Miracle-dz/UniFAR-FTUs huggingface dataset:
Contrasting beta diversity among regions: how do classical and multivariate approaches compare?

Aim: Approaches to calculating beta diversity (β) include classical measures based on alpha (α) and gamma (γ) diversity, and multivariate distance-based measures. Species-area relationships cause measurements of γ to vary, making comparisons of classical β among regions contingent on sampling effort. A recent null-modelling approach has attempted to account for variation in γ by calculating the degree to which β deviates from a random expectation. Here, we clarify the mathematical links between classical and multivariate approaches to measuring β, to derive predictions regarding the reliability of classical, null-model and multivariate approaches. Next, we use four ecological datasets and simulated data to test the consistency of these approaches across sampling effort and γ. We focus on an issue that arises when making comparisons among regions, namely that even small changes to the area sampled can differentially increase measured γ in each region, potentially causing artefacts in β that are driven by methodology rather than biology. Innovation: Comparisons among regions using classical and null-model measures change dramatically as sampling effort and γ increase. This change is understood for classical β because of species-area relationships, but not for null-model measures, making comparisons among regions impossible using the null-model approach. Multiple-site dissimilarity shows a similar sensitivity to γ as classical measures. In contrast, pairwise multivariate distances show no systematic effect of sampling effort and γ: increasing the number of sample plots decreases variability but does not alter mean β. Main conclusions: Multivariate pairwise distances are independent of sample size, offering the most robust comparison among regions. The widespread influence of sampling effort and γ indicate that only scale-dependent measures of classical and multiple-site β are comparable, whereas null-model β may not be comparable among regions. However, in cases where γ is well known, multiple-site dissimilarity metrics offer several advantages, and should be strongly considered.
Work Package 4 Methodological guidance , recommendations and illustrative case studies for ( network ) meta-analysis and modelling to predict real-world effectiveness using individual participant and / or aggregate data

Noemi Hummela, Thomas P. A. Debrayb,c, Eva-Maria Diddena, Orestis Efthimioua, Matthias Eggera,d, Christine Fletchere, Karel G. M. Moonsb,c, Hans J. B. Reitsmab,c, Yann Ruffieuxa, Georgia Salantia,d, Gert van Valkenhoeff on behalf of WP4 a Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland b Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands c Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
The Effects of the Timing of Commercial Breaks by the Measurement of Brain Activity using fNIRS and Autonomic Nervous Activity

Recently commercial breaks are often inserted just before the climax of stories in TV programs in Japan. One article reports that commercials inserted just before the climax will dissatisfy the audience and discourage their concentration. In this research, we study the effects of the timing of commercial breaks by the measurement of brain activity and autonomic nervous activity. As a result, it is suggested that the involuntary disengagement of attention is caused the abrupt onset of the commercial break just before the climax giving audiences an unpleasant feeling. Furthermore, the results show the possibility that presenting the climax of the story just before the onset of the commercial break increases the working memory load of watching the commercial break after the climax.
Purification of Haemophilus parasuis Neuraminidase , Candidate Subunit Vaccine

While new swine production technologies are making inroads into controlling many swine pathogens, Haemophilus parasuis-induced disease has unexpectedly emerged as an increasing problem (Nicolet, 1992; Boeckman, 1995; Radle, 1996; Zimmerman et al., 1997; Rapp-Gabrielson, 1999; Dee, 2000). Innovative new strategies of disease control are needed to meet the challenges associated with new production technologies for high health herds, including segregated early weaning and all-in all-out pig flow in production facilities.
The toxicity effect of cerium oxide nanoparticles on ALT, AST and ALP enzymes in male Rat

Like nanoorganisms (viruses), nanoparticles are able to enter cells and interact with cellular structures. Human exposure to toxic nanoparticles can be reduced through identifying creation-exposure pathways of toxins. In this work, we investigated the toxicity effect of cerium oxide nanoparticles on ALT, ALP and AST enzymes of male Rat. The cerium oxide nanoparticles synthesized and morphological properties of it such as UV-Vis spectrum characterization and transmission electron microscopy (TEM) were investigated. The enzymology studies were performed on 40 male rats that divided into five octet groups. The results showed that with increasing concentration of nanoparticles also increased levels of these three enzymes. And found linear equation between concentration of nanoparticles and levels of these three enzymes.
Characterization of the “a” determinant region of the hepatitis B virus genome in Iranian patients at different clinical phases of chronic infection

Aim: To determine the distribution of important mutations of the “a” determinant region in the HBV genome among patients in different clinical phases of HBV infection. Background: Variations in Hepatitis B infection not only change the outcome of the disease but also the symptoms from which the chronic HBV patients are suffering. Methods: We have meticulously selected a total of 40 chronic HBV patients from four different subclasses of chronic HBV clinical phases including immune tolerant (IT), immune active (IA), inactive carrier (IC) and hepatitis B e antigen (HBeAg)-negative (ENEG); 10 samples per each phase. Mutations of the “a” determinant region were identified using PCR-Direct sequencing method. Results: 17 amino-acid substitutions at 12 positions inside the “a” determinant were identified in all forty samples; 3 mutations in the IT group, 6 mutations in the IA phase, 3 mutations in the IC patients and 5 mutations in the ENEG phase. Different substitutions were observed in all four clinical phases. The IA phase was the most variant group with the highest number of amino-acid substitutions. Conclusion: These results did not reveal a strong pattern to distinguish different clinical phases of Chronic HBV infection, but there are some obvious differences regarding the number and position of mutations between these four clinical phases.
Acute Effects of Sugar-Sweetened Beverage Consumption on Hemodynamics and Reactive Hyperemia in Young, Healthy Humans

Background: Previously, the consumption of sugar-sweetened beverages (SSBs) has been associated with the onset of cardiovascular disease. In addition, reactive hyperemia (RH), a measure of microvascular function, has been associated with cardiovascular disease risk. Purpose: Therefore, the purpose of this study was to test the hypothesis that consumption of a SSB would acutely mitigate microvascular responses. Methods: Thirteen subjects consumed 24 fluid ounces of water or SSB (68g mixture of fructose and dextrose). Prior to, immediately after, and 1-hr post beverage consumption, venous occlusion plethysmography was used to measure the forearm blood flow (FBF) during baseline and post-ischemia (5 min) RH conditions. Whole blood [glucose] was determined via finger-stick samples with rapid glucometry. Heart rate and blood pressure were monitored throughout the experiment. Results : Despite significant elevations in blood glucose levels, there was no significant change in forearm blood flow at rest or during reactive hyperemia in any of the conditions (p=0.823). Slight elevations in heart rate and mean arterial pressure were observed immediately following consumption of SSB. Conclusions: The present findings indicated that young, healthy humans maintained microvascular function following acute consumption of a SSB. Future studies should address whether the ability to maintain microvascular function following acute SSB consumption persists in at-risk populations as well as whether chronic SSB consumption can attenuate RH responses. Journal of Nature and Science (JNSCI), 4(2):e486, 2018
Induced immune response of Escherichia coli BL21 expressing recombinant MSP1a and MSP1b proteins of Anaplasma marginale

This work aims to evaluate the potential of immunization with E. coli BL21 expressing the recombinant rMSP1a and rMSP1b proteins of Anaplasma marginale. E. coli BL21 was transformed with recombinant plasmids pET102/msp1α and pET101/msp1β, and rMSP1a and rMSP1b were expressed after induction by IPTG. BALB/c mice were vaccinated with formolized BL21/rMSP1a and BL21/rMSP1b, and the production in mice sera of whole IgG was determined by ELISA. The mice immunized with BL21/rMSP1a showed a better humoral response for whole IgG when compared to the mice immunized with BL21/rMSP1b; these mice exhibited a small response after the second vaccination. Sera of mice immunized with BL21/rMSP1a reacted via western blot with BL21 and rMSP1a, with molecular masses varying from 70 to 105 kDa. Sera of mice immunized with BL21/rMSP1b reacted with BL21 and rMSP1b with a molecular mass of 100 kDa. These results demonstrate that BL21 containing rMSP1a and rMSP1b in the outer membrane were able to produce an immune response in mice, reinforcing its use in vaccine models against bovine anaplasmosis.
Melatonin induces mechanisms of brain resilience against neurodegeneration

Melatonin is an endogenous pleiotropic molecule which orchestrates regulatory functions and protective capacity against age‐related ailments. The increase in circulating levels of melatonin through dietary supplements intensifies its health benefits. Investigations in animal models have shown that melatonin protects against Alzheimer's disease (AD)‐like pathology, although clinical studies have not been conclusive. We hypothesized that melatonin induces changes in the brain that prevent or attenuate AD by increasing resilience. Therefore, we treated healthy nontransgenic (NoTg) and AD transgenic (3xTg‐AD) 6‐month‐old mice with a daily dose of 10 mg/kg of melatonin until 12 months of age. As expected, melatonin reversed cognitive impairment and dementia‐associated behaviors of anxiety and apathy and reduced amyloid and tau burden in 3xTg‐AD mice. Remarkably, melatonin induced cognitive enhancement and higher wellness level‐related behavior in NoTg mice. At the mechanism level, NF‐κB and proinflammatory cytokine expressions were decreased in both NoTg and 3xTg‐AD mice. The SIRT1 pathway of longevity and neuroprotection was also activated in both mouse strains after melatonin dosing. Furthermore, we explored new mechanisms and pathways not previously associated with melatonin treatment such as the ubiquitin‐proteasome proteolytic system and the recently proposed neuroprotective Gas6/TAM pathway. The upregulation of proteasome activity and the modulation of Gas6 and its receptors by melatonin were similarly displayed by both NoTg and 3xTg‐AD mice. Therefore, these results confirm the potential of melatonin treatment against AD pathology, by way of opening new pathways in its mechanisms of action, and demonstrating that melatonin induces cognitive enhancement and brain resilience against neurodegenerative processes.
Horizontally transferred genes in the ctenophore Mnemiopsis leidyi

Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.
Free Range Kids? Using GPS-Derived Activity Spaces to Examine Children’s Neighborhood Activity and Mobility

This study examines the neighborhood activity spaces (NAS) of 9- to 13-year-old children (n = 143) from seven schools in London, Canada. Data from Global Positioning System (GPS) loggers worn for 7 days were used to isolate and test measures for children’s pedestrian-based neighborhood activity: the maximum distance traveled from home and relative time spent in neighborhood settings. Descriptive and linear regression analyses examined the influence of individual, perceptual, and environmental factors on neighborhood use and travel. Participants spent a large portion of their out-of-school time (75%) in their NAS. Although traveling far from home on occasion, 94.5% of children’s time on average was spent within a short distance of home; participants spent little of their free time in broader neighborhood settings. School travel mode and independent mobility were among the strongest predictors of both distance traveled and time spent close to home. Perceptions of neighborhood safety, neighborhood type, and nearby land uses also influenced local activity.
Interactive Refactoring for GPU Parallelization of Affine Loops

—Considerable recent attention has been given to the problem of porting existing code to heterogeneous computing architectures, such as GPUs. In this paper, we describe a novel, interactive refactoring tool that allows for quick and easy transformation of afﬁne loops to execute on GPUs. Compared to previous approaches, our refactoring approach interactively combines the user’s knowledge with that of an automated parallelizer to produce parallel CUDA GPU code. The generated code retains the structure of the original loop in order to remain maintainable. The refactoring tool also computes and displays proﬁtability metrics, intended to advise the user of the performance potential of the generated code.
Phytochemical Compositions, Antioxidant Properties, and Colon Cancer Antiproliferation Effects of Turkish and Oregon Hazelnut

Roasted and raw Turkish and Oregon hazelnuts were examined. Whole nuts, skins, and skinless nuts of both hazelnut varieties were tested for fat contents, fatty acid profiles. Hazelnut and other byproducts were extracted with 50% ace- tone and examined for total phenolic contents (TPC), antioxidant activities against the peroxyl (ORAC) and DPPH radicals, and were also administered in vitro to the human colon cancer HT-29 cell line to determine antiproliferative effects. The Turkish hazelnuts contained over 65% total oil while the Oregon roasted variety contained 43.8%. The primary fatty acid in both was oleic acid (18:1n-9) comprising 76.7 g/100 g oil in the Oregon variety and 83.3 g/100 g oil in the Turkish variety. The TPC were 91.4 and 102.16 mg gallic acid equivalents/ g sample for the Turkish roasted hazelnut skin and Oregon roasted hazelnut skin respectively, at least 30-folds as high as the hazelnut without skin. Turkish roasted hazelnut skin had the highest ORAC value of 1166.27 Trolox equivalents (TE) mmol/g sample (TE mmol/g), it is 38 times as high as the Oregon roasted hazelnut no skin which as a value of 30.2 TE mmol/g sample. The range of ED50 of DPPH? is from 118.22 to 0.075 mg sample equivalents/ mL among the samples, Oregon roasted hazelnut skin and Turkish raw hazelnut no skin exhibit the weakest and strongest ability to reduce DPPH? respectively. At 6 mg/mL media Oregon roasted hazelnut skin extract significantly inhibited the growth of the HT-29 cells by 96h following 4 days of treatment, and no effect was seen from the Turkish roasted skinned hazelnut extract. The Turkish raw hazelnut had significantly higher antioxidant activities compared to the Oregon roasted variety which may be explained by chemical changes during heating or possibly the total oil to flour ratio.
Evaluation of Artery Sequential Interventional Therapy on Pernicious Placenta Previa

Objective: To evaluate the effect of artery sequential interventional therapy (internal iliac artery catheterization and occlusion/ uterine artery or internal iliac artery embolization) on the hemorrhage of pernicious placenta previa. Method: The total of 29 patients with pernicious placenta previa and risk factor of placenta accreta from March 2012 to June 2013 in our hospital were included as control group, who were given traditional method of treatment, while 40 patients with the same disease status from July 2013 to October 2014 as treatment group with artery sequential interventional therapy. The amount of blood loss during operation and red blood cell suspension transfusion, the rate of hysterectomy cesarean time, the amount of cesarean section hemorrhage after 24 hours, duration of postopera tive hospital stay, the time of postoperative antibiotic usage and the prevalence of complications (pain, fever, infection and others) of patients in two groups were evaluated, respectively. Result: The significant difference of amount of blood loss during operation [(868.5±549.77) ml vs. (1506.90±1417.39) ml for treatment group and control group, respectively)] and red blood cell suspension transfusion [(1.50±1.40) U vs. (2.72±2.00) U], the rate of hysterectomy (2.50% vs. 17.24%), cesarean time [(58.86±20.33) min vs. (70.83±29.26) min)] and the prevalence of pain (81.25% vs. 48.28%) and other complications (0.00% vs. 10.35%) (all p values 0.05). All patients resumed normal menstruation after weaned for 1 to 3 month and the routine newborn physical examination on 42 days after birth, blood analysis, liver function and neurological examination of infants were normal without blood diseases. Conclusion: Artery sequential interventional therapy for patients with pernicious placenta previa was safe, effective and feasible for pregnant and newborn.
Environmental Kuznets curve for CO2 emissions: a literature survey

Purpose The purpose of this paper is to provide a survey of the empirical literature on environmental Kuznets curve (EKC) estimation of carbon dioxide (CO2) emissions over the period of 1991–2017. Design/methodology/approach This survey categorizes the studies on the basis of power of income in empirical models of EKC. It has been hypothesized that the EKC shows an inverted U-shaped association between economic growth and CO2 emissions. Findings For all the contexts, the results of EKC estimation for CO2 emissions are inconclusive in nature. The reasons behind this discrepancy can be attributed to the choice of contexts, time period, explanatory variables, and methodological adaptation. Research limitations/implications The future studies in this context should not only consider new set of variables (e.g. corruption index, social indicators, political scenario, energy research and development expenditures, foreign capital inflows, happiness, population education structure, public investment toward alternate energy exploration, etc.), but also the data set should be refined, so that the EKC estimation issues raised by Stern (2004) can be addressed. Originality/value By far, no study in the literature of ecological economics has focused on the empirical estimation of EKC for CO2 emissions. This particular context has been used for this study, as CO2 is one of the highest studied pollutants in the ecological economics, and especially within the EKC hypothesis framework.
Physically Based Simulation of Potential Effects of Carbon Dioxide–Altered Climates on Groundwater Recharge

Increasing concentrations of atmospheric CO2 will alter regional rainfall and evapotranspiration regimes that drive groundwater recharge. Improved methods of simulation and analysis are needed for assessing the potential sensitivities of soil–water–vegetation systems to climate change. This study demonstrates methods for generating climates and simulating soil–water and vegetation dynamics in response to current and double CO2 climate sequences. Climate change scenarios came from dynamic equilibrium (constant CO2) runs of a general circulation model (GCM). Based on historical climate and GCM output, a stochastic point weather generator produced realizations of the cross‐correlated daily climate variables. A numerical model of infiltration, variably saturated flow, and evapotranspiration produced temporal distributions of groundwater recharge rates for various soil–vegetation environments. Climate change scenarios were simulated for two climatic zones in Australia: subtropical (North Stradbroke Island, Queensland) and Mediterranean (Gnangara, Swan Coastal Plain, Western Australia) having summer‐ and winter‐dominated rainfall regimes, respectively. In these simulations, groundwater recharge values were affected by the dynamic growth and senescence of vegetation, as changes in temperature and rainfall regimes affected growth rates and leaf areas. The temperature regime dominated the hydrologic response in the Mediterranean climate, and the rainfall frequency–duration regime dominated in the subtropical climate. For the simulated Mediterranean climate change (14% rainfall increase), changes in mean recharge values ranged from −34% to +119%, while subtropical climate change (37% rainfall increase) caused increases from 74 to > 500%. Changes in mean recharge rate, interannual variability, and temporal persistence were related to the soil and vegetation characteristics. The model was useful for quantifying complex, nonlinear responses to climate change that require further exploration.
Mapping Process to Pattern in the Landscape Change of the Amazonian Frontier

Abstract Changes in land use and land cover are dynamic processes reflecting a sequence of decisions made by individual land managers. In developing economies, these decisions may be embedded in the evolution of individual households, as is often the case in indigenous areas and agricultural frontiers. One goal of the present article is to address the land-use and land-cover decisions of colonist farmers in the Amazon Basin as a function, in part, of household characteristics. Another goal is to generalize the issue of tropical deforestation into a broader discussion on forest dynamics. The extent of secondary forest in tropical areas has been well documented in South America and Africa. Agricultural-plot abandonment often occurs in tandem with primary forest clearance and as part of the same decision-making calculus. Consequently, tropical deforestation and forest succession are not independent processes in the landscape. This article presents a framework that integrates them into a model of forest dynamics at household level, and in so doing provides an account of the spatial pattern of deforestation that has been observed in the Amazon's colonization frontiers.