bluuebunny/crossref_metadata_2025 huggingface dataset:
Local tradition of mountain farmers in Japan and Batak area in industrial era 4.0
Authors: Situmorang F C , Ginting N M , Dawapa M , Duli A
Published: November 2019

Traditional societies have local knowledge in managing human relations with humans, human relationships with nature and human relations with God. Modern Japanese society recently still maintains its tradition, so it is often called Japan runs on two sides of culture, namely modern and traditional. In mountain farming in Japan, now agricultural activities are still carrying out ritual events such as the ritual of planting rice, rites weeding and repelling pests and rites of harvest and post-harvest. Japanese farmers do not kill wild animals in their fields but take precautions, so that wild animals do not come in to disturb their agriculture. Compared to mountain farming in North Sumatra, the traditional beliefs of the people have changed; they no longer carry out the traditional rites. Now farmers have hunted wild animals such as birds, bats, and snakes. Therefore, this situation is damaging the ecosystem because wild animals have been used as food so that there are many mice and planthopper pests/insects and for that, they use a lot of chemical poisons. This results in poor harvests and consequently, farmers being poor. Researchers use Fudo’s theory (The relationship of climate with the way of life of Watsuji Tetsuro) and the historical development theory of Saburo Ienaga and theories of comparative culture in examining the local wisdom of farming communities in these two ethnicities. This research shows how two nations which have relatively similar natural conditions but in historical development have different ways of life.
Heligman-pollard modification by using the makeham death rate to predict the life table of the elderly
Authors: Riyana M , Belwawin S M , Hasanah N , Ahmad M
Published: November 2019

Increasing the number of elderly people in the world is increasing every year, indicating that the economic factors of the community are getting better and also improving services and public health sciences and other factors. The purpose of this research is to find out the number of elderly people in a country. This can be seen by using a complete life table. But in some developing countries in the world do not have a complete life table and only have a abriged life table with an age interval of 5 years or 10 years. Based on the increase in the elderly population in the world researchers want to make the life table of the elderly based on a complete life table by using the interpolation method. Interpolation methods, for example, are the Heligman-Pollard, Elandt-Johnson, Kostaki, and others. In this study, the researchers tried to modify the Heligman-Pollard interpolation method by flexing it with the death rate of the Gompertz distribution. Thus formed the Heligman-Pollard modification using the death rate of the Gompertz distribution. Based on the modification, the result is that the method can predict the complete life table by the original complete life table data from the United States of America in 2014. With the R2 result of 0.985017
Prototype design of wind power water pump for irrigation
Authors: Jamaludin  , Parjono  , Permadi M G , Andari G , Sapsal M T
Published: November 2019

The main objective of this research was to produce a prototype of a simple water pump using a TSAV (vertical axis wind turbine) wind turbine as a prime mover and to analyze the relationship between wind speed and speed of windmill spin with the dependent variable in the form of water flow from the pump. The study used experimental and design methods. The test results obtained a wind speed of 3.6 m/s in an average windmill rotation of 5.6 rpm. Based on ANOVA test, the wind speed in the morning, afternoon, evening, and night had a significant difference. The highest wind speed occurred during the day at 4.3 m/s while the lowest wind speed occurred at night at 2.2 m/s. Water discharge generated by the pump was 2.0347 liters/minute with an efficiency of 89.7% pump. The results of the analysis showed that wind speed, windmill spin, and water discharge could change linearly. The higher the wind speed, the greater the number of spinning windmills, and the more water discharge produced. Therefore, the results of testing the pump can work well and has the potential to be developed in the region with the existing wind speed.
Comparison of competitive model advantage tools in the economic potential of north Kolaka Regency
Authors: Meilvidiri W , Ulita A S , Asrudi  , Alzarliani Wa Ode
Published: November 2019

The purpose of this study was to identify superior sectors in North Kolaka Regency. The study used competitive model advantage tools (LQ, DLQ, MRP, Tress Index, Shift Share, multiplier effects and compounding factors). Comparative results Sector of the economic potential in North Kolaka Regency that was; agriculture, forestry and fisheries, and construction sector are the base sectors that have a multiplier effect> 1. According to DLQ analysis, some sectors were experiencing rapid development namely the real estate sector, company services, government administration, defense and compulsory social security and health services and social activities. As Carvalho Classification Analysis like agriculture, forestry and fisheries sectors were classified as very high. Meanwhile, the mining and quarrying sector, water supply, waste management, and re-leaf; construction, wholesale and retail trade, Car and Motorcycle Repair, and other services were in the medium classification. According to MRP analysis, information and communication sector were in Classification 1. Tress index analysis during this period experienced an increasing trend.
The use of reading material based contextual approach to improve environmental concern attitude of elementary school students
Authors: Rahayu D P , Lieung K W , Fredy
Published: November 2019

This research objective was to improve the environmental concern attitude of grade 4 students by using reading materials. This research is a classroom action research. The research was conducted in two cycles with each cycle consisting of planning, action, observation, and reflection. The subject of this study was the grade 4 students of SDN 5 Panjer which amounted to 24 students. The data sources used in this research were students, teachers, and observers. Data analysis using quantitative and qualitative techniques, including data reduction, data presentation, and drawing conclusions. The results of this research indicate that students environmental concern attitude improved from pre-cycles, cycle 1 and cycle 2. The results of this research indicate that students environmental concern attitude improved from pre-cycles 25%, cycle 1, 48% to cycles 2, 82%. In learning, the teacher uses a reading material based contextual approach with steps: (a) constructivism, (b) inquiry, (c) questioning, (d) learning community, (e) modeling, (f) reflection, (g) authentic assessment. The conclusion of this study is the use of reading materials based contextual approach can improve environmental concern attitude of grade 4 elementary school students.
The effectiveness of applying contextual approach based on environment toward chemistry learning achievement and scientific attitude
Authors: Nurvitasari E , Maarebia R Z , Sumanik N B
Published: November 2019

This research aimed to know the effectiveness of applying contextual approach based on environment toward chemistry learning achievement and scientific attitude students in aspect (a) differences of students chemistry learning achievement if the early knowledge chemistry uses statistically (b) differences of students scientific attitude in experiment class after the teaching-learning process with contextual approach based on environment (c) differences of students scientific attitude between experiment and control class. The method of this research is to experiment with one-factor design (chemistry learning), two samples (control and experiment class) and one covariable (early knowledge students). In the experiment class using a contextual approach based on the environment while in control class using a conventional approach. Chemistry learning achievement measured with an achievement test and then analyzed with one way ANCOVA. Scientific attitude measured with scientific attitude questionnaire and then analyzed with one sample and two-sample t-test. Base on the ANCOVA analysis get value F0 = 4,431 with Ftable = 3.96. This matter shows that significant differences in students chemistry learning achievement with the contextual base on environment approach if the early knowledge chemistry uses statistically. Result of one sample t-test shows that the value t = 0,465 with t table = 1,67, it can be concluded that is no significant differences of students scientific attitude in experiment class after teaching-learning process with the contextual base on environment approach. Result of two-sample t-test shows that the value t = 0,05 with t table = 1,67, it can be concluded that is no significant differences of students scientific attitude between experiment and control class.
Effectiveness formulation made from PGPR Bacillus spp. in the protection of shallot plants from fusarium wilt
Authors: Suyono  , Baharuddin
Published: November 2019

Fusarium wilt disease (Fusarium oxysporum f. Sp. Cepae) is one of the critical and dominant diseases in shallots in South Sulawesi, which can reduce production by up to 60 percent. This study aims to determine the ability of the PGPR Bacillus spp. in protecting the onion plants from fusarium wilt (F. o. cepae) in the onion plants produced. The implementation method consists of; preparation of planting media, preparation of onion planting, supply and propagation of microbes (fungi F. o. cepae and PGPR bacteria Bacillus spp.), manufacture of PGPR bacteria Bacillus spp. formulations, and application of PGPR bacteria Bacillus spp. on planting. The study was conducted using a Completely Randomized Design (CRD) consisting of 5 treatments and three replications. Data were analyzed with ANOVA at the level of 5% and 1%. If it shows any treatment effect, then it is continued with BNJ test at 1% level. The results showed that treatment C showed the results of the emphasis on the intensity of the attack F. o. the best cepae with an average suppression of 83.44% compared to other treatments at the last observation.
Diversification of processed cocoa using coconut to increase the added value
Authors: Langkong J , Latief R , Rahman A N F , Dirpan A , Sapsal M T , Kamaruddin I , Marselia
Published: November 2019

Chocolate bar is one of secondary product of cocoa beans which are ready to consume. The aim of this research is to know the effect of shredded copra addition as a filler of chocolate bar. The method of this research started from the processing of beans into fats and cocoa powder, the making of shredded copra as a filler, and the making of chocolate bar. The evaluation done based on carbohydrate content, moisture content, ash content, fat content, fat blooming, and organoleptic in terms of color, odor, taste, and texture. The design of research used was completely randomized design in 3 repetition. Sample used is shredded copra (A1 = 6%, A2 = 9%, and A3 = 12%). The results shows that addition of shredded copra is significant at the 5% level of ash content and fat content. While organoleptic test shows that A1 (addition of 6% shredded copra) is most preferred by panellist in terms of color and texture, while A3 (addition of 12% shredded copra) is most preferred by panellist in terms of aroma and taste parameter.
Gauge invariant resolution of the A⃗ · p⃗ versus r⃗ · E⃗ controversy
Authors: Chou Hsiang Shun
Published: November 2019

We delve into the problem of the choice of the interaction Hamiltonian in quantum transitions by using the gauge invariant formalism. We demonstrate that the gauge invariant transition amplitudes for the bare-bare transitions, which is the case in the majority of experiments, are identical to the conventional results with the velocity form interaction Hamiltonian. Under the electric dipole approximation, the gauge invariant formalism derives the modified length form interaction Hamiltonian in any gauge. We propose a simple experiment that one can perform to verify our prediction. On the other hand, the gauge invariant transition amplitudes for the dressed-dressed transitions, which is the case in the Lamb shift experiment, are identical to the conventional results with the length form interaction Hamiltonian. There is no preferred gauge in the calculations of transition amplitudes. The present investigation resolves the long-standing

A

⃗

·

p

⃗

versus

r

⃗

·

E

⃗

controversy and clarifies the prevailing misconception in the literature.
Eigenvalue bounds for Stark operators with complex potentials
Authors: Korotyaev Evgeny , Safronov Oleg
Published: November 2019

We consider the three-dimensional Stark operator perturbed by a complex-valued potential. We obtain an estimate for the number of eigenvalues of this operator as well as for the sum of imaginary parts of eigenvalues situated in the upper half-plane.
On planar Cayley graphs and Kleinian groups
Authors: Georgakopoulos Agelos
Published: November 2019

Let

G
G

be a finitely generated group acting faithfully and properly discontinuously by homeomorphisms on a planar surface

X
⊆

S

2

X \subseteq \mathbb {S}^2

. We prove that

G
G

admits such an action that is in addition co-compact, provided we can replace

X
X

by another surface

Y
⊆

S

2

Y \subseteq \mathbb {S}^2

.

We also prove that if a group

H
H

has a finitely generated Cayley (multi-) graph

C
C

equivariantly embeddable in

S

2

\mathbb {S}^2

, then

C
C

can be chosen so as to have no infinite path on the boundary of a face.

The proofs of these facts are intertwined, and the classes of groups they define coincide. In the orientation-preserving case they are exactly the (isomorphism types of) finitely generated Kleinian function groups. We construct a finitely generated planar Cayley graph whose group is not in this class.

In passing, we observe that the Freudenthal compactification of every planar surface is homeomorphic to the sphere.
Optimized Delta Check Rules for Detecting Misidentified Specimens in Children
Authors: Tan Rui Zhen , Markus Corey , Choy Kay Weng , Doery James C G , Loh Tze Ping
Published: November 2019

Objectives

Preanalytical processes in pediatric patients are generally manual and associated with a higher risk of error. The optimized delta check rules for detecting misidentified children samples are examined.

Methods

Relative difference and absolute different delta check limits were applied on original and reshuffled (to simulate sample mislabeling/mix-up) paired deidentified pediatric results of 57 laboratory tests. The sensitivity, specificity, and accuracy of a range of delta check limits were determined. The delta check limit associated with the highest accuracy was considered optimal.

Results

In general, the delta check limits had poor to moderate accuracy (0.50-0.81) in detecting misidentified patient samples. The sensitivity (rule out misidentified sample) quickly deteriorated at increasing delta check limits. At the same time, the specificity (rule in misidentified sample) of the delta check limit was also low. The performance of the relative difference and absolute difference delta check rules was similar.

Conclusions

Our findings showed poor delta check performance in the pediatric population. The high false-positive flag rate may lead to wasteful resource-intensive investigations and delay in result reporting. In addition, we observed that the optimized pediatric delta check correlated strongly with within-subject biologic variation, whereas delta check accuracy correlated poorly with index of individuality.
Clinicopathologic Features of Small Renal Masses Associated With Distant Metastatic Disease
Authors: Gallan Alexander J , Antic Tatjana
Published: November 2019

Objectives

To assess the clinicopathologic features of small renal masses (≤4 cm) associated with distant metastatic disease.

Methods

We identified radical or partial nephrectomies with renal cell carcinomas (RCCs) measuring 4 cm or less in size (pT1a or pT3a) from 2005 to 2015. Clinicopathologic features were compiled.

Results

A total of 590 RCCs 4 cm or less were identified, of which 3.9% were associated with distant metastatic RCC. Metastasis was more common in pT3a tumors 4 cm or less than pT1a tumors (19% vs 2.7%; P < .01). Seventy percent of tumors were clear cell RCCs. Overall, 43% of patients had previously (30%) or subsequently (13%) diagnosed RCC prior to development of metastasis, 80% of which were the same histologic subtype as the small renal mass.

Conclusions

Distant metastatic disease was rarely encountered in patients with small renal masses. Many of the patients with distant metastases had previously or subsequently diagnosed RCC, which could represent the true source of metastatic disease.
Prevalence and Determinants of Hypertension in India Based on the 2017 ACC/AHA Guideline: Evidence from the India National Family Health Survey
Authors: Abariga Samuel A , Khachan Hamed , Al Kibria Gulam Muhammed
Published: November 2019

OBJECTIVE

To estimate the prevalence and determinants of hypertension in India based on a new definition by the 2017 American College of Cardiology/American Heart Association (2017 ACC/AHA) Guideline for the Prevention, Detection, Evaluation and Management of High Blood Pressure in Adults, and compare prevalence estimates with those of the Seventh Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure (JNC7).

METHODS

We used the National Family Health Survey (NFHS-4) conducted in India (n = 212,007). We accounted for the sampling strategy by applying survey weights.

RESULTS

Prevalence of hypertension among Indians aged 15–49 years was 40.6% (95% confidence interval [CI]: 40.3–41.0) and 13.0% (95% CI: 12.8–13.2) based on 2017 ACC/AHA and JNC7 guidelines respectively. The overall absolute increase in prevalence was 27.6% (95% CI:27.3–27.9). The absolute changes in crude prevalence of hypertension between the JNC7 and 2017 ACC/AHA guidelines for men and women were 31.4% (95% CI: 30.9–31.9) and 23.7% (95% CI: 23.5–23.9), respectively. As per both guidelines, the overall prevalence was significantly higher among older people, age, male sex, overweight/obesity, higher wealth status, and urban residence.

CONCLUSION

Applying the 2017 ACC/AHA guideline to the Indian population led to a significant increase in the proportion of Indians with hypertension. There is also socioeconomic differences in the prevalence of hypertension as per both guidelines. Implementation and expansion of public health efforts for prevention and control strategies for hypertension is warranted.
scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis
Authors: Cai James J
Published: November 2019

Motivation

Single-cell RNA sequencing (scRNA-seq) technology has revolutionized the way research is done in biomedical sciences. It provides an unprecedented level of resolution across individual cells for studying cell heterogeneity and gene expression variability. Analyzing scRNA-seq data is challenging though, due to the sparsity and high dimensionality of the data.

Results

I developed scGEAToolbox—a Matlab toolbox for scRNA-seq data analysis. It contains a comprehensive set of functions for data normalization, feature selection, batch correction, imputation, cell clustering, trajectory/pseudotime analysis and network construction, which can be combined and integrated to building custom workflow. Although most of the functions are implemented in native Matlab, wrapper functions are provided to allow users to call the ‘third-party’ tools developed in Matlab or other languages. Furthermore, scGEAToolbox is equipped with sophisticated graphical user interfaces generated with App Designer, making it an easy-to-use application for quick data processing.

Availability and implementation

https://github.com/jamesjcai/scGEAToolbox.

Supplementary information

Supplementary data are available at Bioinformatics online.
Roles of Positive Psychology for Mental Health in UK Social Work Students: Self-Compassion as a Predictor of Better Mental Health
Authors: Kotera Y , Green P , Sheffield D
Published: November 2019

Despite high shame about mental health symptoms among UK social work students, positive psychological approaches to their mental health have not been investigated in depth. Emotional resilience has been a core skill in social work practice; however, its relationship with mental health is still unclear. Therefore, the primary purposes of this cross-sectional study were to (i) examine the relationships between mental health and positive psychological constructs, namely resilience, self-compassion, motivation and engagement and (ii) determine predictors of mental health in UK social work students. An opportunity sampling of 116 UK social work students (102 females, 14 males; 96 undergraduates, 20 postgraduates) completed 5 measures about these constructs. Correlation and regression analyses were conducted. Mental health was associated with resilience, self-compassion and engagement. Self-compassion was a negative predictor, and intrinsic motivation was a positive predictor of mental health symptoms. Resilience did not predict mental health symptoms. The findings highlight the importance of self-compassion to the challenging mental health of UK social work students; they caution against the overuse and misunderstanding of resilience in the social work field.
Local cold adaption increases the thermal window of temperate mussels in the Arctic
Authors: Thyrring J , Tremblay R , Sejr M K
Published: November 2019

Species expand towards higher latitudes in response to climate warming, but the pace of this expansion is related to the physiological capacity to resist cold stress. However, few studies exist that have quantified the level of inter-population local adaptation in marine species freeze tolerance, especially in the Arctic. We investigated the importance of cold adaptation and thermal window width towards high latitudes from the temperate to the Arctic region. We measured upper and lower lethal air temperatures (i.e. LT and LT50) in temperate and Arctic populations of blue mussels (Mytilus edulis), and analysed weather data and membrane fatty acid compositions, following emersion simulations. Both populations had similar upper LT (~38 °C), but Arctic mussels survived 4°C colder air temperatures than temperate mussels (−13 vs. −9°C, respectively), corresponding to an 8% increase in their thermal window. There were strong latitudinal relationships between thermal window width and local air temperatures, indicating Arctic mussels are highly adapted to the Arctic environment where the seasonal temperature span exceeds 60°C. Local adaptation and local habitat heterogeneity thus allow leading-edge M. edulis to inhabit high Arctic intertidal zones. This intraspecific pattern provides insight into the importance of accounting for cold adaptation in climate change, conservation and biogeographic studies.
Screening Drought-Tolerant Native Plants for Attractiveness to Arthropod Natural Enemies in the U.S. Great Lakes Region
Authors: Gibson Daniel R , Rowe Logan , Isaacs Rufus , Landis Douglas A
Published: November 2019

Arthropods provide a variety of critical ecosystem services in agricultural landscapes; however, agricultural intensification can reduce insect abundance and diversity. Designing and managing habitats to enhance beneficial insects requires the identification of effective insectary plants that attract natural enemies and provide floral resources. We tested the attractiveness of 54 plant species with tolerance to dry soils, contrasting perennial forbs and shrubs native to the Great Lakes region to selected non-native species in three common garden experiments in Michigan during 2015–2016. Overall, we found 32 species that attracted significantly more natural enemies than associated controls. Among these, Achillea millefolium and Solidago juncea were consistently among the most attractive plants at all three sites, followed by Solidago speciosa, Coreopsis tripteris, Solidago nemoralis, Pycnanthemum pilosum, and Symphyotrichum oolantangiense. Species which attracted significantly more natural enemies at two sites included: Asclepias syriaca, Asclepias tuberosa, Monarda fistulosa, Oligoneuron rigidum, Pycnanthemum virginianum, Dasiphora fruticosa, Ratibida pinnata, Asclepias verticillata, Monarda punctata, Echinacea purpurea, Helianthus occidentalis, Silphium integrifolium, Silphium terebinthinaceum, Helianthus strumosus, and Symphyotrichum sericeum. Two non-native species, Lotus corniculatus, and Centaurea stoebe, were also attractive at multiple sites but less so than co-blooming native species. Parasitic Hymenoptera were the most abundant natural enemies, followed by predatory Coleoptera and Hemiptera, while Hemiptera (Aphidae, Miridae, and Tingidae) were the most abundant herbivores. Collectively, these plant species can provide floral resources over the entire growing season and should be considered as potential insectary plants in future habitat management efforts.
Do the Quality and Quantity of Honey Bee-Collected Pollen Vary Across an Agricultural Land-Use Gradient?
Authors: Simanonok Michael P , Otto Clint R V , Smart Matthew D
Published: November 2019

Pollen is the source of protein for most bee species, yet the quality and quantity of pollen is variable across landscapes and growing seasons. Understanding the role of landscapes in providing nutritious forage to bees is important for pollinator health, particularly in areas undergoing significant land-use change such as in the Northern Great Plains (NGP) region of the United States where grasslands are being converted to row crops. We investigated how the quality and quantity of pollen collected by honey bees (Apis mellifera L. [Hymenoptera: Apidae]) changed with land use and across the growing season by sampling bee-collected pollen from apiaries in North Dakota, South Dakota, and Minnesota, USA, throughout the flowering season in 2015–2016. We quantified protein content and quantity of pollen to investigate how they varied temporally and across a land-use gradient of grasslands to row crops. Neither pollen weight nor crude protein content varied linearly across the land-use gradient; however, there were significant interactions between land use and sampling date across the season, particularly in grasslands. Generally, pollen protein peaked mid-July while pollen weight had two maxima in late-June and late-August. Results suggest that while land use itself may not correlate with the quality or quantity of pollen resources collected by honey bees among our study apiaries, the nutritional landscape of the NGP is seasonally dynamic, especially in certain land covers, and may impose seasonal resource limitations for both managed and native bee species. Furthermore, results indicate periods of qualitative and quantitative pollen dearth may not coincide.
Friendship and Female Education: Evidence from a Field Experiment in Bangladeshi Primary Schools
Authors: Hahn Youjin , Islam Asadul , Patacchini Eleonora , Zenou Yves
Published: November 2019

We randomly assigned 115 primary schools in Bangladesh to one of two settings: children studying in groups with friends and children studying in groups with peers. The groups consisted of four people with similar average cognitive abilities and household characteristics. While the achievement of male students was not affected by the group assignment, low-ability females with friends outperformed low-ability females working with peers by roughly 0.4 standard deviations of the test score distribution. This is not due to the fact that friends tend to be of the same gender or to a higher frequency of interactions among friends.
Changing Global Dynamics and International Competition Law: Considering China’s Potential Impact
Authors: Ng Wendy
Published: November 2019

Competition law is increasingly international in its scope and application. Today, over 130 jurisdictions have competition law. Although most competition laws are national in scope and no formalized competition law-related rules apply globally, international norms for competition law have been created and fostered. These norms largely reflect the perspectives and approaches of the USA, European Union and developed countries more generally. However, developing countries now constitute the majority of competition law jurisdictions, and Brazil, Russia, India, China and South Africa – which all have competition laws – have risen as important economic powers. Whether and how these changing global dynamics will impact international competition law norms is an important issue that remains under-explored. This article considers this question by examining China and its competition law. It examines the extent to which China has adopted and incorporated international norms into its competition law and evaluates whether China’s approach to, and understanding of, competition law might challenge or change the development of international competition law norms in the future.
Illuminating the dynamic rare biosphere of the Greenland Ice Sheet's Dark Zone
Authors: Gokul Jarishma K , Cameron Karen A , Irvine-Fynn Tristram D L , Cook Joseph M , Hubbard Alun , Stibal Marek , Hegarty Matt , Mur Luis A J , Edwards Arwyn
Published: November 2019

Greenland's Dark Zone is the largest contiguous region of bare terrestrial ice in the Northern Hemisphere and microbial processes play an important role in driving its darkening and thereby amplifying melt and runoff from the ice sheet. However, the dynamics of these microbiota have not been fully identified. Here we present joint 16S rRNA gene and 16S rRNA (cDNA) comparison of input (snow), storage (cryoconite), and output (supraglacial stream water) habitats across the Dark Zone over the melt season. We reveal that all three Dark Zone communities have a preponderance of rare taxa exhibiting high protein synthesis potential (PSP). Furthermore, taxa with high PSP represent highly connected ‘bottlenecks’ within community structure, consistent with their roles as metabolic hubs. Finally, low abundance-high PSP taxa affiliated with Methylobacterium within snow and stream water suggest a novel role for Methylobacterium in the carbon cycle of Greenlandic snowpacks, and importantly, the export of potentially active methylotrophs to the bed of the Greenland Ice Sheet. By comparing the dynamics of bulk and potentially active microbiota in the Dark Zone of the Greenland Ice Sheet we provide novel insights into the mechanisms and impacts of the microbial colonization of this critical region of our melting planet.
Ethnicity-specific and overlapping alterations of brain hydroxymethylome in Alzheimer’s disease
Authors: Qin Lixia , Xu Qian , Li Ziyi , Chen Li , Li Yujing , Yang Nannan , Liu Zhenhua , Guo Jifeng , Shen Lu , Allen Emily G , Chen Chao , Ma Chao , Wu Hao , Zhu Xiongwei , Jin Peng , Tang Beisha
Published: November 2019

5-Methylcytosine (5mC), generated through the covalent addition of a methyl group to the fifth carbon of cytosine, is the most prevalent DNA modification in humans and functions as a critical player in the regulation of tissue and cell-specific gene expression. 5mC can be oxidized to 5-hydroxymethylcytosine (5hmC) by ten–eleven translocation (TET) enzymes, which is enriched in brain. Alzheimer’s disease (AD) is the most common neurodegenerative disorder, and several studies using the samples collected from Caucasian cohorts have found that epigenetics, particularly cytosine methylation, could play a role in the etiological process of AD. However, little research has been conducted using the samples of other ethnic groups. Here we generated genome-wide profiles of both 5mC and 5hmC in human frontal cortex tissues from late-onset Chinese AD patients and cognitively normal controls. We identified both Chinese-specific and overlapping differentially hydroxymethylated regions (DhMRs) with Caucasian cohorts. Pathway analyses revealed specific pathways enriched among Chinese-specific DhMRs, as well as the shared DhMRs with Caucasian cohorts. Furthermore, two important transcription factor-binding motifs, hypoxia-inducible factor 2α (HIF2α) and hypoxia-inducible factor 1α (HIF1α), were enriched in the DhMRs. Our analyses provide the first genome-wide profiling of DNA hydroxymethylation of the frontal cortex of AD patients from China, emphasizing an important role of 5hmC in AD pathogenesis and highlighting both ethnicity-specific and overlapping changes of brain hydroxymethylome in AD.
Brexit and the UN Security Council: declining British influence?
Authors: Gifkins Jess , Jarvis Samuel , Ralph Jason
Published: November 2019

The United Kingdom's decision to leave the European Union has ramifications beyond the UK and the EU. This article analyses the impact of the Brexit referendum on the UK's political capital in the United Nations Security Council; a dimension of Brexit that has received little attention thus far. Drawing on extensive elite interviews we show that the UK has considerable political capital in the Council, where it is seen as one of the most effective actors, but the reputational costs of Brexit are tarnishing this image. With case-studies on the UK's role in Somalia and Yemen we show how the UK has been able to further its interests with dual roles in the EU and Security Council, and the risks posed by tensions between trade and human rights after Brexit. We also analyse what it takes to be influential within the Security Council and argue that more attention should be paid to the practices of diplomacy. Influence is gained via penholding, strong diplomatic skill and a well-regarded UN permanent representative. The UK accrues political capital as a leader on the humanitarian and human rights side of the Council's agenda, but this reputation is at risk as it exits the EU.
The Kauffman Skein Module at 1st Order
Authors: Marché Julien
Published: November 2019

For a three-manifold $M$ with boundary, we study the Kauffman module with indeterminate equal to $-1+\epsilon $ where $\epsilon ^2=0$. We conjecture an explicit relation between this module and the Reidemeister torsion of $M$, which we prove in particular cases. As a maybe-useful tool, we then introduce a notion of twisted self-linking and prove that it satisfies the Kauffman relations at 1st order. These questions come from considerations on asymptotics of quantum invariants.
Molecular characterization and antimicrobial susceptibility of bacterial isolates present in tap water of public toilets
Authors: Kaur Rajanbir , Singh Drishtant , Kesavan Anup Kumar , Kaur Rajinder
Published: November 2019

Background

The present study was carried out to investigate the tap water quality of public toilets in Amritsar, Punjab, India.

Methods

Water samples from the taps of the public toilets were collected in sterile containers and physicochemical and bacteriological analysis was performed using standard methods. Also, genotypic and phenotypic characterization of the bacterial isolates was performed using different biochemical tests and 16S ribosomal RNA analysis. An antibiotic susceptibility test was performed using antibiotics based on their mode of action. A biofilm assay was performed to assess the adhesion potential of the isolates.

Results

A total of 25 bacterial isolates were identified from the water samples, including Acinetobacter junii, Acinetobacter pittii, Acinetobacter haemolyticus, Bacillus pumilus, Bacillus megaterium, Bacillus marisflavi, Bacillus flexus, Bacillus oceanisediminis, Pseudomonas otitidis, Pseudomonas sp. RR013, Pseudomonas sp. RR021, Pseudomonas sp. RR022, Escherichia coli and Enterobacter cloacae. The results of the antimicrobial susceptibility test revealed that the antibiotics cefodroxil, aztreonam, nitrofurantoin, cefepime, ceftazidime and amoxyclav were found to be mostly ineffective against various isolates. The biofilm assay revealed the weak, moderate and strong biofilm producers among them.

Conclusions

The tap water in the public toilets was microbially contaminated and needs to be monitored carefully. The antibiotic susceptibility profile showed that of 25 bacterial isolates, 5 were multidrug resistant. Bacterial isolates exhibited strong to weak adhesion potential in the biofilm assay.
In vitro activity of ceftazidime/avibactam against isolates of carbapenem-non-susceptible Enterobacteriaceae collected during the INFORM global surveillance programme (2015–17)
Authors: Spiliopoulou Iris , Kazmierczak Krystyna , Stone Gregory G
Published: November 2019

Objectives

To report data for ceftazidime/avibactam and comparators against meropenem-non-susceptible Enterobacteriaceae collected globally (excluding centres in the USA) from 2015 to 2017 as part of the International Network For Optimal Resistance Monitoring (INFORM) surveillance programme.

Methods

MICs and susceptibility were determined using EUCAST broth microdilution methodology and EUCAST breakpoints. Isolates were screened to detect genes encoding β-lactamases using multiplex PCR assays. MBL-positive isolates were those in which one or more of the IMP, VIM and/or NDM genes were detected.

Results

A total of 1460 meropenem-non-susceptible isolates were collected and, of the agents on the panel, susceptibility was highest to ceftazidime/avibactam, colistin and tigecycline [73.0%, 77.0% (1081/1403) and 78.1%, respectively]. Ceftazidime/avibactam was not active against MBL-positive isolates (n=367); these isolates showed the highest rates of susceptibility to colistin (92.1%, 303/329), tigecycline (71.9%) and amikacin (46.6%). A total of 394 isolates were resistant to ceftazidime/avibactam and, of the 369 isolates that were screened, 98.4% were found to carry a gene encoding an MBL enzyme. Among isolates that were identified as carbapenemase positive and MBL negative (n=910), susceptibility was highest to ceftazidime/avibactam (99.8%). Susceptibility was also highest to ceftazidime/avibactam among isolates that were carbapenemase negative and MBL negative (94/98, 95.9%).

Conclusions

These data highlight the need for continued surveillance of antimicrobial activity as well as the need for new antimicrobials to treat infections caused by meropenem-non-susceptible Enterobacteriaceae, for which the options are extremely limited.
Agreement Forthcoming? A Comparison of EU, US, and Chinese RTAs in Times of Plurilateral E-Commerce Negotiations
Authors: Willemyns Ines
Published: November 2019

This paper discusses the results of a study into the evolution of electronic commerce-related provisions in regional trade agreements (RTAs) and supplements them with a tripartite comparison of the e-commerce provisions in Chinese, EU, and US RTAs. As trade barriers related to electronic commerce are becoming ever more important in the global trade landscape and no explicit provisions exist at the multilateral level, it can be expected that WTO Members increasingly include provisions addressing such barriers, and electronic commerce more generally, at the bilateral and regional levels. This study applies a term-frequency analysis to the whole body of RTAs that contain e-commerce-related provisions, mapping the evolution of e-commerce chapters over time. Subsequently, a legal analysis is conducted on the e-commerce terms that were found in Chinese, EU, and US RTAs. Based on these Members’ position at the multilateral level, the e-commerce topics covered in their RTAs, and the nature of the provisions included, the paper aims to assess the convergences and divergences in their approach to e-commerce at the bilateral level and to draw lessons for the ongoing WTO plurilateral negotiations on the trade-related aspects of electronic commerce.
A Latent Factor Model for Forecasting Realized Variances
Authors: Calzolari Giorgio , Halbleib Roxana , Zagidullina Aygul
Published: November 2019

This article proposes a parsimonious model to forecast large vectors of realized variances (RVar) by exploiting their common dynamics within a latent factor structure. Their long persistence is captured by aggregating latent factors with AR(1) dynamics. The model has obvious advantages over standard autoregressive models not only in terms of parametrization, but also in terms of efficiency, when increasing the dimension of the vector, as it provides more information on the commonality of the series’ dynamics. The model easily accommodates further empirical features of RVars, such as conditional heteroskedasticity. For estimation purposes, we use the maximum likelihood method based on Kalman filter and the efficient method of moments, both being easy to implement and providing accurate estimates. Our empirical illustration on real data shows that the model we propose often outperforms standard models, most of which are, for vectors of RVar series, only implementable under heavy parametric restrictions.
The Practice of Pharmaceutics and the Obligation to Expand Access to Investigational Drugs
Authors: Buckley Michael , O’neil Collin
Published: November 2019

Do pharmaceutical companies have a moral obligation to expand access to investigational drugs to patients outside the clinical trial? One reason for thinking they do not is that expanded access programs might negatively affect the clinical trial process. This potential impact creates dilemmas for practitioners who nevertheless acknowledge some moral reason for expanding access. Bioethicists have explained these reasons in terms of beneficence, compassion, or a principle of rescue, but their arguments have been limited to questions of moral permissibility, leaving for future research the question of whether expanded access is morally obligatory. We take up this further question and argue that pharmaceutical companies have a moral obligation to expand access. Our defense is not based on beneficence, compassion, or rescue, but instead on a reciprocal moral expectation resulting from existing social commitments that help ensure a robust pharmaceutical practice within the broader healthcare system. Our aim is to give this obligation, along with several others, a coherent and plausible structure within the wider clinical trial process so that one might better explain the sources of the dilemmas and their possible resolutions.
On the Mass Assembly History of the Local Group
Authors: Carlesi Edoardo , Hoffman Yehuda , Gottlöber Stefan , Libeskind Noam I , Knebe Alexander , Yepes Gustavo , Pilipenko Sergey V
Published: November 2019

In this work an ensemble of simulated Local Group analogues is used to constrain the properties of the mass assembly history of the Milky Way (MW) and Andromeda (M31) galaxies. These objects have been obtained using the constrained simulation technique, which ensures that simulated LGs live within a large scale environment akin to the observed one. Our results are compared against a standard Λ Cold Dark Matter (ΛCDM) series of simulations which use the same cosmological parameters. This allows us to single out the effects of the constraints on the results. We find that (a) the median constrained merging histories for M31 and MW live above the standard ones at the 1-σ level, (b) the median formation time takes place ≈0.5 Gyr earlier than unconstrained values, while the latest major merger happens on average 1.5 Gyr earlier and (c) the probability for both LG haloes to have experienced their last major merger in the first half of the history of the Universe is $\approx 50\%$ higher for the constrained pairs. These results have been estimated to be significant at the $99\%$ confidence level by means of a Kolmogorov-Simirnov test. These results suggest that the particular environment in which the Milky Way and Andromeda form plays a role in shaping their properties, and favours earlier formation and last major merger time values in agreement with other observational and theoretical considerations.
Extensive cryptic diversity of giant clams (Cardiidae: Tridacninae) revealed by DNA-sequence-based species delimitation approaches with new data from Hainan Island, South China Sea
Authors: Liu Jun , Cui Dan , Wang Hui , Chen Jiawei , Liu Helu , Zhang Haibin
Published: November 2019

Accurate species delimitation is important, especially for endangered species. As one of the most conspicuous bivalve taxa, giant clams are threatened throughout their geographic range. Many phylogeographic studies have revealed strong population structure among giant clams in the Indo-Pacific, suggesting cryptic diversity within these species. However, less attention has been paid to their identification and delimitation. In this study, we assembled a comprehensive dataset of mitochondrial cytochrome c oxidase subunit I (COI) sequences for Tridacna species, focusing on new sequences from Hainan Island in the South China Sea and previously published ones from Japan, Taiwan, Singapore, the Philippines, Indonesia, Australia, the Solomon Islands and the Red Sea. Three nominal species, Tridacna crocea, T. squamosa and T. noae, were recognized at Hainan Island on the basis of distance-based DNA barcoding, with mean interspecific K2P distances of 10.6–24.7% for seven Tridacna species (T. crocea, T. squamosa, T. noae, T. maxima, T. mbalavuana, T. derasa and T. gigas). The most abundant species, T. noae, represents the first record of this species from Hainan Island. Using a combination of phylogenetic and DNA-based species delimitation analyses (automatic barcode gap discovery, generalized mixed Yule coalescent and Bayesian Poisson tree processes), we found strong support for a total of 13 operational taxonomic units (OTUs) for the seven nominal Tridacna species. These results, coupled with the fact that each OTU occupies different regions in the Indo-Pacific, strongly suggest multiple cryptic species of giant clams. Our findings point to the need for taxonomic revisionary work on giant clams throughout the Indo-Pacific; such work will have important conservation implications.
BioModels—15 years of sharing computational models in life science
Authors: Malik-Sheriff Rahuman S , Glont Mihai , Nguyen Tung V N , Tiwari Krishna , Roberts Matthew G , Xavier Ashley , Vu Manh T , Men Jinghao , Maire Matthieu , Kananathan Sarubini , Fairbanks Emma L , Meyer Johannes P , Arankalle Chinmay , Varusai Thawfeek M , Knight-Schrijver Vincent , Li Lu , Dueñas-Roca Corina , Dass Gaurhari , Keating Sarah M , Park Young M , Buso Nicola , Rodriguez Nicolas , Hucka Michael , Hermjakob Henning
Published: November 2019

Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform allows submission of models encoded in diverse modelling formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication. The curation also involves encoding models in standard formats and annotation with controlled vocabularies following MIRIAM (minimal information required in the annotation of biochemical models) guidelines. BioModels now accepts large-scale submission of auto-generated computational models. With gradual growth in content over 15 years, BioModels currently hosts about 2000 models from the published literature. With about 800 curated models, BioModels has become the world’s largest repository of curated models and emerged as the third most used data resource after PubMed and Google Scholar among the scientists who use modelling in their research. Thus, BioModels benefits modellers by providing access to reliable and semantically enriched curated models in standard formats that are easy to share, reproduce and reuse.