bluuebunny/crossref_metadata_2025_split huggingface dataset:
From metabarcoding to metaphylogeography: separating the wheat from the chaff
Authors: Turon Xavier , Antich Adrià , Palacín Creu , Præbel Kim , Wangensteen Owen Simon 
Published: May 2019

AbstractMetabarcoding is by now a well-established method for biodiversity assessment in terrestrial, freshwater and marine environments. Metabarcoding datasets are usually used for α- and β-diversity estimates, that is, interspecies (or inter-MOTU) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra-MOTU) information - mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding datasets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field which we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra-MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co-occurrence patterns of sequences. Using a dataset of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two-step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole dataset. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between-seas component as well. There were inter-group differences in the amount of variability between and within communities in each sea. For two species the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra- and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.
Temporally coherent perturbation of neural dynamics during retention alters human multi-item working memory
Authors: Li Jiaqi , Huang Qiaoli , Han Qiming , Mi Yuanyuan , Luo Huan 
Published: May 2019

SummaryTemporarily storing a list of items in working memory (WM), a fundamental ability in cognition, has been posited to rely on the temporal dynamics of multi-item neural representations during retention. Here, we develop a “dynamic perturbation” approach to manipulate the relative memory strength of a list of WM items, by interfering with their neural dynamics during the delay period in a temporally correlated way. Six experiments on human subjects confirm the effectiveness of this WM manipulation method. A computational model combining continuous attractor neural network (CANN) and short-term synaptic plasticity (STP) principles further reproduces all the empirical findings. The model shows that the “dynamic perturbation” modifies the synaptic efficacies of WM items through STP principles, eventually leading to changes in their relative memory strengths. Our results support the causal role of temporal dynamics of neural network in mediating multi-item WM and offer a promising, non-invasive approach to manipulate WM.
Integration of Structured Biological Data Sources using Biological Expression Language
Authors: Hoyt Charles Tapley , Domingo-Fernández Daniel , Mubeen Sarah , Llaó Josep Marin , Konotopez Andrej , Ebeling Christian , Birkenbihl Colin , Muslu Özlem , English Bradley , Müller Simon , de Lacerda Mauricio Pio , Ali Mehdi , Colby Scott , Türei Dénes , Palacio-Escat Nicolàs , Hofmann-Apitius Martin 
Published: May 2019

AbstractBackgroundThe integration of heterogeneous, multiscale, and multimodal knowledge and data has become a common prerequisite for joint analysis to unravel the mechanisms and aetiologies of complex diseases. Because of its unique ability to capture this variety, Biological Expression Language (BEL) is well suited to be further used as a platform for semantic integration and harmonization in networks and systems biology.ResultsWe have developed numerous independent packages capable of downloading, structuring, and serializing various biological data sources to BEL. Each Bio2BEL package is implemented in the Python programming language and distributed through GitHub (https://github.com/bio2bel) and PyPI.ConclusionsThe philosophy of Bio2BEL encourages reproducibility, accessibility, and democratization of biological databases. We present several applications of Bio2BEL packages including their ability to support the curation of pathway mappings, integration of pathway databases, and machine learning applications.TweetA suite of independent Python packages for downloading, parsing, warehousing, and converting multi-modal and multi-scale biological databases to Biological Expression Language
Hierarchical transcriptional control regulatesPlasmodium falciparumsexual differentiation
Authors: van Biljon Riëtte , van Wyk Roelof , Painter Heather J. , Orchard Lindsey , Reader Janette , Niemand Jandeli , Llinás Manuel , Birkholtz Lyn-Marie 
Published: May 2019

AbstractMalaria pathogenesis relies on sexual gametocyte forms of the malaria parasite to be transmitted between the infected human and the mosquito host but the molecular mechanisms controlling gametocytogenesis remains poorly understood. Here we provide a high-resolution transcriptome ofPlasmodium falciparumas it commits to and develops through gametocytogenesis. The gametocyte-associated transcriptome is significantly different from that of the asexual parasites, with dynamic gene expression shifts characterizing early, intermediate and late-stage gametocyte development and results in differential timing for sex-specific transcripts. The striking transcriptional dynamics suggest strict transcriptional control during gametocytogenesis inP. falciparum, which we propose is mediated by putative regulators including epigenetic mechanisms (driving active repression of proliferation-associated processes) and a cascade-like expression of ApiAP2 transcription factors. The gametocyte transcriptome serves as the blueprint for sexual differentiation and will be a rich resource for future functional studies on this critical stage ofPlasmodiumdevelopment, as the intraerythrocytic transcriptome has been for our understanding of the asexual cycle.
The determinants of aggregate and dis-aggregated import demand in Ghana
Authors: Vacu Nomfundo Portia , Odhiambo Nicholas 
Published: May 2019

Purpose
The purpose of this paper is to examine the determinants of aggregate and dis-aggregated import demand for Ghana for the period from 1985 to 2015.

Design/methodology/approach
The study employed the autoregressive distributed lag bounds testing approach.

Findings
The long-run finding show that aggregate import demand (AIMD) is positively determined by exports of goods and services and consumer spending, but negatively determined by foreign exchange reserves. It is found that consumer spending is the key positive determinant of the import demand of consumer goods, while foreign exchange reserves, trade liberalisation policy and relative import price are negative determinants. It is found that import demand of intermediate goods is positively determined by consumer spending, government spending and investment spending. The long-run findings further confirm that import demand of capital goods is negatively determined by relative import price. In the short run, the findings suggest that AIMD is positively affected by exports of goods and services, investment spending and consumer spending, but negatively affected by foreign exchange reserves. Import demand of consumer goods is positively influenced by consumer spending, but negatively determined by relative import price. Finally, import demand for intermediate goods is found to be positively determined by investment spending and government spending, while import demand for capital goods is positively associated with exports of goods and services and trade liberalisation policy in the previous period.

Originality/value
A number of studies have looked at the determinants of import demand, focussing on the aggregated import demand. This study adds the component of dis-aggregated import demand, as it assist in dealing with the issues of bias.
Must attic ventilation be preserved in energy retrofits?
Authors: Rose William 
Published: May 2019

Purpose
The addition of thermal insulation into attics along with air-tightening of the ceiling plane is a common first step in making homes more energy efficient. Attic ventilation was introduced decades ago on the assumption that air leakage across the ceiling was inevitable and not correctible – this was before the era of spray-applied foams. Often attic ventilation is provided at roof eaves, and ensuring good insulation in their location is critical to avoid cold corners in the rooms below. So may vents be blocked in the course of energy retrofits? The paper aims to discuss this issue.

Design/methodology/approach
This study consists of a simple spreadsheet model of attic performance. The model is built using material from ASHRAE Handbook Fundamentals and ASHRAE Standards. It includes: Glaser calculations for temperature, vapor pressure and vapor pressure excess; radiation exchange – solar and sky; buoyancy flow assumption for leakage from indoors; wind flow assumption for leakage from outdoors; and change in attic air RH as assumed indicator of change in sheathing moisture performance.

Findings
The model results show that lowered moisture contributions across air-tightened ceilings may compensate effectively for added insulation (which lowers the attic air temperature) and reduced moisture dilution from attic ventilation.

Originality/value
These results provide support for the policy of allowing attic ventilation reductions that are proportionate to ceiling air leakage reductions as part of weatherization efforts. Given the limitations of the model, continued field observations remain critical.
Banking regulation - burden or blessing?
Authors: Abildgren Kim 
Published: May 2019

Purpose
The purpose of this paper is to explore the impact of regulation on previously unregulated banks’ balance-sheet growth using the 1880 Danish Savings Bank Act as a natural experiment. With the Act, Danish savings banks became, for the first time, subject to regulation and supervision whereas commercial banks continued as unregulated institutions.

Design/methodology/approach
The main elements of the Act focussed on supervision and provisions to improve information transparency. The paper estimates the impact of the Act on the balance-sheet growth of Danish savings banks using bank-level panel data and a difference-in-differences approach.

Findings
The paper finds no indications that the Act had a negative effect on the balance-sheet growth of savings banks compared to commercial banks in the short run. Furthermore, there are indications of a positive effect after a couple of years. This suggests that regulation is not always a burden for the regulated institutions and might even have a positive impact on their business activity.

Originality/value
This paper is the first study using the introduction of banking supervision and regulation in the 1800s as a natural experiment to evaluate the causal effect of regulation on the balance-sheet growth of previously unregulated financial intermediaries.
The colour stability of natural blue dye extracted from Clitoria ternatea L. in poly(acrylamide-co-acrylic acid) coating film
Authors: Abidin Z.H.Z. , Manah N.S.A. , Hadi A.N. , Saugi N.S. , Fuad F.A. , Mazni N.A. , Hassan H.C. , Careem M.A. , Arof A.K. 
Published: May 2019

Purpose
This paper aims to focus on a comparison study of the visible stability of natural blue dye consisting anthocyanin molecules extracted from Clitoria ternatea in coating films.

Design/methodology/approach
The coating films were prepared by mixing the blue dye with poly(acrylamide-co-acrylic acid) in three different weight ratios. Samples were coded as 10PBA, 15PBA and 20PBA, where PBA is the abbreviation for poly acrylamide-co-acrylic acid, blue dyes and anthocyanin. The number at the beginning of each code represents the weight percentage of poly(acrylamide-co-acrylic acid) to natural blue dye. The mixtures were applied on separate glass substrates to form coating films. Another set of samples were prepared for the comparison study with a commercial acrylic clear coat (cc) applied on the surface of the 10PBA, 15PBA and 20PBA coating films. These coating films were coded 10PBAcc, 15PBAcc and 20PBAcc. The purpose of the clear coat is to observe how it affects the colour stability of the blue coating films with respect to time. All samples were exposed to the ultraviolet (UV) source, an 18 W Philips TL-D 18w/830 UV fluorescent lamp. The UV lamp was placed 15 cm above the surface of the samples for 35 days. The colour of the coatings was measured using CIE L*a*b* colour space coordinate.

Findings
The results obtained show 10PBA and 10PBAcc have the highest colour stability after 35 days of exposure to UV light. The reflectivity of the coating films was also measured during exposure to UV lamp. Reflectivity measurements also showed that 10PBA and 10PBAcc coating films had the highest reflective stabilities.

Research limitations/implications
The potential of using natural blue dye consisting anthocyanin in coating film to obtain high colour stability.

Practical implications
The coating film developed in this work is suitable to be applied on glass substrates.

Originality/value
The application of anthocyanin dye extracted from the Clitoria ternatea L. as a colourant in coating films
Bidens pilosa L.: Exclusive report of vivipary in a non‐mangrove taxa from the eastern Himalayas
Authors: Karmakar Narayan C. , Hazra Anjan , Das Sauren 
Published: May 2019

AbstractVivipary is an extremely evolved type of epigeal germination in seed plants and very common in tropical estuarine plant communities (mangroves), ensuring a greater number of viable settings of offspring. In addition to this, there are some other non‐mangrove angiosperm taxa that have a successful existence, and because of their invasive nature, vivipary has been reported as an attribute of their uncongenial abiotic stress. The present observation confirms the incidence of true vivipary in Bidens pilosa L. (a member of the family Asteraceae) from the eastern Himalayan region.
Decomposing changes in the growth of U.S. prescription drug use and expenditures, 1999‐2016
Authors: Selden Thomas M. , Abdus Salam , Miller G. Edward 
Published: May 2019

AbstractObjectiveTo analyze factors associated with changes in prescription drug use and expenditures in the United States from 1999 to 2016, a period of rapid growth, deceleration, and resumed above‐average growth.Data Sources/Study SettingThe Medical Expenditure Panel Survey (MEPS), containing household and pharmacy information on over five million prescription drug fills.Study DesignWe use nonparametric decomposition to analyze drug use, average payment per fill, and per capita expenditure, tracking the contributions over time of socioeconomic characteristics, health status and treated conditions, insurance coverage, and market factors surrounding the patent cycle.Data Collection/Extraction MethodsMedical Expenditure Panel Survey data were combined with information on drug approval dates and patent status.Principal FindingsPer capita utilization increased by nearly half during 1999‐2016, with changes in health status and treated conditions accounting for four‐fifths of the increase. In contrast, per capita expenditures more than doubled, with individual characteristics only explaining one‐third of the change. Other drivers of spending during this period include the changing pipeline of new drugs, drugs losing exclusivity, and changes in generic competition.ConclusionsLong‐term trends in treated conditions were the fundamental drivers of medication use, whereas factors involving the patent cycle accelerated and decelerated spending growth relative to trends in use.
Cancer risk among patients with type 2 diabetes: A real‐world study in Shanghai, China
Authors: Qi Jiying , He Ping , Yao Huayi , Song Ruogang , Ma Chenglong , Cao Min , Cui Bin , Ning Guang 
Published: May 2019

AbstractBackgroundThe aim of this study was to investigate the risk of 23 common types of cancer among patients with type 2 diabetes (T2D) compared with the general Chinese population.MethodsBased on the Shanghai Hospital Link database, 410 191 patients with T2D (age 20‐99 years) were identified from July 2013 to December 2016, and were followed‐up for cancer incidence until December 2017.ResultsIn all, 8485 cases of newly diagnosed cancer were identified. The standardized incidence ratios (SIRs) of total cancer were 1.34 and 1.62 among males and females, respectively. Among males with T2D, the risk of cancer of the prostate (highest SIR of 1.86), blood (leukemia, lymphoma), skin, thyroid, kidney, liver, pancreas, lung, colorectum, and stomach was increased significantly. There was a significant decrease in the risk of esophageal cancer. In females with T2D, there were significantly greater risks of cancer of the nasopharynx (highest SIR of 2.33), liver, esophagus, thyroid, lung, pancreas, blood (lymphoma, leukemia), uterus, colorectum, breast, cervix, and stomach. In contrast, there was significantly decrease risk of gallbladder cancer in females with T2D.ConclusionsThis study shows significantly increased risks of overall and some site‐specific cancers among patients with T2D. We suggest that establishing strategies for regular cancer‐specific screening and prevention care among patients with T2D are necessary.
A New World Order for the Beer Industry: A Review of the Acquisition of SABMiller by Anheuser‐Busch AB InBev
Authors: Bamber Matthew 
Published: May 2019

ABSTRACTThis case study reviews one of the largest merger and acquisition transactions in corporate history—the acquisition of SABMiller by Anheuser‐Busch InBev. This study provides information to value the post‐transaction combined entity and provide an investment recommendation. Following this, the case discusses the basic details of the funding required to undertake the acquisition and questions which implications of any additional financial risk may arise for AB InBev from a valuation perspective.
Keeping invertebrate research ethical in a landscape of shifting public opinion
Authors: Drinkwater Eleanor , Robinson Elva J. H. , Hart Adam G. 
Published: May 2019

Abstract

Invertebrate study systems are cornerstones of biological and biomedical research, providing key insights into fields from genetics to behavioural ecology. Despite the widespread use of invertebrates in research, there are very few ethical guidelines surrounding their use.

Focussing on two ethical considerations faced during invertebrate studies—collecting methods and euthanasia—we make recommendations for integrating principles of vertebrate research into invertebrate research practice.

We argue, given emerging research on invertebrate cognition and shifting public perception on the use of invertebrates in research, it is vital that the scientific community revisits the ethics of invertebrate use in research.

Without careful consideration and development of the ethics surrounding the use of invertebrates by the scientific community, there is a danger of losing public support. It is imperative that the public understand the significance of research that uses invertebrates and that scientists demonstrate their ethical treatment of their experimental subjects.
Double jeopardy: Comorbid obesity and cigarette smoking are linked to neurobiological alterations in inhibitory control during smoking cue exposure
Authors: Ely Alice V. , Jagannathan Kanchana , Hager Nathan , Ketcherside Ariel , Franklin Teresa R. , Wetherill Reagan R. 
Published: May 2019

AbstractObesity and cigarette smoking are two of the leading preventable causes of death in the United States. Research suggests that overlapping pathophysiology may contribute to obesity and nicotine use disorder (NUD), yet no studies have investigated the effect of obesity on neural response to reward stimuli in NUD. This study used arterial spin‐labeled perfusion functional magnetic resonance imaging (fMRI) to examine neural responses during exposure to smoking versus nonsmoking cues in 79 treatment‐seeking participants with NUD, 26 with normal weight, 28 with overweight, and 25 with obesity. Given that deficits in behavioral inhibitory control have been associated with both obesity and NUD, participants completed an affect‐congruent Go/NoGo task to assess the effect of body mass index (BMI) on this construct in NUD. Analyses revealed that BMI was negatively associated with activation in the right dorsolateral prefrontal cortex (dlPFC) in response to smoking cues, with significantly reduced response in smokers with overweight and smokers with obesity compared with normal‐weight smokers. In addition, greater commission errors on the Go/NoGo task were correlated with reduced neural response to smoking cues in the right dlPFC only among those with obesity. Together, these findings provide evidence that obesity in treatment‐seeking NUDs is related to neurobiological alterations in inhibitory control over cue‐potentiated behaviors, suggesting that smoking cessation may be more difficult in individuals with comorbid NUD and obesity than in those without, requiring treatment strategies tailored to meet their unique needs.
Brain region‐specific neuromedin U signalling regulates alcohol‐related behaviours and food intake in rodents
Authors: Vallöf Daniel , Kalafateli Aimilia Lydia , Jerlhag Elisabet 
Published: May 2019

AbstractAlbeit neuromedin U (NMU) attenuates alcohol‐mediated behaviours, its mechanisms of action are poorly defined. Providing that the behavioural effects of alcohol are processed within the nucleus accumbens (NAc) shell, anterior ventral tegmental area (aVTA), and laterodorsal tegmental area (LDTg), we assessed the involvement of NMU signalling in the aforementioned areas on alcohol‐mediated behaviours in rodents. We further examined the expression of NMU and NMU receptor 2 (NMUR2) in NAc and the dorsal striatum of high compared with low alcohol‐consuming rats, as this area is of importance in the maintenance of alcohol use disorder (AUD). Finally, we investigated the involvement of NAc shell, aVTA and LDTg in the consumption of chow and palatable peanut butter, to expand the link between NMU and reward‐related behaviours. We demonstrated here, that NMU into the NAc shell, but not aVTA or LDTg, blocked the ability of acute alcohol to cause locomotor stimulation and to induce memory retrieval of alcohol reward, as well as reduced peanut butter in mice. In addition, NMU into NAc shell decreased alcohol intake in rats. On a molecular level, we found increased NMU and decreased NMUR2 expression in the dorsal striatum in high compared with low alcohol‐consuming rats. Both aVTA and LDTg, rather than NAc shell, were identified as novel sites of action for NMU's anorexigenic properties in mice based on NMU's ability to selectively reduce chow intake when injected to these areas. Collectively, these data indicate that NMU signalling in different brain areas selectively modulates different behaviours.