bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloud Impacts on Pavement Temperature and Shortwave Radiation
Authors: Walker Curtis L. , Anderson Mark R. 
Published: August 2016

AbstractForecast systems provide decision support for end users ranging from the solar energy industry to municipalities concerned with road safety. Pavement temperature is an important variable when considering vehicle response to various weather conditions. A complex relationship exists between tire and pavement temperatures that affects vehicle performance. Many forecast systems suffer from inaccurate radiation forecasts resulting in part from the inability to model different types of clouds and their influence on radiation. This research focuses on forecast improvement by determining how cloud type impacts pavement temperature and the amount of shortwave radiation reaching the surface. The study region is the Great Plains where surface radiation data were obtained from the High Plains Regional Climate Center’s Automated Weather Data Network stations. Pavement temperature data were obtained from the Meteorological Assimilation Data Ingest System. Cloud-type identification was possible via the Naval Research Laboratory Cloud Classification algorithm, and clouds were subsequently sorted into five distinct groups: clear conditions, low clouds, middle clouds, high clouds, and cumuliform clouds. Statistical analyses during the daytime in June 2011 revealed that cloud cover lowered pavement temperatures by up to approximately 10°C and dampened downwelling shortwave radiation by up to 400 W m−2. These pavement temperatures and surface radiation observations were strongly correlated, with a maximum correlation coefficient of 0.83. A comparison between cloud-type group identified and cloud cover observed from satellite images provided a measure of confidence in the results and identified cautions with using satellite-based cloud detection.
Combining Observations from Multiple Platforms across the Kuroshio Northeast of Luzon: A Highlight on PIES Data
Authors: Mensah Vigan , Andres Magdalena , Lien Ren-Chieh , Ma Barry , Lee Craig M. , Jan Sen 
Published: August 2016

AbstractThis study presents amended procedures to process and map data collected by pressure-sensor-equipped inverted echo sounders (PIESs) in western boundary current regions. The modifications to the existing methodology, applied to observations of the Kuroshio from a PIES array deployed northeast of Luzon, Philippines, consist of substituting a hydrography-based mean travel time field for the PIES-based mean field and using two distinct gravest empirical mode (GEM) lookup tables across the front that separate water masses of South China Sea and North Pacific origin. In addition, this study presents a method to use time-mean velocities from acoustic Doppler current profilers (ADCPs) to reference (or “level”) the PIES-recorded pressures in order to obtain time series of absolute geostrophic velocity. Results derived from the PIES observations processed with the hydrography-based mean field and two GEMs are compared with hydrographic profiles sampled by Seagliders during the PIES observation period and with current velocity measured concurrently by a collocated ADCP array. The updated processing scheme leads to a 41% error decrease in the determination of the thermocline depth across the current, a 22% error decrease in baroclinic current velocity shear, and a 61% error decrease in baroclinic volume transports. The absolute volume transport time series derived from the leveled PIES array compares well with that obtained directly from the ADCPs with a root-mean-square difference of 3.0 Sv (1 Sv ≡ 106 m3 s–1), which is mainly attributed to the influence of ageostrophic processes on the ADCP-measured velocities that cannot be calculated from the PIES observations.
Hindcasts of Integrated Kinetic Energy in Atlantic Tropical Cyclones: A Neural Network Prediction Scheme
Authors: Kozar Michael E. , Misra Vasubandhu , Powell Mark D. 
Published: August 2016

AbstractA new statistical–dynamical scheme is presented for predicting integrated kinetic energy (IKE) in North Atlantic tropical cyclones from a series of environmental input parameters. Predicting IKE is desirable because the metric quantifies the energy across a storm’s entire wind field, allowing it to respond to changes in storm structure and size. As such, IKE is especially useful for quantifying risks in large, low-intensity, high-impact storms such as Sandy in 2012. The prediction scheme, named the Statistical Prediction of Integrated Kinetic Energy, version 2 (SPIKE2), builds upon a previous statistical IKE scheme, by using a series of artificial neural networks instead of more basic linear regression models. By using a more complex statistical scheme, SPIKE2 is able to distinguish nonlinear signals in the environment that could cause fluctuations in IKE. In an effort to evaluate SPIKE2’s performance in a future operational setting, the model is calibrated using archived input parameters from Global Ensemble Forecast System (GEFS) control analyses, and is run in a hindcast mode from 1990 to 2011 using archived GEFS reforecasts. The hindcast results indicate that SPIKE2 performs significantly better than both persistence and climatological benchmarks.
Variable Selection for Tropical Cyclogenesis Predictive Modeling
Authors: Wijnands Jasper S. , Qian Guoqi , Kuleshov Yuriy 
Published: August 2016

AbstractVariable selection for short-term forecasting (up to 72 h) of tropical cyclone (TC) genesis has been investigated. IBTrACS data (1979–2014) are used to identify the genesis time and position of over 2500 TCs between 30°N and 30°S. Tracks are extended using a tropical cloud cluster (TCC) dataset, which is also used to identify over 28 000 nondeveloping TCCs. Subsequently, corresponding local environment states at various atmospheric pressure levels are retrieved from ERA-Interim data. An initial selection of potentially favorable variables for TC genesis is made based on mutual information, which forms the set of nodes for graphical model structure learning using the Peter–Clark (PC) algorithm. Structure learning identifies the variables with the strongest influence on TC genesis, while taking into account the interrelationship with other variables. Variables are ranked based on the maximum observed p value in all (conditional) independence tests of the variable with the TC genesis node. The results indicate that potential vorticity (600 hPa), relative vorticity (925 hPa), and (vector) vertical wind shear (200–700 hPa) are the highest ranked variables for forecasting up to 72 h. These are followed by the basin and zonal wind speed (200 hPa), and for very short lead-time divergence (925 hPa), air temperature (300 hPa), and average vertical velocity. Predictive modeling with logistic regression confirms the superior performance of the top-ranked variables. The presented variable ranking (methodology) can be used as a building block for the creation of genesis indices or predictive models in the future.
The evaluation of off‐loading using a new removable oRTHOsis in DIABetic foot (ORTHODIAB) randomized controlled trial: study design and rationale
Authors: Mohammedi Kamel , Potier Louis , François Maud , Dardari Dured , Feron Marilyne , Nobecourt‐Dupuy Estelle , Dolz Manuel , Ducloux Roxane , Chibani Abdelkader , Eveno Dominique‐François , Crea Avila Teresa , Sultan Ariane , Baillet‐Blanco Laurence , Rigalleau Vincent , Velho Gilberto , Tubach Florence , Roussel Ronan , Dupré Jean‐Claude , Malgrange Dominique , Marre Michel 
Published: August 2016

AbstractBackgroundOff‐loading is essential for diabetic foot management, but remains understudied. The evaluation of Off‐loading using a new removable oRTHOsis in DIABetic foot (ORTHODIAB) trial aims to evaluate the efficacy of a new removable device “Orthèse Diabète” in the healing of diabetic foot.Methods/designORTHODIAB is a French multi‐centre randomized, open label trial, with a blinded end points evaluation by an adjudication committee according to the Prospective Randomized Open Blinded End‐point. Main endpoints are adjudicated based on the analysis of diabetic foot photographs. Orthèse Diabète is a new removable off‐loading orthosis (PROTEOR, France) allowing innovative functions including real‐time evaluation of off‐loading and estimation of patients' adherence. Diabetic patients with neuropathic plantar ulcer or amputation wounds (toes or transmetatarsal) are assigned to one of 2 parallel‐groups: Orthèse Diabète or control group (any removable device) according to a central computer‐based randomization. Study visits are scheduled for 6 months (days D7 and D14, and months M1, M2, M3, and M6). The primary endpoint is the proportion of patients whose principal ulcer is healed at M3. Secondary endpoints are: the proportion of patients whose principal ulcer is healed at M1, M2 and M6; the proportion of patients whose initial ulcers are all healed at M1, M2, M3, and M6; principal ulcer area reduction; time‐related ulcer‐free survival; development of new ulcers; new lower‐extremity amputation; infectious complications; off‐loading adherence; and patient satisfaction. The study protocol was approved by the French National Agency for Medicines and Health Products Safety, and by the ethics committee of Saint‐Louis Hospital (Paris). Comprehensive study information including a Patient Information Sheet has been provided to each patient who must give written informed consent before enrolment. Monitoring, data management, and statistical analyses are providing by UMANIS Life Science (Paris), independently to the sponsor. Since 27/10/2013, 13 centres have agreed to participate in this study, 117 participants were included, and 70 have achieved the study schedules. The study completion is expected for the end of 2016, and the main results will be published in 2017.ConclusionORTHODIAB trial evaluates an innovating removable off‐loading device, seeking to improve diabetic foot healing (ClinicalTrials.gov identifier: NCT01956162).
Generation of a new transgenic mouse model for assessment of tau gene silencing therapies
Authors: Fromholt Susan , Reitano Christian , Brown Hilda , Lewis Jada , Borchelt David R. 
Published: August 2016

Abstract
Background
Targeting the expression of genes has emerged as a potentially viable therapeutic approach to human disease. In Alzheimer’s disease, therapies that silence the expression of tau could be a viable strategy to slow disease progression.

Methods
We produced a novel strain of transgenic mice that could be used to assess the efficacy of gene knockdown therapies for human tau, in live mice. We designed a tetracycline-regulated transgene construct in which the cDNA for human tau was fused to ubiquitin and to luciferase to create a single fusion polyprotein, termed TUL.

Results
When expressed in brain, the TUL polyprotein was cleaved by ubiquitin-processing enzymes to release the luciferase as an independent protein, separating the half-life of luciferase from the long-lived tau protein. Treatment of bigenic tTA/TUL mice with doxycycline produced rapid declines in luciferase levels visualized by in vivo imaging and ex vivo enzyme measurement.

Conclusions
This new mouse model can be used as a discovery tool in optimizing gene targeting therapeutics directed to reduce human tau mRNA levels.
Alzheimer’s Research UK 2016 Conference report
Authors: Sancho Rosa M. , Cox Carla J. , Phipps Laura E. , Ridley Simon H. 
Published: August 2016

AbstractThe annual Alzheimer’s Research UK (ARUK) Conference was hosted by the Manchester and North West Network Centre on March 8–9, 2016. In this report, we provide a summary of the research presented.
Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences
Authors: Tamazian Gaik , Dobrynin Pavel , Krasheninnikova Ksenia , Komissarov Aleksey , Koepfli Klaus-Peter , O'Brien Stephen J 
Published: August 2016

Abstract

Background
As the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study. Since de novo chromosome assemblies are confounded by repeat-mediated artifacts, reference-assisted assemblies that use comparative inference have become widely used, prompting the development of several reference-assisted assembly programs for prokaryotic and eukaryotic genomes.

Findings
We developed Chromosomer – a reference-based genome arrangement tool, which rapidly builds chromosomes from genome contigs or scaffolds using their alignments to a reference genome of a closely related species. Chromosomer does not require mate-pair libraries and it offers a number of auxiliary tools that implement common operations accompanying the genome assembly process.

Conclusions
Despite implementing a straightforward alignment-based approach, Chromosomer is a useful tool for genomic analysis of species without chromosome maps. Putative chromosome assemblies by Chromosomer can be used in comparative genomic analysis, genomic variation assessment, potential linkage group inference and other kinds of analysis involving contig or scaffold mapping to a high-quality assembly.
High-quality genome assembly of channel catfish, Ictalurus punctatus
Authors: Chen Xiaohui , Zhong Liqiang , Bian Chao , Xu Pao , Qiu Ying , You Xinxin , Zhang Shiyong , Huang Yu , Li Jia , Wang Minghua , Qin Qin , Zhu Xiaohua , Peng Chao , Wong Alex , Zhu Zhifei , Wang Min , Gu Ruobo , Xu Junmin , Shi Qiong , Bian Wenji 
Published: August 2016

Abstract

Background
The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world, especially in the United States' aquaculture industry. Since its introduction into China in 1984, both cultivation area and yield of this species have been dramatically increased such that China is now the leading producer of channel catfish. To aid genomic research in this species, data sets such as genetic linkage groups, long-insert libraries, physical maps, bacterial artificial clones (BAC) end sequences (BES), transcriptome assemblies, and reference genome sequences have been generated. Here, using diverse assembly methods, we provide a comparable high-quality genome assembly for a channel catfish from a breeding stock inbred in China for more than three generations, which was originally imported to China from North America.

Findings
Approximately 201.6 gigabases (Gb) of genome reads were sequenced by the Illumina HiSeq 2000 platform. Subsequently, we generated high quality, cost-effective and easily assembled sequences of the channel catfish genome with a scaffold N50 of 7.2 Mb and 95.6 % completeness. We also predicted that the channel catfish genome contains 21,556 protein-coding genes and 275.3 Mb (megabase pairs) of repetitive sequences.

Conclusions
We report a high-quality genome assembly of the channel catfish, which is comparable to a recent report of the “Coco” channel catfish. These generated genome data could be used as an initial platform for molecular breeding to obtain novel catfish varieties using genomic approaches.
Achieving convergence in galaxy formation models by augmenting N-body merger trees
Authors: Benson Andrew J , Cannella Chris , Cole Shaun 
Published: August 2016

AbstractAccurate modeling of galaxy formation in a hierarchical, cold dark matter universe requires the use of sufficiently high-resolution merger trees to obtain convergence in the predicted properties of galaxies. When semi-analytic galaxy formation models are applied to cosmological N-body simulation merger trees, it is often the case that those trees have insufficient resolution to give converged galaxy properties. We demonstrate a method to augment the resolution of N-body merger trees by grafting in branches of Monte Carlo merger trees with higher resolution, but which are consistent with the pre-existing branches in the N-body tree. We show that this approach leads to converged galaxy properties.
HRTEM low dose: the unfold of the morphed graphene, from amorphous carbon to morphed graphenes
Authors: Calderon H. A. , Okonkwo A. , Estrada-Guel I. , Hadjiev V. G. , Alvarez-Ramírez F. , Robles Hernández F. C. 
Published: August 2016

AbstractWe present experimental evidence under low-dose conditions transmission electron microscopy for the unfolding of the evolving changes in carbon soot during mechanical milling. The milled soot shows evolving changes as a function of the milling severity or time. Those changes are responsible for the transformation from amorphous carbon to graphenes, graphitic carbon, and highly ordered structures such as morphed graphenes, namely Rh6 and Rh6-II. The morphed graphenes are corrugated layers of carbon with cross-linked covalently nature and sp2- or sp3-type allotropes. Electron microscopy and numerical simulations are excellent complementary tools to identify those phases. Furthermore, the TEAM 05 microscope is an outstanding tool to resolve the microstructure and prevent any damage to the sample. Other characterization techniques such as XRD, Raman, and XPS fade to convey a true identification of those phases because the samples are usually blends or mixes of the mentioned phases.
Characterization of Tumor Size Changes Over Time From the Phase 3 Study of Lenvatinib in Thyroid Cancer
Authors: Robinson Bruce , Schlumberger Martin , Wirth Lori J. , Dutcus Corina E. , Song James , Taylor Matthew H. , Kim Sung-Bae , Krzyzanowska Monika K. , Capdevila Jaume , Sherman Steven I. , Tahara Makoto 
Published: August 2016

Context:
Lenvatinib improved the progression-free survival (PFS) and overall response rate of patients with radioiodine-refractory differentiated thyroid cancer vs placebo in the Phase 3 Study of (E7080) Lenvatinib in Differentiated Cancer of the Thyroid (SELECT).

Objective:
The objective of the study was to characterize tumor size changes with lenvatinib treatment.

Design:
SELECT was a phase 3, randomized, double-blind, multicenter study.

Setting:
In this clinical trial, tumor assessments of lenvatinib (n = 261) and placebo-treated (n = 131) patients were performed by independent radiological review per Response Evaluation Criteria in Solid Tumors version, 1.1 at 8-week intervals.

Patients:
Patients with complete or partial response were defined as responders to lenvatinib (n = 169). Of the 92 nonresponders, 76 had at least one postbaseline tumor assessment and were included in this analysis.

Interventions:
Lenvatinib (24 mg once daily) or placebo in 28-day cycles until unacceptable toxicity, disease progression, or death.

Main Outcome Measures:
This was an exploratory analysis of key end points from SELECT, including PFS, overall response rate, and tumor reduction.

Results:
The median maximum percentage change in tumor size was −42.9% for patients receiving lenvatinib (responders, −51.9%; nonresponders, −20.2%). Tumor size reduction was most pronounced at first assessment (median, −24.7% at 8 wk after randomization); thereafter, the rate of change was slower but continuous (−1.3% per mo). In a multivariate model, percentage change in tumor size at the first assessment was a marginally significant positive predictor for PFS (P = .06).

Conclusions:
The change in tumor size conferred by lenvatinib was characterized by two phases: an initial, rapid decline, followed by slower, continuous shrinkage.
MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data
Authors: Correia Damien , Doppelt-Azeroual Olivia , Denis Jean-Baptiste , Vandenbogaert Mathias , Caro Valérie 
Published: August 2016

The detection and characterization of emerging infectious agents has been a continuing public health concern. High Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies have proven to be promising approaches for efficient and unbiased detection of pathogens in complex biological samples, providing access to comprehensive analyses. As NGS approaches typically yield millions of putatively representative reads per sample, efficient data management and visualization resources have become mandatory. Most usually, those resources are implemented through a dedicated Laboratory Information Management System (LIMS), solely to provide perspective regarding the available information. We developed an easily deployable web-interface, facilitating management and bioinformatics analysis of metagenomics data-samples. It was engineered to run associated and dedicated Galaxy workflows for the detection and eventually classification of pathogens. The web application allows easy interaction with existing Galaxy metagenomic workflows, facilitates the organization, exploration and aggregation of the most relevant sample-specific sequences among millions of genomic sequences, allowing them to determine their relative abundance, and associate them to the most closely related organism or pathogen. The user-friendly Django-Based interface, associates the users’ input data and its metadata through a bio-IT provided set of resources (a Galaxy instance, and both sufficient storage and grid computing power). Galaxy is used to handle and analyze the user’s input data from loading, indexing, mapping, assembly and DB-searches. Interaction between our application and Galaxy is ensured by the BioBlend library, which gives API-based access to Galaxy’s main features. Metadata about samples, runs, as well as the workflow results are stored in the LIMS. For metagenomic classification and exploration purposes, we show, as a proof of concept, that integration of intuitive exploratory tools, like Krona for representation of taxonomic classification, can be achieved very easily. In the trend of Galaxy, the interface enables the sharing of scientific results to fellow team members.
Inventory, Risk Shifting, and Trade Credit
Authors: Chod Jiri 
Published: August 2016

This paper has two objectives. First, we show how debt financing distorts a retailer’s inventory decision when the retailer orders multiple items that differ in cost, revenue, or demand parameters. Taking advantage of limited liability, a debt-financed retailer favors items with a low salvage value, those with a high profit margin, and those that represent a large proportion of the total inventory investment. Second, we argue that this distortion is mitigated when the financing is provided by the supplier who can observe the actual order quantities before determining the credit terms. Borrowing goods rather than borrowing cash limits the retailer’s ability to deviate from the first-best inventory decision. On the flip side, few suppliers can access capital at the same low cost as banks. We study a combination of bank and supplier financing that allows the retailer to get the best of both worlds. This paper was accepted by Serguei Netessine, operations management.