly used. This study seeks to explore how people who inject PO learn to prepare injections and how health promotion efforts could influence practice...
May 10, 2017: Drug and Alcohol Review
https://www.readbyqxmd.com/read/28466043/scientometric-analysis-of-research-on-zika-virus
#10
Nirmal Singh
The research productivity on Zika virus (ZV) had been evaluated applying scientometrics. The different aspects of scientific literature on the subject under study accessible through 'Scopus' were explored. An advanced search was conducted in the database for 'Zika' and 'Virus' as main operators for analytical purposes. Search terms were connected using Boolean Operator 'AND' to retrieve relevant records. The search results were further filtered for journals articles. A total of 573 ZV associated records were retrieved including 6 duplicate items, after deleting which the relevant results remained 567...
September 2016: Virusdisease
https://www.readbyqxmd.com/read/28450978/beyond-low-rank-sparse-multi-scale-low-rank-matrix-decomposition
#11
Frank Ong, Michael Lustig
We present a natural generalization of the recent low rank + sparse matrix decomposition and consider the decomposition of matrices into components of multiple scales. Such decomposition is well motivated in practice as data matrices often exhibit local correlations in multiple scales. Concretely, we propose a multi-scale low rank modeling that represents a data matrix as a sum of block-wise low rank matrices with increasing scales of block sizes. We then consider the inverse problem of decomposing the data matrix into its multi-scale low rank components and approach the problem via a convex formulation...
June 2016: IEEE Journal of Selected Topics in Signal Processing
https://www.readbyqxmd.com/read/28445243/harmonizing-standardized-uptake-value-recovery-between-two-pet-ct-systems-from-different-manufacturers-when-using-resolution-modelling-and-time-of-flight
#12
Ian S Armstrong, Katharine E Thomson, Lisa M Rowley, Daniel R McGowan
PET iterative reconstruction algorithms with resolution modelling (RM) can be used to improve spatial resolution in the images. However, RM has a significant impact on quantification, which raises issues for harmonization across multicentre networks or collaborations. This investigation compared quantification from two modern time-of-flight (TOF) PET/CT systems from different manufacturers with RM with the intention to harmonize recovery. Images of a National Electrical Manufacturers Association image quality phantom with a sphere-to-background concentration ratio of 4 : 1 were acquired on a GE Discovery 710 and a Siemens Biograph mCT and reconstructed with RM and TOF...
April 25, 2017: Nuclear Medicine Communications
https://www.readbyqxmd.com/read/28430095/window-of-opportunity-for-new-disease-surveillance-developing-keyword-lists-for-monitoring-mental-health-and-injury-through-syndromic-surveillance
#13
Ursula Lauper, Jian-Hua Chen, Shao Lin
Studies have documented the impact that hurricanes have on mental health and injury rates before, during, and after the event. Since timely tracking of these disease patterns is crucial to disaster planning, response, and recovery, syndromic surveillance keyword filters were developed by the New York State Department of Health to study the short- and long-term impacts of Hurricane Sandy. Emergency department syndromic surveillance is recognized as a valuable tool for informing public health activities during and immediately following a disaster...
April 2017: Disaster Medicine and Public Health Preparedness
https://www.readbyqxmd.com/read/28428978/20th-workshop-of-the-international-stroke-genetics-consortium-november-3-4-2016-milan-italy-2016-036-isgc-research-priorities
#14
Daniel Woo, Stephanie Debette, Christopher Anderson
OBJECTIVE: To develop a research priority list for the International Stroke Genetics Consortium (ISGC). BACKGROUND: Previously, stroke progress review groups and other activities provided an opportunity for members within the field to develop priorities for research. These filtered into larger categories which then published the top research priorities of their given field. However, these review groups are no longer forming and thus there has been no clear direction on what the research priorities and needs for stroke genetics research...
March 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28358916/classifying-three-imaginary-states-of-the-same-upper-extremity-using-time-domain-features
#15
Mojgan Tavakolan, Zack Frehlick, Xinyi Yong, Carlo Menon
Brain-computer interface (BCI) allows collaboration between humans and machines. It translates the electrical activity of the brain to understandable commands to operate a machine or a device. In this study, we propose a method to improve the accuracy of a 3-class BCI using electroencephalographic (EEG) signals. This BCI discriminates rest against imaginary grasps and elbow movements of the same limb. This classification task is challenging because imaginary movements within the same limb have close spatial representations on the motor cortex area...
2017: PloS One
https://www.readbyqxmd.com/read/28333627/ultrasound-image-despeckling-using-stochastic-distance-based-bm3d
#16
Cid A N Santos, Diego L N Martins, Nelson D A Mascarenhas
Ultrasound image despeckling is an important research field, since it can improve the interpretability of one of the main categories of medical imaging. Many techniques have been tried over the years for ultrasound despeckling, and more recently, a great deal of attention has been focused on patch-based methods, such as non-local means and block-matching collaborative filtering (BM3D). A common idea in these recent methods is the measure of distance between patches, originally proposed as the Euclidean distance, for filtering additive white Gaussian noise...
June 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28332211/a-multichannel-block-matching-denoising-algorithm-for-spectral-photon-counting-ct-images
#17
Adam P Harrison, Ziyue Xu, Amir Pourmorteza, David A Bluemke, Daniel J Mollura
PURPOSE: We present a denoising algorithm designed for a whole-body prototype photon-counting computed tomography (PCCT) scanner with up to 4 energy thresholds and associated energy-binned images. METHODS: Spectral PCCT images can exhibit low signal to noise ratios (SNRs) due to the limited photon counts in each simultaneously-acquired energy bin. To help address this, our denoising method exploits the correlation and exact alignment between energy bins, adapting the highly-effective block-matching 3D (BM3D) denoising algorithm for PCCT...
March 23, 2017: Medical Physics
https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#18
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28301397/the-michigan-trauma-quality-improvement-program-results-from-a-collaborative-quality-initiative
#19
Mark Richard Hemmila, Jill L Jakubus, Anne H Cain-Nielsen, John P Kepros, Wayne E Vander Kolk, Wendy L Wahl, Judy N Mikhail
BACKGROUND: American College of Surgeons verified trauma centers and a third-party payer within the state of Michigan built a regional collaborative quality initiative (CQI). The Michigan Trauma Quality Improvement Program began as a pilot in 2008 and expanded to a formal program in 2011. Here, we examine the performance of the collaborative over time with regard to patient outcomes, resource utilization, and process measures. METHODS: Data from the initial 23 hospitals that joined the CQI in 2011 were analyzed...
May 2017: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/28296902/multi-vehicle-detection-with-identity-awareness-using-cascade-adaboost-and-adaptive-kalman-filter-for-driver-assistant-system
#20
Baofeng Wang, Zhiquan Qi, Sizhong Chen, Zhaodu Liu, Guocheng Ma
Vision-based vehicle detection is an important issue for advanced driver assistance systems. In this paper, we presented an improved multi-vehicle detection and tracking method using cascade Adaboost and Adaptive Kalman filter(AKF) with target identity awareness. A cascade Adaboost classifier using Haar-like features was built for vehicle detection, followed by a more comprehensive verification process which could refine the vehicle hypothesis in terms of both location and dimension. In vehicle tracking, each vehicle was tracked with independent identity by an Adaptive Kalman filter in collaboration with a data association approach...
2017: PloS One
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