bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters
Authors: Álvarez-Carretero Sandra , Goswami Anjali , Yang Ziheng , dos Reis Mario 
Published: October 2018

AbstractDiscrete morphological data have been widely used to study species evolution, but the use of quantitative (or continuous) morphological characters is less common. Here, we implement a Bayesian method to estimate species divergence times using quantitative characters. Quantitative character evolution is modelled using Brownian diffusion with character correlation and character variation within populations. Through simulations, we demonstrate that ignoring the population variation (or population “noise”) and the correlation among characters leads to biased estimates of divergence times and rate, especially if the correlation and population noise are high. We apply our new method to the analysis of quantitative characters (cranium landmarks) and molecular data from carnivoran mammals. Our results show that time estimates are affected by whether the correlations and population noise are accounted for or ignored in the analysis. The estimates are also affected by the type of data analysed, with analyses of morphological characters only, molecular data only, or a combination of both; showing noticeable differences among the time estimates. Rate variation of morphological characters among the carnivoran species appears to be very high, with Bayesian model selection indicating that the independent-rates model fits the morphological data better than the autocorrelated-rates model. We suggest that using morphological continuous characters, together with molecular data, can bring a new perspective to the study of species evolution. Our new model is implemented in the MCMCtree computer program for Bayesian inference of divergence times.
Comparisons of a Novel Air Sampling Filter Material, Wash Buffers and Extraction Methods in the Detection and Quantification of Influenza Virus
Authors: Thedell Terrance A. , Boles Corey L. , Cwiertny David M. , Qian Jiajie , Brown Grant D. , Nonnenmann Matthew W. 
Published: October 2018

AbstractQuantification of aerosolized influenza virus is used for determining inhalation exposure. Several bioaerosol samplers and analytical methods have been used; however, the detection and quantification of influenza virus among aerosol samples remains challenging. Therefore, improved viral aerosol measurement methods are needed. This study evaluated influenza virus recovery among three filter types polytetrafluoroethylene, polyvinylchloride and polystyrene. Polytetrafluoroethylene, polyvinylchloride are fabricated filter materials and commonly used in the scientific literature to sample for viral aerosols. A novel, electrospun polystyrene filter material may improve viral aerosol recovery during filter-based air sampling. The filter materials were compared across the following conditions: treated with or without air, filter wash buffer (HBSS or PBS), and viral RNA extraction method (QIAamp Viral RNA Mini Kit or Trizol). Twenty trials were completed in a chamber and samples were analyzed using RT-qPCR. Viral recovery was significantly different (p-value < .0001) by filter type. Polystyrene filter use resulted in recovery of the most viral RNA. Air sampling did not affect the recovery of viral RNA from the filter materials (p-values > 0.05). Viral RNA concentrations were significantly different across extraction methods for all comparisons (p-values < 0.05). Our results demonstrated that the novel polystyrene filter material resulted in the highest concentration of extracted RNA compared to the commonly used polytetrafluoroethylene and polyvinylchloride, which we speculate may be related to the chemical composition of the filter material (e.g., polystyrene is an aromatic hydrocarbon whereas polytetrafluoroethylene and polyvinylchloride contain more polar, and thus potentially reactive, carbon-halogen bonds). Air sampling did not have an effect on viral RNA recovery. Using Hanks Balanced Salt Solution with QIAamp Viral RNA Mini Kit, and Phosphate-buffered saline with the Trizol extraction, resulted in the most viral RNA recovery.
The role of climate change education on individual lifetime carbon emissions
Authors: Cordero Eugene C. , Centeno Diana , Marie Todd Anne 
Published: October 2018

AbstractStrategies to mitigate climate change often center on clean technologies such as electric vehicles and solar panels, while the mitigation potential of a quality educational experience is rarely discussed. In this paper, we investigate the long-term impact that an intensive one-year university course had on individual carbon emissions by surveying students at least five years after having taken the course. A majority of course graduates reported pro-environmental decisions (i.e., type of car to buy, food choices) that can be attributed to experiences gained in the course. Furthermore, our carbon footprint analysis demonstrates that for the average course graduate, these decisions reduced their individual carbon emissions by 2.86 tons of CO2 per year. Focus group interviews identify that course graduates have developed a strong personal connection to climate change solutions, and this is realized in their daily behaviors and through their professional careers. The paper discusses in more detail the specific components of the course that are believed to be most impactful, and it shares preliminary outcomes from similar curriculum designs that are being used with K-12 students. Our analysis also demonstrates that if similar education programs were applied at scale, the potential reductions in carbon emissions would be of similar magnitude to other large-scale mitigation strategies such as rooftop solar or electric vehicles.
Conditioned place avoidance using encapsulated calcium propionate as an appetite suppressant for broiler breeders Conditioned place avoidance and calcium propionate
Authors: Arrazola Aitor , Torrey Stephanie 
Published: October 2018

AbstractBroiler breeders, the parent stock of meat chicks, are feed-restricte throughout rearing to avoid obesity-related problems in their health and reproductive performance. Broiler breeders often show signs of chronic hunger, lack of satiety and feeding frustration, and the development of alternative feeding strategies has investigated the inclusion of calcium propionate (CaP) as an appetite suppressant. However, the mechanisms involved in the reduction of voluntary feed intake are unknown, but are thought to be due to low palatability, gastrointestinal discomfort, or both. The objective of this experiment was to examine the effect of CaP as an appetite suppressant on the experience of a negative affective state, using a conditioned place preference test. Twenty four broiler breeders were trained to associate the consumption of CaP or a placebo pill with a red or blue place, depending on inherent colour preference. Pullets consumed two pills followed by 20 g feed allotment. The CaP pill contained 160 mg of CaP and the placebo pill had 160 mg of feed. Conditioning lasted for 90 min/pullet/day over 8 consecutive days at 7 and 9 weeks of age, and pullets’ choice was tested in a T-maze twice on two consecutive days at both 8 and 10 weeks of age. Data were analysed using a linear mixed regression model, with pen nested in the model and age as a repeated measure. Pullets were less likely to choose the place conditioned with the consumption of CaP (P<0.05) and the preference of the placebo linearly increased with training sessions (P<0.05). These results suggest that calcium propionate as an appetite suppressant can induce a negative affective state, with the lower feed intake resulting from a conditioned response to the negative effect of calcium propionate rather than to satiety.
Dosage Matters: A Randomized Controlled Trial of Rehabilitation Dose in the Chronic Phase after Stroke
Authors: Winstein Carolee , Kim Bokkyu , Kim Sujin , Martinez Clarisa , Schweighofer Nicolas 
Published: October 2018

AbstractBackground and PurposeFor stroke rehabilitation, task-specific training in animal models and human rehabilitation trials is considered important to trigger inherent neuroplasticity, promote motor learning, and functional recovery. Little is known, however, about what constitutes an effective dosage of therapy.MethodsThis is a parallel group, four arm, single blind, phase I, randomized control trial of four dosages of upper extremity therapy delivered in an outpatient setting during the chronic phase after stroke. Participants were randomized into groups that varied in total dosage of therapy (i.e., 0, 15, 30, or 60 hours). Seven hundred and four participants were assessed for eligibility, 50 were eligible to enroll, 45 were randomized, 44 participated and 41 completed the study. Planned primary analyses used linear mixed effects regression to model baseline to post-intervention changes in the Motor Activity Log-Quality of Movement rating (MALQ) and the Wolf Motor Function Test (WMFT) time score as a function of therapy dosage. A series of hierarchical models were constructed using the MALQ and WMFT.ResultsWe observed a significant dose response curve: the greater the dosage of training, the greater the change in MALQ, with the dose by week slope parameter of 0.0045 (ΔMAL/hour/week; p = 0.0011; 95% CI = [0.0019; 0.0071]). Over the 3 weeks of therapy, this corresponds to a gain of 0.81 in MALQ for the 60 hour dose.ConclusionsFor mild-to-moderately impaired stroke survivors, the dosage of a patient-centered, task specific motor therapy was shown to systematically influence the gain in quality of arm use in the natural environment, but not functional capacity as measured in the laboratory. We highlight the importance of recovery outcomes that capture arm use vs. functional capacity.Clinical Trial RegistrationURL: http://www.clinicaltrials.gov. Unique identifier: NCT 01749358
Current clinical use of polygenic scores will risk exacerbating health disparities
Authors: Martin Alicia R. , Kanai Masahiro , Kamatani Yoichiro , Okada Yukinori , Neale Benjamin M. , Daly Mark J. 
Published: October 2018

AbstractPolygenic risk scores (PRS) are poised to improve biomedical outcomes via precision medicine. However, the major ethical and scientific challenge surrounding clinical implementation is that they are many-fold more accurate in European ancestry individuals than others. This disparity is an inescapable consequence of Eurocentric genome-wide association study biases. This highlights that—unlike clinical biomarkers and prescription drugs, which may individually work better in some populations but do not ubiquitously perform far better in European populations—clinical uses of PRS today would systematically afford greater improvement to European descent populations. Early diversifying efforts show promise in levelling this vast imbalance, even when non-European sample sizes are considerably smaller than the largest studies to date. To realize the full and equitable potential of PRS, we must prioritize greater diversity in genetic studies and public dissemination of summary statistics to ensure that health disparities are not increased for those already most underserved.
Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers
Authors: Chatterjee Nilanjana , Pazarentzos Evangelos , Hrustanovic Gorjan , Lin Luping , Verschueren Erik , Johnson Jeffrey R. , Hofree Matan , Yan Jenny J. , Olivas Victor , Newton Billy W. , Dollen John V. , Earnshaw Charles H. , Flanagan Jennifer , Chan Elton , Asthana Saurabh , Ideker Trey , Wu Wei , Mayekar Manasi K. , Suzuki Junji , Barad Ben , Kirichok Yuriy , Fraser James , Weiss William A. , Krogan Nevan J. , Tulpule Asmin , Sabnis Amit J. , Bivona Trever G. 
Published: October 2018

SUMMARYPTEN is a tumor suppressor that is often inactivated in cancer and possesses both lipid and protein phosphatase activities. We report the metabolic regulator PDHK1 (pyruvate dehydrogenase kinase1) is a synthetic-essential gene in PTEN-deficient cancer and normal cells. The predominant mechanism of PDHK1 regulation and dependency is the PTEN protein phosphatase dephosphorylates NFκ;B activating protein (NKAP) and limits NFκB activation to suppress expression of PDHK1, a NFκB target gene. Loss of the PTEN protein phosphatase upregulates PDHK1 to drive aerobic glycolysis and induce PDHK1 cellular dependence. PTEN-deficient human tumors harbor increased PDHK1, which is a biomarker of decreased patient survival, establishing clinical relevance. This study uncovers a PTEN-regulated signaling pathway and reveals PDHK1 as a potential target in PTEN-deficient cancers.SIGNIFICANCEThe tumor suppressor PTEN is widely inactivated in cancers and tumor syndromes. PTEN antagonizes PI3K/AKT signaling via its lipid phosphatase activity. The modest success of PI3K/AKT inhibition in PTEN-deficient cancer patients provides rationale for identifying other vulnerabilities in PTEN-deficient cancers to improve clinical outcomes. We show that PTEN-deficient cells are uniquely sensitive to PDHK1 inhibition. PTEN and PDHK1 co-suppression reduced colony formation and induced cell deathin vitroand tumor regressionin vivo. PDHK1 levels were high in PTEN-deficient patient tumors and associated with inferior patient survival, establishing clinical relevance. Our study identifies a PTEN-regulated signaling pathway linking the PTEN protein phosphatase to the metabolic regulator PDHK1 and provides a mechanistic basis for PDHK1 targeting in PTEN-deficient cancers.
Elevatedde novofatty acid biosynthesis gene expression promotes melanoma cell survival and drug resistance
Authors: Wu Su , Näär Anders M. 
Published: October 2018

AbstractElevatedde novofatty acid biosynthesis (DNFA) is a hallmark adaptation in many cancers that supports survival, proliferation, and metastasis. Here we elucidate previously unexplored aspects of transcription regulation and clinical relevance of DNFA in melanomas. We show that elevated expression of DNFA genes is characteristic of many tumor types and correlates with poor prognosis. Elevated DNFA gene expression depends on transcription factor SREBP1 in multiple melanoma cell lines. SREBP1 predominantly binds to the transcription start sites of DNFA genes, directly regulating transcription via RNA polymerase II recruitment and productive elongation. We find that SREBP1-regulated DNFA represents an intrinsic survival mechanism in melanoma cells, regardless of proliferative state and oncogenic mutation status. Indeed, malignant melanoma cells exhibit elevated DNFA gene expression after pro-survival signaling pathways are blocked (e.g. by the BRAF inhibitor vemurafenib). Altogether, these results implicate SREBP1 and DNFA enzymes as enticing therapeutic targets in melanomas.
Citizens of Delhi lead resilience action
Authors: Gupta Manu , Talankar Parag , Chavda Shivangi 
Published: October 2018

Purpose
The purpose of this paper is to illustrate practical approaches to addressing issues of risk reduction and disaster prevention in urban areas. In addition to exposure to natural hazards, urban areas represent complex risks and vulnerabilities together with complicated governance structures.

Design/methodology/approach
To address the challenge, SEEDS mobilised a “Disaster Watch Forum” – a citizens’ platform that brought citizens together to proactively engage with the local government. With hand-holding support from SEEDS, training by domain experts, internal team building and the forum has become a credible people-based institution addressing issues of risk reduction and prevention.

Findings
Urban risk reduction has remained a challenging issue with solutions often sought in high investment structural interventions. These have limited impact on the urban poor living in informal areas. This paper reveals “bottom-up” people-based approach that is able to engage with the “system” from “outside”. It reveals how people relate to day-to-day risks that affect their lives, making it the stepping stone to address higher order societal risks. Finally, the immense power and energy of youth and children work as local “agents of change”. Overall, the work aligns with priorities of the Sendai Framework for Disaster Risk Reduction.

Research limitations/implications
There are three principal implications for further research: with half the world now urbanized, urgent solutions are needed for improving disaster risk governance in cities; taking a “whole of society” approach in addressing a wider canvas of risks; and redirecting investments in urban areas towards managing risks, rather than managing disasters.

Practical implications
The model illustrated is replicable in urban areas facing risk. It worked well in a population catchment of 50,000 residents; to achieve scale would require enabling a federated structure of several localised forums.

Originality/value
The paper presents a hands-on experience in building an alternative approach to urban risk reduction. It has required authors to move from “government to governance” model making citizens active stakeholders in proactively addressing their own underlying vulnerabilities that lead to creation of and exacerbation of risks.
When two existential risks are better than one
Authors: Miller James Daniel 
Published: October 2018

Purpose
The great filter and an unfriendly artificial general intelligence might pose existential risks to humanity, but these two risks are anti-correlated. The purpose of this paper is to consider the implications of having evidence that mankind is at significant peril from both these risks.

Design/methodology/approach
This paper creates Bayesian models under which one might get evidence for being at risk for two perils when we know that we are at risk for at most one of these perils.

Findings
Humanity should possibly be more optimistic about its long-term survival if we have convincing evidence for believing that both these risks are real than if we have such evidence for thinking that only one of these perils would likely strike us.

Originality/value
Deriving implications of being greatly concerned about both an unfriendly artificial general intelligence and the great filter.
Asymmetric characteristics of the shock bifurcation in the reflected shock/boundary layer interaction
Authors: Zhang Yang , Zou Jianfeng , Xie Jiahua , Li Xiaoyue , Ma Zhenhai , Zheng Yao 
Published: October 2018

Purpose
When a reflected shock interacts with the boundary layer in a shock tube, the shock bifurcation occurs near the walls. Although the study of the shock bifurcation has been carried out by many researchers for several decades, little attention has been devoted to investigate the instability pattern of the bifurcation. This research work aims to successfully capture the asymmetry of the whole flow field, and attempt to achieve the instability mechanism of the shock bifurcation by a direct numerical simulation of the reflected shock wave/boundary layer interaction at Ma = 1.9. In addition, the reason for the formation of the bifurcated structure is also explored.

Design/methodology/approach
The spatial and temporal evolution of the shock bifurcation is obtained by solving the two-dimensional compressible Navier–Stokes equations using a seventh-order accurate weighted essentially non-oscillatory (WENO) scheme and a three-step Runge–Kutta time advancing approach.

Findings
The results show that the formation of shock bifurcation is mainly because of the shock/gradient field interaction, and the height of the bifurcated foot increases with the growth of the shock intensity and the gradient field. The unsteady asymmetry of the upper and bottom shock bifurcated structures is because of the vortex shedding with high frequency in the rear recirculation zone, which leads to the fluctuation of the recirculation area. The vortex shedding process behind the bifurcated structure closely resembles the Karman vortex street formed by the flow around the cylinder. The dimensionless vortex shedding frequency varies between 0.01 and 0.02. In comparison to the scenario at Ma = 1.9, the occurring time of instability is delayed and the upper and bottom bifurcated feet intersect in a relatively short time at Ma = 3.5. The region behind the bifurcated shock is a transitional flow field containing obvious cell structures and “isolated islands.”

Originality/value
This paper discovers an unsteady flow pattern of the shock bifurcation, and the mechanism of this instability in the reflected shock/boundary layer interaction is revealed in detail.
Numerical simulation of wet steam transonic condensation flow in the last stage of a steam turbine
Authors: Han Xu , Han Zhonghe , Zeng Wei , Li Peng , Qian Jiangbo 
Published: October 2018

Purpose
The purpose of this paper is to study the condensation flow of wet steam in the last stage of a steam turbine and to obtain the distribution of condensation parameters such as nucleation rate, Mach number and wetness.

Design/methodology/approach
Because of the sensitivity of the condensation parameter distribution, a double fluid numerical model and a realizable k-ε-kd turbulence model were applied in this study, and the numerical solution for the non-equilibrium condensation flow is provided.

Findings
The simulation results are consistent with the experimental results of the Bakhtar test. The calculation results indicate that the degree of departure from saturation has a significant impact on the wet steam transonic condensation flow. When the inlet steam deviates from the saturation state, shock wave interference and vortex mixing also have a great influence on the distribution of water droplets.

Originality/value
The research results can provide reference for steam turbine wetness losses evaluation and flow passage structure optimization design.
Influence of external head cooling on the head, core body and blood temperatures using 3D whole-body model
Authors: Devarakonda Surendra Balaji , Bulusu Pallavi , Al-rjoub Marwan , Bhattacharya Amit , Banerjee Rupak Kumar 
Published: October 2018

Purpose
The purpose of this study is to evaluate the impact of external head cooling on alleviating the heat stress in the human body by analyzing the temperatures of the core body (Tc), blood (Tblood) and head (Th) during exercise conditions using 3D whole body model.

Design/methodology/approach
Computational study is conducted to comprehend the influence of external head cooling on Tc, Tblood and Th. The Pennes bioheat and energy balance equations formulated for the whole-body model are solved concurrently to obtain Tc, Tblood and Th for external head cooling values from 33 to 233 W/m2. Increased external head cooling of 404 W/m2 is used to compare the numerical and experimental Th data.

Findings
Significant reductions of 0.21°C and 0.38°C are observed in Th with external head cooling of 233 and 404 W/m2, respectively. However, for external head cooling of 233 W/m2, lesser reductions of 0.03°C and 0.06°C are found in Tc and Tblood, respectively. Computational results for external head cooling of 404 W/m2 show a difference of 15 per cent in Th compared to experimental values from literature.

Originality/value
The development of stress because of heat generated within human body is major concern for athletes exercising at high intensities. This study provides an insight into the effectiveness of external head cooling in regulating the head and body temperatures during exercise conditions.