bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Microwave Radiative Properties of Falling Snow Derived from Nonspherical Ice Particle Models. Part II: Initial Testing Using Radar, Radiometer and In Situ Observations
Authors: Olson William S. , Tian Lin , Grecu Mircea , Kuo Kwo-Sen , Johnson Benjamin T. , Heymsfield Andrew J. , Bansemer Aaron , Heymsfield Gerald M. , Wang James R. , Meneghini Robert 
Published: January 2016

AbstractIn this study, two different particle models describing the structure and electromagnetic properties of snow are developed and evaluated for potential use in satellite combined radar–radiometer precipitation estimation algorithms. In the first model, snow particles are assumed to be homogeneous ice–air spheres with single-scattering properties derived from Mie theory. In the second model, snow particles are created by simulating the self-collection of pristine ice crystals into aggregate particles of different sizes, using different numbers and habits of the collected component crystals. Single-scattering properties of the resulting nonspherical snow particles are determined using the discrete dipole approximation. The size-distribution-integrated scattering properties of the spherical and nonspherical snow particles are incorporated into a dual-wavelength radar profiling algorithm that is applied to 14- and 34-GHz observations of stratiform precipitation from the ER-2 aircraftborne High-Altitude Imaging Wind and Rain Airborne Profiler (HIWRAP) radar. The retrieved ice precipitation profiles are then input to a forward radiative transfer calculation in an attempt to simulate coincident radiance observations from the Conical Scanning Millimeter-Wave Imaging Radiometer (CoSMIR). Much greater consistency between the simulated and observed CoSMIR radiances is obtained using estimated profiles that are based upon the nonspherical crystal/aggregate snow particle model. Despite this greater consistency, there remain some discrepancies between the higher moments of the HIWRAP-retrieved precipitation size distributions and in situ distributions derived from microphysics probe observations obtained from Citation aircraft underflights of the ER-2. These discrepancies can only be eliminated if a subset of lower-density crystal/aggregate snow particles is assumed in the radar algorithm and in the interpretation of the in situ data.
Stochastic Convection Parameterization with Markov Chains in an Intermediate-Complexity GCM
Authors: Dorrestijn Jesse , Crommelin Daan T. , Siebesma A. Pier , Jonker Harmen J. J. , Selten Frank 
Published: January 2016

Abstract
Conditional Markov chain (CMC) models have proven to be promising building blocks for stochastic convection parameterizations. In this paper, it is demonstrated how two different CMC models can be used as mass flux closures in convection parameterizations. More specifically, the CMC models provide a stochastic estimate of the convective area fraction that is directly proportional to the cloud-base mass flux. Since, in one of the models, the number of CMCs decreases with increasing resolution, this approach makes convection parameterizations scale aware and introduces stochastic fluctuations that increase with resolution in a realistic way. Both CMC models are implemented in a GCM of intermediate complexity. It is shown that with the CMC models, trained with observational data, it is possible to improve both the subgrid-scale variability and the autocorrelation function of the cloud-base mass flux as well as the distribution of the daily accumulated precipitation in the tropics. Hovmöller diagrams and wavenumber–frequency diagrams of the equatorial precipitation indicate that, in this specific GCM, convectively coupled equatorial waves are more sensitive to the mean cloud-base mass flux than to stochastic fluctuations. A smaller mean mass flux tends to increase the power of the simulated MJO and to diminish equatorial Kelvin waves.
Reconceptualizing Consent for Direct-to-Consumer Health Services
Authors: Spector-Bagdady Kayte 
Published: January 2016

The market for direct-to-consumer (DTC) health services continues to grow rapidly with former patients converting to customers for the opportunity to purchase varied diagnostic tests without the involvement of their clinician. For the first time a DTC genetic testing company is advertising health-related reports “that meet [Food and Drug Administration] standards for being clinically and scientifically valid.” Ethicists and regulatory agencies alike have recognized the need for a more informed transaction in the DTC context, but how should we classify a commercial transaction for something normally protected by a duty of care? How can we assure informed agreements in an industry with terms and conditions as varied as the services performed? The doctrine of “informed consent” began as an ethical construct building on the promise of beneficence in the clinical relationship and elevating the principle of autonomy—but in the DTC context should we hold providers to legal standards of informed consent and associated medical malpractice liability, or contractual obligations where consumers would seek remedy for breach?This Article analyzes the fine balance that must be struck in an industry where companies are selling services for entertainment or non-medical purposes that possess the capacity to produce serious and disquieting medical information. It begins by reviewing current standards of consent in the clinical setting from both a legal and ethical perspective and then lays forth current standards for DTC consent using two currently controversial case studies: that of keepsake fetal ultrasound and genetic testing.DTC keepsake ultrasound and genetic testing providers attempt to de-medicalize the devices used for these procedures from their intended medical uses to non-medical uses. But while keepsake ultrasound is marketed as “intended for entertainment purposes only,” it can provide medical information as an incidental finding. 23andMe currently purports to be the only DTC genetics service that “includes” reports that meet FDA qualifications, despite disclaimers of intent to “provide medical advice.” The attempted de-medicalization of these devices, therefore, has not been fully transformative, and DTC providers should have more robust ethical and legal duties than the average goods and services seller.This Article delineates these responsibilities, beginning with ethical duties surrounding marketing, entering into, and providing DTC services. It then turns to the legal paradigms necessary to enable, or at least allow for, DTC providers to meet these ethical obligations. While it argues that contractual, as opposed to fiduciary, requirements are most appropriate and that waivers of liability will likely be upheld, it also advocates for a heightened expectation of disclosure during contracting.
Efficacy of Maxillomandibular Advancement Examined with Drug‐Induced Sleep Endoscopy and Computational Fluid Dynamics Airflow Modeling
Authors: Liu Stanley Yung‐Chuan , Huon Leh‐Kiong , Iwasaki Tomonori , Yoon Audrey , Riley Robert , Powell Nelson , Torre Carlos , Capasso Robson 
Published: January 2016

ObjectivesTo use drug‐induced sedation endoscopy (DISE) and computational fluid dynamics (CFD) modeling to study dynamic airway and airflow changes after maxillomandibular advancement (MMA), and how the changes correlate with surgical success based on polysomnography parameters.Study DesignRetrospective cohort study.SettingUniversity medical center.MethodsDISE was rated with the VOTE (velum, oropharynx, tongue, epiglottis) classification, and CFD was used to model airflow velocity and negative pressure exerted on pharyngeal wall. Changes in VOTE score by site and CFD measurements were correlated with perioperative polysomnography outcomes of apnea‐hypopnea index (AHI), apnea index (AI), oxygenation desaturation index (ODI), and lowest oxygen saturation.ResultsAfter MMA, 20 subjects (17 males, 3 females) with a mean age of 44 ± 12 years and body mass index of 27.4 ± 4.6 kg/m2 showed mean decreases in AHI (53.6 ± 26.6 to 9.5 ± 7.4 events/h) and ODI (38.7 ± 30.3 to 8.1 ± 9.2 events/h; P <. 001). Improvement in lateral pharyngeal wall collapse during DISE based on VOTE score correlated with the most decrease in AHI (60.0 ± 25.6 to 7.5 ± 3.4 events/h) and ODI (46.7 ± 29.8 to 5.3 ± 2 events/h; P =. 002). CFD modeling showed significant positive Pearson correlations between reduction of retropalatal airflow velocity and AHI (r = 0.617, P =. 04) and ODI (r = 0.773, P =. 005).ConclusionAHI and ODI improvement after MMA is best correlated with (1) decreased retropalatal airflow velocity modeled by CFD and (2) increased lateral pharyngeal wall stability based on VOTE scoring from DISE.
The Finance Curse: Britain and the World Economy
Authors: Christensen John , Shaxson Nick , Wigan Duncan 
Published: January 2016

Outlines harms caused to countries hosting an oversized financial sector Argues Britain is subject to a Finance Curse, which carries many similarities with the Resource Curse, afflicting mineral-exporting countries Provides a narrative and framework to analyse the political economy of finance and financialisation The Global Financial Crisis placed the utility of financial services in question. The crash, great recession, wealth transfers from public to private, austerity and growing inequality cast doubt on the idea that finance is a boon to the host economy. This article systematizes these doubts to highlight the perils of an oversized financial sector. States failing to harness natural resources for development led to the concept of the Resource Curse. In many countries, resource dependence generated slower growth, crowding out, reduced economic diversity, lost entrepreneurialism, unemployment, economic instability, inequality, conflict, rent-seeking and corruption. The Finance Curse produces similar effects, often for similar reasons. Beyond a point, a growing financial sector can do more harm than good. Unlike the Resource Curse, these harms transcend borders. The concept of a Finance Curse starkly illuminates the condition of Britain’s political economy and the character of its relations with the rest of the world.
What is the relationship among penumbra volume, collaterals, and time since onset in the first 6 h after acute ischemic stroke?
Authors: Cheripelli Bharath Kumar , Huang Xuya , McVerry Ferghal , Muir Keith W 
Published: January 2016

Background The steep, time-dependent loss of benefit from reperfusion in clinical trials is consistent with loss of penumbra over the early hours of ischemia, as observed in animal models. Human imaging studies, however, show persistent penumbra for up to 48 h. We investigated core and penumbra volumes and collateral status in relation to time after stroke onset within the first 6 h. Methods Using data from three multimodal computer tomography-based studies in acute ischemic stroke patients <6 h after onset, we measured core and penumbra volumes, collateral status, and target mismatch (defined as core volume < 50 ml, perfusion lesion volume > 15 ml, mismatch ratio > 1.8). Patients were grouped by onset to imaging time (<3, 3–4.5, 4.5–6 h). We explored correlates of penumbra proportion by multivariable linear regression. Results Analysis included 144 subjects. Across time epochs, neither proportions of penumbra (59%, 64%, 75% at <3, 3–4.5, >4. 5 h, respectively, p = 0.4) nor poor collaterals (15/56 (27%), 14/47 (30%), 4/15 (27%) at <3, 3–4.5, >4.5 h, p = 0.9) differed significantly. Penumbra proportion was not clearly related to time to imaging ( R2 = 0.003; p = 0.5) but a trend for divergent effects by collateral status was seen (slight increase in penumbra over time with good collaterals versus reduced with poor, interaction = 0.08). The proportion of patients with target mismatch did not vary by time (56%, 74%, and 67% at <3, 3–4.5, >4.5 h, p = 0.09). Conclusions In a cross-sectional sample imaged within 6 h, neither the proportions of penumbral tissue nor “target mismatch” varied by time from onset. A trend for reducing penumbra proportion only among those with poor collaterals may have pathophysiological and therapeutic importance.
A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads
Authors: Le Vinh Van , Tran Lang Van , Tran Hoai Van 
Published: January 2016

Abstract
Background
Taxonomic assignment is a crucial step in a metagenomic project which aims to identify the origin of sequences in an environmental sample. Among the existing methods, since composition-based algorithms are not sufficient for classifying short reads, recent algorithms use only the feature of similarity, or similarity-based combined features. However, those algorithms suffer from the computational expense because the task of similarity search is very time-consuming. Besides, the lack of similarity information between reads and reference sequences due to the length of short reads reduces significantly the classification quality.

Results
This paper presents a novel taxonomic assignment algorithm, called SeMeta, which is based on semi-supervised learning to produce a fast and highly accurate classification of short-length reads with sufficient mutual overlap. The proposed algorithm firstly separates reads into clusters using their composition feature. It then labels the clusters with the support of an efficient filtering technique on results of the similarity search between their reads and reference databases. Furthermore, instead of performing the similarity search for all reads in the clusters, SeMeta only does for reads in their subgroups by utilizing the information of sequence overlapping. The experimental results demonstrate that SeMeta outperforms two other similarity-based algorithms on different aspects.

Conclusions
By using a semi-supervised method as well as taking the advantages of various features, the proposed algorithm is able not only to achieve high classification quality, but also to reduce much computational cost. The source codes of the algorithm can be downloaded at http://it.hcmute.edu.vn/bioinfo/metapro/SeMeta.html
TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation
Authors: Wolfien Markus , Rimmbach Christian , Schmitz Ulf , Jung Julia Jeannine , Krebs Stefan , Steinhoff Gustav , David Robert , Wolkenhauer Olaf 
Published: January 2016

AbstractBackgroundTechnical advances in Next Generation Sequencing (NGS) provide a means to acquire deeper insights into cellular functions. The lack of standardized and automated methodologies poses a challenge for the analysis and interpretation of RNA sequencing data. We critically compare and evaluate state-of-the-art bioinformatics approaches and present a workflow that integrates the best performing data analysis, data evaluation and annotation methods in aTransparent,Reproducible andAutomatedPipeLINE(TRAPLINE) for RNA sequencing data processing (suitable for Illumina, SOLiD and Solexa).ResultsComparative transcriptomics analyses with TRAPLINE result in a set of differentially expressed genes, their corresponding protein-protein interactions, splice variants, promoter activity, predicted miRNA-target interactions and files for single nucleotide polymorphism (SNP) calling. The obtained results are combined into a single file for downstream analysis such as network construction. We demonstrate the value of the proposed pipeline by characterizing the transcriptome of our recently described stem cell derived antibiotic selected cardiac bodies ('aCaBs').ConclusionTRAPLINE supports NGS-based research by providing a workflow that requires no bioinformatics skills, decreases the processing time of the analysis and works in the cloud. The pipeline is implemented in the biomedical research platform Galaxy and is freely accessible viawww.sbi.uni-rostock.de/RNAseqTRAPLINEor the specific Galaxy manual page (https://usegalaxy.org/u/mwolfien/p/trapline---manual).
Comparative ethnobotany of the Wakhi agropastoralist and the Kyrgyz nomads of Afghanistan
Authors: Soelberg Jens , Jäger Anna K. 
Published: January 2016

Abstract
Background
The mountainous Wakhan and Pamir in northeastern Afghanistan is one of the most isolated yet inhabited places in Asia. It is home to the agropastoralist Wakhi and the last Afghan semi-nomadic Kyrgyz. We present a study of plant names and uses, along with comparisons of plant name etymology, origins of plant resources, intra- and intercultural exchanges and relations, and the relative availability of the known and used plants.

Methods
The fieldwork was conducted as an expedition in the summer of 2010, and visited settlements and pastures in Upper Wakhan and Big and Little Pamir. Semi-structured group interviews, talks and observations gave initial data on names, uses and the relative availability of used plants, and provided foundation for individual interviews using an interview-herbarium containing vouchers of the 72 most frequently used plants or plant groups.

Results
Wakhi and Kyrgyz plant names are recorded in western transcription, the new Wakhi alphabet, phonetically and in Cyrillic. The present study documents a large body of endemic, indigenous plant knowledge; on crops, fuel, fodder, cosmetics, dyes, vegetables, veterinary medicine, traditional medicines and other plant uses which sustain life in Wakhan and Pamir. Overall, the Wakhi use considerably more plants than the Kyrgyz, and their materia medica and use thereof is more complex. Although the Wakhi and Kyrgyz are close neighbours, there are few indications of direct knowledge transfer between them. Most shared plant uses are strictly necessary for survival in the mountains. While there are few differences between genders and cultural subgroups within the two cultures, the Wakhi and Kyrgyz exhibit great differences both in their total number of use-plants and the distance from which they obtain them. The agropastoralist Wakhi appear to have their basic needs for wild natural resources covered within half a days travel, while the relatively plant-derived environment of the high Pamir appears to have necessitated the nomadic Kyrgyz to adapt by developing uses and obtaining plants that are comparatively remote.

Conclusion
The comparative differences in plant uses between the agropastoralist Wakhi and nomadic Kyrgyz appear to be accentuated by an environment at the extreme of what is humanly possible.
Foodways in transition: food plants, diet and local perceptions of change in a Costa Rican Ngäbe community
Authors: D’Ambrosio Ugo , Puri Rajindra K. 
Published: January 2016

Abstract
Background
Indigenous populations are undergoing rapid ethnobiological, nutritional and socioeconomic transitions while being increasingly integrated into modernizing societies. To better understand the dynamics of these transitions, this article aims to characterize the cultural domain of food plants and analyze its relation with current day diets, and the local perceptions of changes given amongst the Ngäbe people of Southern Conte-Burica, Costa Rica, as production of food plants by its residents is hypothesized to be drastically in recession with an decreased local production in the area and new conservation and development paradigms being implemented.

Methods
Extensive freelisting, interviews and workshops were used to collect the data from 72 participants on their knowledge of food plants, their current dietary practices and their perceptions of change in local foodways, while cultural domain analysis, descriptive statistical analyses and development of fundamental explanatory themes were employed to analyze the data.

Results
Results show a food plants domain composed of 140 species, of which 85 % grow in the area, with a medium level of cultural consensus, and some age-based variation. Although many plants still grow in the area, in many key species a decrease on local production–even abandonment–was found, with much reduced cultivation areas. Yet, the domain appears to be largely theoretical, with little evidence of use; and the diet today is predominantly dependent on foods bought from the store (more than 50 % of basic ingredients), many of which were not salient or not even recognized as ‘food plants’ in freelists exercises. While changes in the importance of food plants were largely deemed a result of changes in cultural preferences for store bought processed food stuffs and changing values associated with farming and being food self-sufficient, Ngäbe were also aware of how changing household livelihood activities, and the subsequent loss of knowledge and use of food plants, were in fact being driven by changes in social and political policies, despite increases in forest cover and biodiversity.

Conclusions
Ngäbe foodways are changing in different and somewhat disconnected ways: knowledge of food plants is varied, reflecting most relevant changes in dietary practices such as lower cultivation areas and greater dependence on food from stores by all families. We attribute dietary shifts to socioeconomic and political changes in recent decades, in particular to a reduction of local production of food, new economic structures and agents related to the State and globalization.
Ethnoichthyology of the indigenous Truká people, Northeast Brazil
Authors: Santos Carlos Alberto Batista , Nóbrega Alves Rômulo Romeu 
Published: January 2016

AbstractBackgroundHistorically, fishing is an important activity for riverine communities established along the São Francisco River, including indigenous communities. In the present study, we researched fishing activities in two villages of the Truká ethnic group, both located in the State of Pernambuco along the sub-middle section of the São Francisco River, Northeast Brazil. We recorded the richness and uses of the fished species and the ecological knowledge on these species, the fishing techniques employed and the perception of the indigenous people regarding current environmental impacts on the São Francisco River that influence local fishing.MethodThe information was obtained through interviews with 33 Truká fishers (27 men and six women), including 17 interviewees from Central Village (Cabrobó) and 16 from Tapera Village (Orocó).ResultsUsing five fishing techniques, the interviewees caught 25 fish species, including 21 native and four exotic species. All species are used as food, and two species are used in traditional Truká medicine. The interviewees revealed that fishing currently has less importance in their subsistence. They indicated that this situation is occurring because of several factors, such as the introduction of exotic species, pollution and urbanization, that have impacted the São Francisco River, resulting in a decline of fishing resources. Nevertheless, we found that the indigenous people who are still fishing have a broad knowledge of the habitat and ecology of the target fishing.ConclusionAlthough fishing is declining in importance among the Truká, we found that the individuals who are still practicing this activity have a broad knowledge about the habitat and ecology of the target species and apply that knowledge to fishing methods. Knowledge about the ecology of the species and the environmental impacts that have affected them can support basic research on local fish populations and research investigating the environmental impacts, resource management and sustainable exploitation of fisheries resources.