bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward deterministic and semiautomated SPADE analysis
Authors: Qiu Peng 
Published: February 2017

AbstractSPADE stands for spanning‐tree progression analysis for density‐normalized events. It combines downsampling, clustering and a minimum‐spanning tree to provide an intuitive visualization of high‐dimensional single‐cell data, which assists with the interpretation of the cellular heterogeneity underlying the data. SPADE has been widely used for analysis of high‐content flow cytometry data and CyTOF data. The downsampling and clustering components of SPADE are both stochastic, which lead to stochasticity in the tree visualization it generates. Running SPADE twice on the same data may generate two different tree structures. Although they typically lead to the same biological interpretation of subpopulations present in the data, robustness of the algorithm can be improved. Another avenue of improvement is the interpretation of the SPADE tree, which involves visual inspection of multiple colored versions of the tree based on expression of measured markers. This is essentially manual gating on the SPADE tree and can benefit from automated algorithms. This article presents improvements of SPADE in both aspects above, leading to a deterministic SPADE algorithm and a software implementation for semiautomated interpretation. © 2017 International Society for Advancement of Cytometry
Temperature rise may explain grass depletion in the Chihuahuan Desert
Authors: Kidron Giora J. , Gutschick Vincent P. 
Published: February 2017

AbstractA consistent encroachment of shrubs into the northern Chihuahuan Desert (NM, USA) has been well documented since the mid‐1800s. This phenomenon is mainly attributed to overgrazing followed by nutrient depletion, which impedes successful grass establishment. Significantly, higher grass cover that were measured by us during 1998 and 2005 in plots at the Sevilleta National Wildlife Refuge, SEV (60.5–62%), than in plots at the Jornada Experimental Range, JER (4.7–4.9%), lead us to hypothesize that climatological factors that may affect soil moisture may account for the differences in grass cover in both sites. We carried out a 10‐year analysis (1994–2004) of rain, temperature, wind speed, relative humidity, and potential evaporation at the 2 sites. Total summer rainstorm duration in JER was shorter (43 hr in comparison to 46 hr in SEV), and the temperature in JER was higher (by ~3 °C), relative humidity lower (by 3–6%) and vapor pressure deficit higher (by 0.5–0.6 kPa) in comparison to SEV. In addition, during the summer growing period, hourly wind speed was by 18.0% higher and monthly pan A evaporation was by 9.1% higher in JER, pointing out that time duration during which the soil remains wet during the summer is apparently much shorter in JER. Our results indicate that surface wetness in JER following rainstorms is apparently below the necessary threshold needed for successful grass establishment in JER. This in turn has broad consequences on the ecosystem hydrology, structure, and function.
Comparative effectiveness of transitional care services in patients discharged from the hospital with heart failure: a systematic review and network meta‐analysis
Authors: Van Spall Harriette G.C. , Rahman Tahseen , Mytton Oliver , Ramasundarahettige Chinthanie , Ibrahim Quazi , Kabali Conrad , Coppens Michiel , Brian Haynes R. , Connolly Stuart 
Published: February 2017

AbstractAimsTo compare the effectiveness of transitional care services in decreasing all‐cause death and all‐cause readmissions following hospitalization for heart failure (HF).Methods and resultsWe searched PubMed, Embase, CINAHL, and Cochrane Clinical Trials Register for randomized controlled trials (RCTs) published in 2000–2015 that tested the efficacy of transitional care services in patients hospitalized for HF, provided ≥1 month of follow‐up, and reported all‐cause mortality or all‐cause readmissions. Our network meta‐analysis included 53 RCTs (12 356 patients). Among services that significantly decreased all‐cause mortality compared with usual care, nurse home visits were most effective [ranking P‐score 0.6794; relative risk (RR) 0.78, 95% confidence intervals (CI) 0.62–0.98], followed by disease management clinics (DMCs) (ranking P‐score 0.6368; RR 0.80, 95% CI 0.67–0.97). Among services that significantly decreased all‐cause readmission, nurse home visits were most effective [ranking P‐score 0.8365; incident rate ratio (IRR) 0.65, 95% CI 0.49–0.86], followed by nurse case management (NCM) (ranking P‐score 0.6168; IRR 0.77, 95% CI 0.63–0.95), and DMCs (ranking P‐score 0.5691; IRR 0.80, 95% CI 0.66–0.97). There was no significant difference in the comparative effectiveness of services that improved each outcome. Nurse home visits had the greatest pooled cost‐savings (3810 USD, 95% CI 3682–3937), followed by NCM (3435 USD, 95% CI 3224–3645), and DMCs (245 USD, 95% CI −70 to 559). Telephone, telemonitoring, pharmacist, and education interventions did not significantly improve clinical outcomes.ConclusionNurse home visits and DMCs decrease all‐cause mortality after hospitalization for HF. Along with NCM, they also reduce all‐cause readmissions, with no significant difference in comparative effectiveness. These services reduce healthcare system costs to varying degrees.
Sediment transport in high‐speed flows over a fixed bed: 1. Particle dynamics
Authors: Auel Christian , Albayrak Ismail , Sumi Tetsuya , Boes Robert M. 
Published: February 2017

AbstractParticle dynamics are investigated experimentally in supercritical high‐speed open channel flow over a fixed planar bed of low relative roughness height simulating flows in high‐gradient non‐alluvial mountain streams and hydraulic structures. Non‐dimensional equations were developed for transport mode, particle velocity, hop length and hop height accounting for a wide range of literature data encompassing sub‐ and supercritical flow conditions as well as planar and alluvial bed configurations. Particles were dominantly transported in saltation and particle trajectories on planar beds were rather flat and long compared with alluvial bed data due to (1) increased lift forces by spinning motion, (2) strongly downward directed secondary currents, and (3) a planar flume bed where variation in particle reflection and damping effects were minor. The analysis of particle saltation trajectories revealed that the rising and falling limbs were almost symmetrical contradicting alluvial bed data. Furthermore, no or negligible effect of particle size and shape on particle dynamics were found. Implications of experimental findings for mechanistic saltation‐abrasion models are briefly discussed. Copyright © 2017 John Wiley & Sons, Ltd.
Sediment transport in high‐speed flows over a fixed bed: 2. Particle impacts and abrasion prediction
Authors: Auel Christian , Albayrak Ismail , Sumi Tetsuya , Boes Robert M. 
Published: February 2017

AbstractSingle bed load particle impacts were experimentally investigated in supercritical open channel flow over a fixed planar bed of low relative roughness height simulating high‐gradient non‐alluvial mountain streams as well as hydraulic structures. Particle impact characteristics (impact velocity, impact angle, Stokes number, restitution and dynamic friction coefficients) were determined for a wide range of hydraulic parameters and particle properties. Particle impact velocity scaled with the particle velocity, and the vertical particle impact velocity increased with excess transport stage. Particle impact and rebound angles were low and decreased with transport stage. Analysis of the particle impacts with the bed revealed almost no viscous damping effects with high normal restitution coefficients exceeding unity. The normal and resultant Stokes numbers were high and above critical thresholds for viscous damping. These results are attributed to the coherent turbulent structures near the wall region, i.e. bursting motion with ejection and sweep events responsible for turbulence generation and particle transport. The tangential restitution coefficients were slightly below unity and the dynamic friction coefficients were lower than for alluvial bed data, revealing that only a small amount of horizontal energy was transferred to the bed. The abrasion prediction model formed by Sklar and Dietrich in 2004 was revised based on the new equations on vertical impact velocity and hop length covering various bed configurations. The abrasion coefficient kv was found to be vary around kv ~ 105 for hard materials (tensile strength ft > 1 MPa), one order of magnitude lower than the value assumed so far for Sklar and Dietrich's model. Copyright © 2017 John Wiley & Sons, Ltd.
Reflections on bird and mammal risk assessment for plant protection products in the European Union: Past, present, and future
Authors: Brooks Amy C. , Fryer Mike , Lawrence Alan , Pascual Juan , Sharp Rachel 
Published: February 2017

Abstract

The use of plant protection products on agricultural crops can result in exposure of birds and mammals to toxic chemicals. In the European Union, the risks from such exposures are assessed under the current (2009) guidance document from the European Food Safety Authority (EFSA), designed to increase the realism of the theoretical risk assessments in comparison to its predecessor (SANCO/4145/2000). Since its adoption over 7 yr ago, many plant protection products have been evaluated successfully using the 2009 EFSA guidance document. However, there are still significant areas of improvement recommended for future revisions of this guidance. The present Focus article discusses experiences to date with the current scheme, including levels of conservatism in input parameters and interpretation by regulatory authorities together with proposals for how the guidance document could be improved when it is revised in the not too distant future. Several areas for which further guidance is recommended have been identified, such as the derivation of ecologically relevant bird and mammal reproductive endpoints and the use of modeling approaches to contextualize risk assessments. Areas where existing databases could be improved were also highlighted, including the collation of relevant focal species across Europe and expansion of the residue database for food items. To produce a realistic and useable guidance document in the future, it is strongly recommended that there is open and constructive communication between industry, regulatory authorities, and the EFSA. Such collaboration would also encourage harmonization between member states, thus reducing workloads for both industry and regulatory authorities. Environ Toxicol Chem 2017;36:565–575. © 2017 SETAC
Promotion of invasion by mutant RAS is dependent on activation of the WASF3 metastasis promoter gene
Authors: Teng Yong , Ngoka Lambert , Cowell John K 
Published: February 2017

AbstractMetastasis represents an end stage in the evolution of cancer progression and has been related to specific genetic pathways. Overexpression of mutant RAS in particular appears to promote invasion and metastasis, although exactly how this occurs has not been well characterized. It was previously showed that activation of the WASF3 protein regulates actin cytoskeleton dynamics that promote invasion. In this report, how WASF3 overexpression interacts with mutant RAS to increase invasion and metastasis was investigated. The ability of RAS to promote invasion and metastasis was shown to be dependent on WASF3 activation in a PI3K and AKT dependent manner. Proteomics analysis demonstrates the presence of AKT in the WASF3 immunocomplex which is enhanced by overexpression of mutant RAS. During these processes activation of ERK1/2 is not affected by loss of WASF3 expression. Analysis of the relative involvement of p85 and p110 in the WASF3 complex demonstrates that mutant RAS promotes dissociation of p85 promoting activation of p110. These studies provide a deeper understanding of the critical role for WASF3 in facilitating increased invasion potential in cancer cells expressing mutant RAS and supports the idea that targeting WASF3 in metastatic cells overexpressing RAS may be used to suppress invasion and metastasis.
ETV transcriptional upregulation is more reliable than RNA sequencing algorithms and FISH in diagnosing round cell sarcomas with CIC gene rearrangements
Authors: Kao Yu‐Chien , Sung Yun‐Shao , Chen Chun‐Liang , Zhang Lei , Dickson Brendan C , Swanson David , Vaiyapuri Sumathi , Latif Farida , Alholle Abdullah , Huang Shih‐Chiang , Hornick Jason L. , Antonescu Cristina R 
Published: February 2017

AbstractCIC rearrangements have been reported in two‐thirds of EWSR1‐negative small blue round cell tumors (SBRCTs). However, a number of SBRCTs remain unclassified despite exhaustive analysis. Fourteen SBRCTs lacking driver genetic events by RNA sequencing (RNAseq) analysis were collected. Unsupervised hierarchical clustering was performed using samples from our RNAseq database, including 13 SBRCTs with non‐CIC genetic abnormalities and 2 CIC‐rearranged angiosarcomas among others. Remarkably, all 14 study cases showed high mRNA levels of ETV1/4/5, and by unsupervised clustering most grouped into a distinct cluster, separate from other tumors. Based on these results indicating a close relationship with CIC‐rearranged tumors, we manually inspected CIC reads in RNAseq data. FISH for CIC and DUX4 abnormalities and immunohistochemical stains for ETV4 were also performed. In the control group, only 2 CIC‐rearranged angiosarcomas had high ETV1/4/5 expression. Upon manual inspection of CIC traces, 7 of 14 cases showed CIC‐DUX4 fusion reads, 2 cases had DUX4‐CIC reads, while the remaining 5 were negative. FISH showed CIC break‐apart in 7 cases, including 5 cases lacking CIC‐DUX4 or DUX4‐CIC fusion reads on RNAseq manual inspection. However, no CIC abnormalities were detected by FISH in 6 cases with CIC‐DUX4 or DUX4‐CIC reads. ETV4 immunoreactivity was positive in 7 of 11 cases. Our results highlight the underperformance of FISH and RNAseq methods in diagnosing SBRCTs with CIC gene abnormalities. The downstream ETV1/4/5 transcriptional up‐regulation appears highly sensitive and specific and can be used as a reliable molecular signature and diagnostic method for CIC fusion positive SBRCTs.
Parental health and children's cognitive and noncognitive development: New evidence from the longitudinal survey of Australian children
Authors: Le Huong Thu , Nguyen Ha Trong 
Published: February 2017

SummaryThis paper examines the effects of parental health on cognitive and noncognitive development in Australian children. The underlying nationally representative panel data and a child fixed effects estimator are used to deal with unobserved heterogeneity. We find that only father's serious mental illness worsens selected cognitive and noncognitive skills of children. Maternal poor health also deteriorates some cognitive and noncognitive outcomes of children of lone mothers only. Our results demonstrate that either failing to account for parent–child fixed effects or using child noncognitive skills reported by parents could overestimate the harmful impact of poor parental health on child development.
Association of tumor necrosis factor‐α ‐308 G/A gene polymorphism with coronary artery diseases: An evidence‐based study
Authors: Kazemi Elaheh , Jamialahmadi Khadijeh , Avan Amir , Mirhafez Seyed Reza , Mohiti Javad , Pirhoushiaran Maryam , Hosseini Nedasadat , Mohammadi Akram , Ferns Gordon A. , Pasdar Alireza , Ghayour‐Mobarhan Majid 
Published: February 2017

BackgroundCoronary artery disease (CAD) is the leading cause of death worldwide and remains a major health problem, providing the rationale for identification of molecular markers for detection of individuals at high risk of developing CAD. Tumor necrosis factor‐α (TNF‐α) plays a crucial role in the pathogenesis of CAD. We have therefore explored the association of TNF‐α 308 (G/A) gene polymorphism in 903 individuals with/without CAD.MethodsTNF‐α 308 gene polymorphism was analyzed in 903 subjects of whom 222 were healthy controls. Among the 681 patients who were investigated angiographically, 468 had ≧50% stenosis and 213 patients had <50% stenosis. Biochemical profiles (eg, triglycerides, high‐density lipoprotein cholesterol, low‐density lipoprotein cholesterol, fasting blood glucose, and CRP) were evaluated. Associations between TNF‐α genotypes with biochemical and anthropometric characteristics were determined.ResultsThe frequencies of TNF‐α‐AA or AG genotypes were significantly lower in patients classified as CAD patients with ≥ or <50% obstruction in at least one coronary artery, compared to the control group. We observed that CAD patients with ≥50% stenosis and with AA genotype were associated with higher risk of CAD with OR of 3.56 (95%CI: 1.02‐12.41; P=.046) using multivariate analysis. Moreover, we found that TNF‐α‐308‐AA genotype was associated with blood pressure and CRP level in CAD patients, compared to the wild type‐genotype.ConclusionOur data showed an association of TNF‐α‐308G/A polymorphism with CAD patients with ≥50% obstruction, supporting the need for further investigations on the role of TNF‐α‐308G/A polymorphism with hypertension.
Inhibitory effect of 2,4‐dichlorophenoxyacetic acid on ROS, autophagy formation, and mRNA replication for influenza virus infection
Authors: Enkhtaivan Gansukh , Muthuraman Pandurangan , Kim Doo Hwan 
Published: February 2017

AbstractInfluenza virus has had a high rate of antigenic shift and drift that causes significant morbidity and mortality in humans and animals. The lack of excellent pharmacological treatment underlines the importance of the development of the novel antiviral drugs. We investigated the anti‐influenza A and B viruses of 2,4‐dichlorophenoxyacetic acid (2,4‐D), which is the synthetic analog to auxin and is used as a popular herbicide in the agricultural practices. 2,4‐D was evaluated using a cytopathic effect reduction method; assay results showed that 2,4‐D possessed strong anti‐influenza A and B viruses inhibiting the formation of a visible cytopathic effect. Influenza viral RNA expression was performed by quantitative real‐time polymerase chain reaction. 2,4‐D also inhibited virus replication in the early stage of influenza virus infection without direct interaction with virus particles. Additionally, 2,4‐D significantly inhibited various factors occur during influenza virus infection as the acidic vesicular formation and reactive oxygen species production. Moreover, 2,4‐D represented no cytotoxicity in normal kidney cell. Therefore, these findings provide an understanding of the mechanism and efficient use of 2,4‐D in pharmacological applications against influenza virus infection.
Identification of the compositional changes in Orthosiphon stamineus leaves triggered by different drying techniques using 1H NMR metabolomics
Authors: Pariyani Raghunath , Ismail Intan Safinar , Ahmad Azam Amalina , Abas Faridah , Shaari Khozirah 
Published: February 2017

AbstractBACKGROUNDJava tea is a well‐known herbal infusion prepared from the leaves of Orthosiphon stamineus (OS). The biological properties of tea are in direct correlation with the primary and secondary metabolite composition, which in turn largely depends on the choice of drying method. Herein, the impact of three commonly used drying methods, i.e. shade, microwave and freeze drying, on the metabolite composition and antioxidant activity of OS leaves was investigated using proton nuclear magnetic resonance (1H NMR) spectroscopy combined with multivariate classification and regression analysis tools.RESULTSA total of 31 constituents comprising primary and secondary metabolites belonging to the chemical classes of fatty acids, amino acids, sugars, terpenoids and phenolic compounds were identified. Shade‐dried leaves were identified to possess the highest concentrations of bioactive secondary metabolites such as chlorogenic acid, caffeic acid, luteolin, orthosiphol and apigenin, followed by microwave‐dried samples. Freeze‐dried leaves had higher concentrations of choline, amino acids leucine, alanine and glutamine and sugars such as fructose and α‐glucose, but contained the lowest levels of secondary metabolites.CONCLUSIONMetabolite profiling coupled with multivariate analysis identified shade drying as the best method to prepare OS leaves as Java tea or to include in traditional medicine preparation. © 2017 Society of Chemical Industry
Quality and readability assessment of websites related to recurrent respiratory papillomatosis
Authors: San Giorgi Michel R.M. , de Groot Olivier S.D. , Dikkers Frederik G. 
Published: February 2017

ObjectiveRecurrent respiratory papillomatosis (RRP) is a rare disease for which a limited number of information sources for patients exist. The role of the Internet in the patient–physician relationship is increasing. More and more patients search for online health information, which should be of good quality and easy readable. The study aim was to investigate the quality and readability of English online health information about RRP.Study DesignQuality and readability assessment of online information.MethodsRelevant information was collected using three different search engines and seven different search terms. Quality was assessed with the DISCERN instrument. The Flesch Reading Ease Score (FRES) and average grade level (AGL) were determined to measure readability of the English websites.ResultsFifty‐one English websites were included. The mean DISCERN score of the websites is 28.1 ± 9.7 (poor quality); the mean FRES is 41.3 ± 14.9 (difficult to read); and the mean AGL is 12.6 ± 2.3.ConclusionThe quality and readability of English websites about RRP is alarmingly poor.Level of EvidenceNA. Laryngoscope, 127:2293–2297, 2017
Root Characteristics of Herbaceous Species for Topsoil Stabilization in Restoration Projects
Authors: Federica Gilardelli , Chiara Vergani , Rodolfo Gentili , Anne Bonis , Pierre Chanteloup , Sandra Citterio , Chiaradia Enrico A. 
Published: February 2017

AbstractQuarries are highly heterogeneous and constraining environments because of man‐induced disturbances associated with soil erosion and shallow mass movements. Recognizing the importance of plant root systems to overcome stability problems, we investigated the contributions of three different herbaceous species typical of calcareous grasslands, that is, Anthyllis vulneraria, Bromus erectus and Stachys recta, to the stability of the superficial layers of dump deposits at limestone quarries in the Botticino extractive basin (Lombardy, Italy). We analysed (i) the root mechanical properties and root diameter distributions of the selected species and estimated (ii) the lateral root reinforcement they can provide through the fibre bundle model. To assess the effective contribution of a species to the topsoil stabilization, we implemented the results obtained in a stability model based on the ordinary method of slices. Our results showed that using species such as B. erectus and S. recta with a density of 100 plants per square metre guarantees a better stability of the superficial layers. Copyright © 2017 John Wiley & Sons, Ltd.