bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Fluorescence Spectroscopy to Assess Organic Matters in Activated Persulfate
Authors: Hidayah E N , Cahyonugroho O H 
Published: July 2020

Abstract
Surface water contains organic matters from human activities, discharged industrial wastewater, and generated from microbial activities in water body. Persulfate is one of the strongest oxidants and could be used to oxidize organic matters. Fluorescence excitation emission matrices is one of the qualitative methods to identify organic matters properties, instead of chromatography and ultraviolet visible detection. The objective of this study was to identify dissolved organic matter in source and treated water by using peroxidation activated persulfate followed by coagulation. Sampel was analysed by using fluorescence excitation emission matrices (FEEMs) to assess its properties. The results showed that Activated persulfate has a good performance as pretreatment, in order to oxidize organic matters, further the coagulation is suitable treatment to combine with peroxidation activated persulfate. Those treatment resulted lower fluorescence intensity in all regions, including aromatic protein, fulvic acid-like, soluble microbial products, and humic acid-like.
Resistance of Loading Loads in Surabaya River and Its Branch with Qual2KW Model.
Authors: Hendrasarie N , Swandika I D A 
Published: July 2020

Abstract
Pollution of Surabaya River from year to year is increasing, the increase in pollution is the main problem of Surabaya River which is caused by the entry of most of the liquid waste from industrial, agricultural, and domestic activities. Continuous pollution can reduce water quality for rivers and creeks. One solution that can be applied to reduce the level of pollution is by calculating the capacity of pollution loads. This research was conducted to find out the quality of Kali Surabaya and tributaries of Surabaya River and the calculation of pollution load capacity with the QUAL2KW model. The study analysed the parameters of DO, BOD, COD, and phosphate. From the results of the study, the water quality values for Surabaya river and its branch were above the Class I quality standard Government Regulation Number 82 of 2010 and from the calculation results obtained the maximum capacity values BOD load were 23-1355 kg/day, and COD load were 23-6830 kg/days, while phosphate load were 2,5-125 kg/day.
Application of remotely sensed data and maximum entropy model in detecting potential fishing zones of Yellowfin tuna (Thunnus albacares) in the eastern Indian Ocean off Sumatera
Authors: Syah Achmad Fachruddin , Yanti Siregar Emma Suri , Siregar Vincetius P , Agus Syamsul B 
Published: July 2020

Abstract
Yellowfin tuna (Thunnus obesus) is one of the most important and most caught fish in the eastern Indian Ocean off west Sumatera and has extensive migration. To develop an appropriate prediction model and to understand the contribution of oceanographic parameters in the potential habitat of Yellowfin tuna, remotely sensed data and habitat modeling were used. Daily data of sea-surface temperature (SST), sea-surface salinity (SSS) and sea-surface height (SSH) were downloaded from the marine copernicus website, meanwhile fishing vessel position for Yellowfin tuna were obtained from fishing port Samudera, Bungus, west Sumatera, from January through December 2015. Daily fishing vessel position and environmental parameters were used for maximum entropy model construction. The model predictive performance was then evaluated using a threshold-independent metric, the area under the curve (AUC) metric of the receiver operating characteristic (ROC). Maximum entropy model results (AUC > 0.90) indicated its potential to figure out the spatial distribution of Yellowfin tuna. In general, SST (50.5%) is the most affective variable in the Yellowfin tuna distribution, followed by SSS (37%) and SSH (12.5%). This study showed that integration multi remotely sensed data and a modeling approach provide an innovative way to decide the potential fishing zones of the Yellowfin tuna in the eastern Indian Ocean off west Sumatera.
Effect of using chemsketch on teaching molecular shape of hydrocarbon to increase student’s achievement
Authors: Marpaung D N , Siregar L F , Pongkendek J J 
Published: July 2020

Abstract
This research aim to know the effectiveness of using chemsketch on the teaching molecular shape of hydrocarbon to increase student achievement. Hydrocarbon is very interesting to be discussed. Technology utilized need to solve this problem which is by using chemsketch. Chemsketch implemented by powerpoint. Research conducted in SMAN 5 Medan sample that used consists of two classes, that consist of experiment class and control class. The average pretest score in control is 33.33 and posttest score is 73.03. Percentage of passed students post-test is 69.70% from 33 students only 23students. While experiment class average pretest score is 32.12 and posttest score is 81.21. Percentage of passed students post-test is 85.71%, from 35 students only 30 students. The gain percentage between the post-test score in the experiment and the control class is 16.01%. The result showed that chemsketch with PowerPoint effective to increase student’s achievement in hydrocarbon and suitable following industrial revolution 4.0 to prepare student face globalization era education.
PyRice: a Python package for querying Oryza sativa databases
Authors: Do Quan , Bich Hai Ho , Larmande Pierre 
Published: July 2020

Abstract

Summary
Currently, gene information available for Oryza sativa species is located in various online heterogeneous data sources. Moreover, methods of access are also diverse, mostly web-based and sometimes query APIs, which might not always be straightforward for domain experts. The challenge is to collect information quickly from these applications and combine it logically, to facilitate scientific research. We developed a Python package named PyRice, a unified programing API to access all supported databases at the same time with consistent output. PyRice design is modular and implements a smart query system, which fits the computing resources to optimize the query speed. As a result, PyRice is easy to use and produces intuitive results.

Availability and implementation
https://github.com/SouthGreenPlatform/PyRice.

Supplementary information
Supplementary data are available at Bioinformatics online.
Global, regional, and national prevalence, incidence, mortality, and risk factors for atrial fibrillation, 1990–2017: results from the Global Burden of Disease Study 2017
Authors: Dai Haijiang , Zhang Quanyu , Much Arsalan Abu , Maor Elad , Segev Amit , Beinart Roy , Adawi Salim , Lu Yao , Bragazzi Nicola Luigi , Wu Jianhong 
Published: July 2020

Abstract

Aims
To estimate the prevalence, incidence, mortality, and risk factors for atrial fibrillation (AF) in 195 countries and territories from 1990 to 2017.

Methods and results
Following the methodologies used in the Global Burden of Disease Study 2017, the prevalence, incidence, and mortality of AF were analysed by age, sex, year, socio-demographic index (SDI), and location. The percentage contributions of major risk factors to age-standardized AF deaths were measured by population attributable fractions. In 2017, there were 37.57 million [95% uncertainty interval (UI) 32.55–42.59] prevalent cases and 3.05 million (95% UI 2.61–3.51) incident cases of AF globally, contributing to 287 241 (95% UI 276 355–304 759) deaths. The age-standardized rates of prevalent cases, incident cases, and deaths of AF in 2017 and their temporal trends from 1990 to 2017 varied significantly by SDI quintile and location. High systolic blood pressure was the leading risk factor for AF age-standardized deaths [34.3% (95% UI 27.4–41.5)] in 2017, followed by high body mass index [20.7% (95% UI 11.5–32.2)] and alcohol use [9.4% (95% UI 7.0–12.2)].

Conclusion
Our study has systematically and globally assessed the temporal trends of AF, which remains a major public heath challenge. Although AF mainly occurred in developed countries, the unfavourable trend in countries with lower SDI also deserves particular attention. More effective prevention and treatment strategies aimed at counteracting the increase in AF burden should be established in some countries.
Adoption of outgroup norms provides evidence for social transmission in perinatal care practices among rural Namibian women
Authors: Hagen Renée V , Scelza Brooke A 
Published: July 2020

Abstract

Background and objectives
How do new ideas spread in social groups? We apply the framework of cultural evolution theory to examine what drives change in perinatal care norms among Himba women in the Kunene region of Namibia. Access to formal medical care is on the rise in this region, and medical workers regularly visit communities to promote WHO-recommended perinatal care practices. This study investigates how various forms of social transmission affect women’s uptake of medical recommendations concerning perinatal care.

Methodology
Based on interviews with one hundred Himba mothers, we used Bayesian multi-level logistical regression models to examine how perceptions of group preferences, prestige ascribed to outgroup conformers, interaction with the outgroup and access to resources affect norm adoption.

Results
Women who perceive medical recommendations as common in their group prefer, plan and practice these recommendations more often themselves. We observed a shift toward medical recommendations regarding birth location and contraception use that was in line with conformity bias predictions. Practices that serve as cultural identity markers persist in the population.

Conclusions and implications
Norm changes, and the cultural evolutionary processes that can lead to them, are not uniform, either in process or pace. Empirical studies like this one provide important examples of how these changes reflect local culture and circumstance and are critical for better understanding the models that currently predominate in cultural evolution work. These cases can also help bridge the gap between evolutionary anthropology and public health by demonstrating where promotion and prevention campaigns might be most effective.

Lay Summary
The recent promotion of WHO-recommended perinatal care practices in Namibia provides an opportunity to empirically study norm change using a cultural evolution framework. We found women adopt medical recommendations when they believe these are common in their social group. Local norms that were not discouraged persisted in the study group.
A glimpse of potential transposable element impact on adaptation of the industrial yeast Saccharomyces cerevisiae
Authors: Liu Z Lewis , Huang Xiaoqiu 
Published: July 2020

ABSTRACT
The adapted industrial yeast strain Saccharomyces cerevisiae NRRL Y-50049 is able to in situ detoxify major toxic aldehyde compounds derived from sugar conversion of lignocellulosic biomass while producing ethanol. Pathway-based studies on its mechanisms of tolerance have been reported previously, however, little is known about transposable element (TE) involvement in its adaptation to inhibitory compounds. This work presents a comparative dynamic transcription expression analysis in response to a toxic treatment between Y-50049 and its progenitor, an industrial type strain NRRL Y-12632, using a time-course study. At least 77 TEs from Y-50049 showed significantly increased expression compared with its progenitor, especially during the late lag phase. Sequence analysis revealed significant differences in TE sequences between the two strains. Y-50049 was also found to have a transposons of yeast 2 (Ty2) long terminal repeat-linked YAT1 gene showing significantly higher copy number changes than its progenitor. These results raise awareness of potential TE involvement in the adaptation of industrial yeast to the tolerance of toxic chemicals.
PhaseME: Automatic rapid assessment of phasing quality and phasing improvement
Authors: Majidian Sina , Sedlazeck Fritz J 
Published: July 2020

Abstract

Background
The detection of which mutations are occurring on the same DNA molecule is essential to predict their consequences. This can be achieved by phasing the genomic variations. Nevertheless, state-of-the-art haplotype phasing is currently a black box in which the accuracy and quality of the reconstructed haplotypes are hard to assess.

Findings
Here we present PhaseME, a versatile method to provide insights into and improvement of sample phasing results based on linkage data. We showcase the performance and the importance of PhaseME by comparing phasing information obtained from Pacific Biosciences including both continuous long reads and high-quality consensus reads, Oxford Nanopore Technologies, 10x Genomics, and Illumina sequencing technologies. We found that 10x Genomics and Oxford Nanopore phasing can be significantly improved while retaining a high N50 and completeness of phase blocks. PhaseME generates reports and summary plots to provide insights into phasing performance and correctness. We observed unique phasing issues for each of the sequencing technologies, highlighting the necessity of quality assessments. PhaseME is able to decrease the Hamming error rate significantly by 22.4% on average across all 5 technologies. Additionally, a significant improvement is obtained in the reduction of long switch errors. Especially for high-quality consensus reads, the improvement is 54.6% in return for only a 5% decrease in phase block N50 length.

Conclusions
PhaseME is a universal method to assess the phasing quality and accuracy and improves the quality of phasing using linkage information. The package is freely available at https://github.com/smajidian/phaseme.
An Overview of Competition Law Enforcement in Hong Kong
Authors: Snyder Brent 
Published: July 2020

Abstract
The Hong Kong Competition Commission is a young enforcement agency, enforcing a competition law that has been in effect less than five years. Despite its relative youth, the Competition Commission is quickly gaining experience as the pace and breadth of its enforcement is increasing in the aftermath of its first trial wins, its policy advisory work with the Hong Kong Government is gaining traction, and its advocacy is succeeding in educating a wide variety of Hong Kong stakeholders about the benefits of competition and the requirements of the law.
Reduced Hospital Costs for Ultrasound-guided Vacuum-assisted Excision Compared with Open Surgery in Patients with Benign Breast Masses and High-risk Lesions
Authors: Whitworth Pat , Hogan Andrew , Ferko Nicole , Son Daniel , Wang Faye , Xiong Yan , Suri Himanshu , Barclay Ben 
Published: July 2020

Abstract

Objective
Benign breast masses represent a substantial proportion of breast cancer screening results and may require multiple follow-up visits and biopsy. Even with a preceding benign core biopsy, benign masses have been excised via open surgery for a variety of reasons. This study compared the procedural costs of US-guided vacuum-assisted excision (US-VAE) versus open surgical excisions for benign breast masses and high-risk lesions (HRL).

Methods
In this retrospective cohort study, female outpatients receiving US-VAE or open excision of benign breast masses between 2015 and 2018 were identified within the Premier Healthcare Database. A secondary analysis was conducted for patients with HRLs. Propensity score matching and multivariate regression adjusted for patient demographics, encounter level covariates, and hospital characteristics. The total procedural costs were reported from a hospital perspective.

Results
A total of 33 724 patients underwent excisions for benign breast masses (8481 US-VAE and 25 242 open surgery). Procedural costs were significantly lower in unmatched patients who received US-VAE ($1350) versus open surgery ($3045) (P &lt; 0.0001). After matching, a total of 5499 discharges were included in each group, with similar findings for US-VAE ($1348) versus open surgery ($3101) (P &lt; 0.0001). A secondary analysis of matched HRL patients (41 discharges in each group) also showed significantly lower procedural costs with US-VAE ($1620) versus open surgery ($3870) (P &lt; 0.0001).

Conclusion
Among patients with benign breast masses or HRLs, US-VAE was associated with significantly lower procedural costs versus open surgery. If excision is performed and expected clinical outcomes are equal, US-VAE is preferable to reduce costs without compromising the quality of care.
Population-Based Evidence From a Western Canadian Province of the Decreasing Incidence Rates and Trends of Inflammatory Bowel Disease Among Adults
Authors: Osei Jessica Amankwah , Peña-Sánchez Juan Nicolás , Fowler Sharyle A , Muhajarine Nazeem , Kaplan Gilaad G , Lix Lisa M 
Published: July 2020

Abstract

Background and Aims
Canada has one of the highest inflammatory bowel disease (IBD) incidence rates worldwide. Higher IBD incidence rates have been identified among urban regions compared to rural regions. The study objectives were to (i) estimate IBD incidence rates in Saskatchewan from 1999 to 2016 and (ii) test for differences in IBD incidence rates for rural and urban regions of Saskatchewan.

Methods
A population-based study was conducted using provincial administrative health databases. Individuals aged 18+ years with newly diagnosed Crohn’s disease or ulcerative colitis were identified using a validated case definition. Generalized linear models with a negative binomial distribution were used to estimate incidence rates and incidence rate ratios (IRRs) adjusted for age group, sex and rurality with 95% confidence intervals (CIs).

Results
The average annual incidence rate of IBD among adults in Saskatchewan decreased from 75/100,000 (95% CI 67 to 84) in 1999 to 15/100,000 (95% CI 12 to 18) population in 2016. The average annual incidence of IBD declined significantly by 6.9% (95% CI −7.6 to −6.2) per year. Urban residents had a greater overall risk of IBD (IRR = 1.19, 95% CI 1.11 to 1.27) than rural residents. This risk difference was statistically significant for Crohn’s disease (IRR = 1.25, 95% CI 1.14 to 1.36), but not for ulcerative colitis (IRR = 1.08, 95% CI 0.97 to 1.19).

Conclusions
The incidence of IBD in Saskatchewan dropped significantly from 1999 to 2016 with urban dwellers having a 19% higher risk of IBD onset compared to their rural counterparts. Health care providers and decision-makers should plan IBD-specific health care programs considering these specific IBD rates.
Planetary systems in a star cluster II: intermediate-mass black holes and planetary systems
Authors: Flammini Dotti Francesco , Kouwenhoven M B N , Shu Qi , Hao Wei , Spurzem Rainer 
Published: July 2020

ABSTRACT
Most stars form in dense stellar environments. It is speculated that some dense star clusters may host intermediate-mass black holes (IMBHs), which may have formed from runaway collisions between high-mass stars, or from the mergers of less massive black holes. Here, we numerically explore the evolution of populations of planets in star clusters with an IMBH. We study the dynamical evolution of single-planet systems and free-floating planets, over a period of 100 Myr, in star clusters without an IMBH, and in clusters with a central IMBH of mass $100\, \mathrm{M}_\odot$ or $200\, \mathrm{M}_\odot$. In the central region ($r\lesssim 0.2$ pc), the IMBH’s tidal influence on planetary systems is typically 10 times stronger than the average neighbour star. For a star cluster with a $200\, \mathrm{M}_\odot$ IMBH, the region in which the IMBH’s influence is stronger within the virial radius (∼1 pc). The IMBH quenches mass segregation, and the stars in the core tend to move towards intermediate regions. The ejection rate of both stars and planets is higher when an IMBH is present. The rate at which planets are expelled from their host star rate is higher for clusters with higher IMBH masses, for t &lt; 0.5trh, while remains mostly constant while the star cluster fills its Roche lobe, similar to a star cluster without an IMBH. The disruption rate of planetary systems is higher in initially denser clusters, and for wider planetary orbits, but this rate is substantially enhanced by the presence of a central IMBH.
Is there large convective-core overshooting in Kepler targets KIC 2837475 and 11081729?
Authors: Zhang Jianwei 
Published: July 2020

ABSTRACT
The ratio of small-to-large separations r010 has been widely used in helioseismology and asteroseismology to investigate the internal structure of a star, as it is approximately independent of the structure of the outer layers. Several studies have used this tool to constrain the convective-core overshooting of main-sequence stars (i.e. 0.0 ≤ δov ≤ 0.2). This is consistent with the generally accepted values. However, Yang et al. have proposed that there is large convective-core overshooting in the Kepler targets KIC 2837475 and 11081729: 1.2 ≤ δov ≤ 1.6 and 1.7 ≤ δov ≤ 1.8, respectively. These are much larger than the normal values. Thus, the aim of this study is to re-investigate the ratios of the two stars using a model-independent method with the latest p-mode observations. Our results indicate that there is no robustness for including such a large convective-core overshooting while modelling these two stars. In fact, this leads to over-fitting, and the observational constraints of r010 prefer models with a normal convective-core overshooting (i.e. 0.0 ≤ δov ≤ 0.2) as the candidates for the best-fitting model of KIC 2837475 and 11081729.
A commercial grain-free diet does not decrease plasma amino acids and taurine status but increases bile acid excretion when fed to Labrador Retrievers
Authors: Donadelli Renan A , Pezzali Julia G , Oba Patricia M , Swanson Kelly S , Coon Craig , Varney Jessica , Pendlebury Christine , Shoveller Anna K 
Published: July 2020

AbstractGrain-free diets tend to have greater inclusions of pulses in contrast to grain-based diets. In 2018, the Food and Drug Administration (FDA) released a statement that grain-free diets may be related to the development of canine dilated cardiomyopathy (DCM). However, all dog foods met regulatory minimums for nutrient inclusion recommended by the Association of American Feed Controls Official. In some FDA case reports, but not all, dogs diagnosed with DCM also had low concentrations of plasma or whole blood taurine; thus, we hypothesized that feeding these diets will result in reduced taurine status from baseline measures. The objective of this study was to determine the effects of feeding a grain-free diet to large-breed dogs on taurine status and overall health. Eight Labrador Retrievers (four males and four females; Four Rivers Kennel, MO) were individually housed and fed a commercial complete and balanced grain-free diet (Acana Pork and Squash formula; APS) for 26 wk. Fasted blood samples were collected prior to the start of the trial (baseline; week 0) and at weeks 13 and 26 for analyses of blood chemistry, hematology, plasma amino acids, and whole blood taurine. Urine was collected by free catch at weeks 0 and 26 for taurine and creatinine analyses. Fresh fecal samples were collected at weeks 0 and 26 for bile acid analyses. Data were analyzed using the GLIMMIX procedure with repeated measures in SAS (v. 9.4). Plasma His, Met, Trp, and taurine and whole blood taurine concentrations increased over the course of the study (P &lt; 0.05). Urinary taurine to creatinine ratio was not affected by diet (P &gt; 0.05). Fecal bile acid excretion increased after 26 wk of feeding APS to dogs. Despite the higher fecal excretion of bile acids, plasma and whole blood taurine increased over the 26-wk feeding study. These data suggest that feeding APS, a grain-free diet, over a 26-wk period improved taurine status in Labrador Retrievers and is not the basis for the incidence of DCM for dogs fed APS. Other factors that may contribute to the etiology of DCM should be explored.