bluuebunny/crossref_metadata_2025 huggingface dataset:
A New approximate matching compression algorithm for DNA sequences
Authors: Lázaro-Guevara J.M. , Garrido K.M.
Published: November 2019

1.

Undeveloped countries like Guatemala, where access to high-speed internet connections is limited, downloading and sharing Biological information of thousands of Mega Bits is a huge problem for the beginning and development of Bioinformatics. Based on that information is an urgent necessity to find a better way to share this biological data. There is when the compression algorithms become relevant. With all this information in mind, born the idea of creating a new algorithm using redundancy and approximate selection.

Methods:

Using the probability given by the transition matrix of the three-word tuple and relative frequencies. Calculating the relative and total frequencies given by the permutation formula (nr) and compressing 6 bits of information into 1 implementing the ASCII table code (0…255 characters, 28), using clusters of 102 DNA bases compacted into 17 string sequences. For decompressing, the inverse process must be done, except that the triplets must be selected randomly (or use a matrix dictionary, 4102).

Conclusion:

The compression algorithm has a better compression ratio than LZW and Huffman’s algorithm. However, the time needed for decompressing makes this algorithm incompatible for massive data. The functionality as MD5sum need more research but is a promising helpful tool for DNA checking.
Distinct neural contributions to metacognition for detecting (but not discriminating) visual stimuli
Authors: Mazor Matan , Friston Karl J. , Fleming Stephen M.
Published: November 2019

Being confident in whether a stimulus is present or absent (a detection judgment) is qualitatively distinct from being confident in the identity of that stimulus (a discrimination judgment). In particular, in detection, evidence can only be available for the presence, not the absence, of a target object. This asymmetry suggests that higher-order cognitive and neural processes may be required for confidence in detection, and more specifically, in judgments about absence. In a within-subject, pre-registered and performance-matched fMRI design, we observed quadratic confidence effects in frontopolar cortex for detection but not discrimination. Furthermore, in the right temporoparietal junction, confidence effects were enhanced for judgments of target absence compared to judgments of target presence. We interpret these findings as reflecting qualitative differences between the neural basis of metacognitive evaluation of detection and discrimination, potentially in line with counterfactual or higher-order models of confidence formation in detection.
Climatic niche change of fish is faster at high latitude and in marine environments
Authors: Bourgeaud Luana , Rolland Jonathan , Carvajal-Quintero Juan David , Jézéquel Céline , Tedesco Pablo A. , Murienne Jérôme , Grenouillet Gaël
Published: November 2019

Change in species’ climatic niches is a key mechanism influencing species distribution patterns. The question of which factors impact niche change remains a highly debated topic in evolutionary biology. Previous studies have proposed that rates of climatic niche change might be correlated with climatic oscillations at high latitude or adaptation to new environmental conditions. Yet, very few studies have asked if those factors are also predominant in aquatic environments. Here, we reconstruct the climatic niche changes of fish species on a new phylogeny encompassing 12,616 species. We first confirm that the rate of niche change is faster at high latitude and show that this association is steeper for freshwater than for marine species. We also show that freshwater species have slower rates of niche change than marine species. These results may be explained by the fact that freshwater species have larger climatic niche breadth and thermal safety margin than marine species at high latitude. Overall, our study sheds a new light on the environmental conditions and species features impacting rates of climatic niche change in aquatic habitats.
Spexin and a novel cichlid-specific spexin paralog both inhibit FSH and LH through a specific galanin receptor (Galr2b) in tilapia
Authors: Cohen Yaron , Hausken Krist , Bonfil Yoav , Gutnick Michael , Levavi-Sivan Berta
Published: November 2019

Spexin (SPX) is a 14 amino acid peptide hormone that has pleiotropic functions across vertebrates, one of which is involvement in the brain-pituitary-gonad axis of fish. SPX(1) has been identified in each class of vertebrates, and a second SPX (named SPX2) has been found in some non-mammalian species. We have cloned two spexin paralogs, designated as Spx1a and Spx1b, from Nile tilapia (Oreochromis niloticus) that have varying tissue distribution patterns. Spx1b is a novel peptide only identified in cichlid fish, and is more closely related to Spx1 than Spx2 homologs as supported by phylogenetic, synteny, and functional analyses. Kisspeptin, Spx, and galanin (Gal) peptides and their corresponding kiss receptors and Gal receptors (Galrs), respectively, are evolutionarily related. Cloning of six tilapia Galrs (Galr1a, Galr1b, Galr2a, Galr2b, Galr type 1, and Galr type 2) and subsequentin vitrosecond-messenger reporter assays for Gαs, Gαq, and Gαisuggests that Gal and Spx activate Galr1a/Galr2a and Galr2b, respectively. A decrease in plasma follicle stimulating hormone and luteinizing hormone concentrations was observed with injections of Spx1a or Spx1bin vivo. Additionally, application of Spx1a to pituitary slices decreased the firing rate of LH cells, suggesting direct inhibition at the pituitary level. These data collectively suggest an inhibitory mechanism of action against the secretion of gonadotropins for a traditional and a novel spexin paralog in cichlid species.
Inhibition of gonadotropin-stimulated steroidogenesis by the erk cascade
Authors: Seger Rony , Hanoch Tamar , Rosenberg Revital , Dantes Ada , Merz Wolfgang E. , Strauss Jerome F. , Amsterdam Abraham
Published: November 2019

LH and FSH are two important hormones in the regulation of granulosa cells. Their effects are mediated mainly by cAMP/PKA signaling, bit the activity of the extracellular signal-regulated kinase (ERK) signaling cascade is elevated as well. We studied the involvement of the ERK cascade in LH and FSH-induced steroidogenesis in two granulosa-derived cell lines, rLHR-4 and rFSHR-17, respectively. We found that stimulation of these cells with the appropriate gonadotropin induced ERK activation as well as progesterone production, downstream of PKA. Inhibition of ERK activity enhanced gonadotropin-stimulated progesterone production, which was correlated with increased-expression of the steroidogenic acute regulatory (StAR) protein, a key regulator of progesterone synthesis. Therefore, it is likely that gonadotropin-stimulated progesterone formation is regulated by a pathway that includes PKA and StAR, and this process is downregulated by ERK, due to attenuation of StAR expression. Our results suggest that activation of PKA signaling by gonadotropins not only induces steroidogenesis, but also activates downregulation machinery involving the ERK cascade. The activation of ERK by gonadotropins as well as by other agents, may be a key mechanism for the modulation of gonadotropin-induced steroidogenesis.
Event-related dynamics of brain oscillations during perception of verbal information in patients with paranoid schizophrenia
Authors: Garakh Zhanna V. , Larionova Ekaterina V.
Published: November 2019

We studied the evoked changes in brain rhythmic activity during reading semantic (words) and meaningless verbal information (pseudowords) in patients with paranoid schizophrenia (n= 40) and in control group of healthy subjects (n= 64). Patients with paranoid schizophrenia showed the decrease in the event-related synchronization (ERS) of alpha and theta rhythms compared to controls when reading semantic verbal information. Reduced event-related synchronization of the alpha rhythm in time window 105 – 145 ms may be associated with the severity of hallucinations (P3 scale) by PANSS. In contrast to the control group, the patients had no differences in the gamma range when reading words and pseudowords. This fact may indicate that patients with paranoid schizophrenia assign significance to those stimuli that are not normally considered as significant (pseudowords).
Visual landmarks calibrate auditory space across eye movements
Authors: Aagten-Murphy David , Szinte Martin , Taylor Robert , Deubel Heiner
Published: November 2019

Visual objects that are present both before and after eye movements can act as landmarks, aiding localization of other visual stimuli. We investigated whether visual landmarks would also influence auditory localization – despite participants’ head position remaining unchanged. Participants made eye-movements from central fixation to a peripheral visual landmark, which either remained stationary or was covertly displaced. Following the movement, participants judged whether a stimulus (auditory or visual) was shifted in location relative to before the movement. Visual localization estimates shifted along with the landmark, although the landmark displacement itself went unnoticed. Interestingly, auditory localization estimates were also displaced. Thus, despite identical auditory input reaching the ears, two auditory stimuli originating from the same position were perceived as spatially distinct when the visual landmark moved. These results are consistent with the idea that auditory spatial information is encoded within an eye-centered reference frame and subject to spatial recalibration by visual landmarks.

Highlights

Visual landmarks affect stimulus localization across eye movements

We show this also for auditory stimuli, even when the head remains stable

Due to a visual landmark displacement, identical auditory stimuli are perceived as shifted

This suggests that auditory space is calibrated on eye-centered maps across saccades
Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach
Authors: Kuwahara Hiroyuki , Gao Xin
Published: November 2019

Two-dimensional (2D) chemical fingerprints are widely used as numerical features for the quantification of structural similarity of chemical compounds, which is an important step in similarity-based virtual screening (VS). Here, using an eigenvalue-based entropy approach, we sought to identify 2D fingerprints with little to no contribution to shaping the eigenvalue distribution of the feature matrix as related fingerprints and examined the degree to which these related 2D fingerprints influence molecular similarity scores via Tanimoto coefficient. We found that there are many related fingerprints in publicly available fingerprint schemes and that their presence in the feature set tends to decrease the similarity scores. Our results have implication in the optimal selection of 2D fingerprints and the identification of potential hits for compounds with target biological activity in VS.
On the spillover effect and optimal size of marine reserves for sustainable fishing yields
Authors: Takashina Nao
Published: November 2019

Marine reserves are an essential component of modern fishery management. Marine reserves, which represent a management tradeoff between harvesting and conservation, are fundamental to maintenance of fisheries. Finding optimal reserve sizes that improve fishing yields is not only of theoretical interest, but also of practical importance to facilitate decision making. Also, since the migratory behavior of some species influences the spillover effect of a marine reserve, this is a key consideration when assessing performance of marine reserves. The relationship between optimal reserve size and migration rate/mode has not been well studied, but it is fundamental to management success. Here, I investigate optimal reserve size and its management outcome with different levels of spillover via a simple two-patch mathematical model. In this model, one patch is open to fishing, and the other is closed. The two-patch model is aggregated by single-population dynamics when the migration rate is sufficiently larger than the growth rate of a target species. At this limit, I show that an optimal reserve size exists when pre-reserve fishing occurs at fishing mortality larger thanfMSY, the fishing mortality at the maximum sustainable yield (MSY). Also, the fishing yield at an optimal reserve size becomes as large as MSY at the limit. Numerical simulations at various migration rates between the two patches suggest that the maximum harvest under management with a marine reserve is achieved at this limit. This contrasts with the conservation benefit which is maximized at an intermediate migration rate. Numerical simulations show that the above-mentioned condition derived from the aggregated model is necessary when the migration rate is not sufficiently large, and that a moderate migration rate is further necessary for an optimal reserve size to exist. However, high fishing mortality reduces this requirement.
Dynamics of host glutathione and glutathione related enzymes in Macrophomina phaseolina-sorghum bicolor interaction
Authors: Bandara Ananda Y. , Weerasooriya Dilooshi K. , Liu Sanzhen , Little Christopher R.
Published: November 2019

Glutathione and its related enzymes play an integral role in cellular detoxification processes and redox buffering. A genome wide transcriptome profiling was conducted through RNA sequencing to investigate the dynamics of glutathione and related enzymes in sorghum bicolor (L.) Moench in response to Macrophomina phaseolina (MP) infection. Compared to mock inoculated control treatment, MP significantly upregulated the glutathione synthetase, glutamate cysteine ligase (involved in glutathione biosynthesis), glutathione s-transferase (GST), glutathione peroxidase (GPX), and glutathione reductase (GR) genes in a charcoal rot susceptible sorghum genotype (Tx7000), but not in a resistant genotype (SC599) at 7 days post- inoculation. The net log2 fold up-regulation of the aforesaid genes in MP-inoculated Tx7000 was 1.9, 0.9, 120.0, 9.0, and 4.5, respectively. To confirm the gene expression data, cell extracts were acquired from MP- and mock-inoculated resistant (SC599, SC35) and susceptible (Tx7000, BTx3042) sorghum genotypes and their reduced (GSH), oxidized (GSSG) glutathione, GST, GPX, and GR activities were measured using standard protocols. A significantly reduced GSH/GSSG ratio was observed in Tx7000 and BTx3042 indicating the strong oxidative stress experienced by charcoal rot susceptible genotypes under MP infection. MP significantly increased the GST, GPX, and GR activities of Tx7000 and BTx3042. Although augmented GR activity contributes to cellular GSH restoration, the enhanced GST activity leads to diminishing GSH pools through vacuolar sequestration of GSH-S-conjugates. This eases the oxidative stress confronted by susceptible genotypes under MP infection and in turn contributes to reduced charcoal rot susceptibility. The importance of GSH in controlling the MP infection associated oxidative stress was further supported by the significantly reduced disease severity observed in Tx7000 and BTx3042 upon exogenous GSH application.
CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single-cells
Authors: Perez-Rathke Alan , Sun Qiu , Wang Boshen , Boeva Valentina , Shao Zhifeng , Liang Jie
Published: November 2019

Chromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions can play important roles in condensing super-enhancer regions into a cohesive transcriptional apparatus. Chromosome conformation studies using Hi-C are limited to pairwise, population-averaged interactions; therefore, not suitable for direct assessment of many-body interactions. We describe a computational model, CHROMATIX, that reconstructs structural ensembles based on Hi-C data and identifies significant many-body interactions. For a diverse set of highly-active transcriptional loci with at least 2 super-enhancers, we detail the many-body functional landscape and show DNase-accessibility, POLR2A binding, and decreased H3K27me3 are predictive of interaction-enriched regions.
Addressing dereplication crisis: Taxonomy-free reduction of massive genome collections using embeddings of protein content
Authors: Viehweger A. , Hoelzer M. , Brandt C.
Published: November 2019

Many recent microbial genome collections curate hundreds of thousands of genomes. This volume complicates many genomic analyses such as taxon assignment because the associated computational burden is substantial. However, the number of representatives of each species is highly skewed towards human pathogens and model organisms. Thus many genomes contain little additional information and could be removed. We created a frugal dereplication method that can reduce massive genome collections based on genome sequence alone, without the need for manual curation nor taxonomic information.

We recently created a genome representation for bacteria and archaea called “nanotext”. This method embeds each genome in a low-dimensional vector of numbers. Extending nanotext, our proposed algorithm called “thinspace” uses these vectors to group and dereplicate similar genomes.

We dereplicated the Genome Taxonomy Database (GTDB) from about 150 thousand genomes to less than 22 thousand. The resulting collection increases the percent of classified reads in a metagenomic dataset by a factor of 5 compared to NCBI RefSeq and performs equal to both a larger as well as a manually curated GTDB subset.

With thinspace, massive genome collections can be dereplicated on regular hardware, without affecting downstream results. It is released under a BSD-3 license (github.com/phiweger/thinspace).
How and when AR technology affects product attitude
Authors: Xu Lan , Zhang Lei , Cui Nan , Yang Zhilin
Published: November 2019

Purpose

Augmented reality (AR) has emerged as a novel communication tool, which adds virtual computer-generated information to a viewer’s real life. The purpose of this paper is to investigate the effect of AR technology on consumers’ experience.

Design/methodology/approach

Four experiments were performed to test the effect of AR-based product display on the consumer’s attitude and the underlying mechanism of the effect.

Findings

The results have demonstrated that self-referencing reality simulation mediates the effect of AR technology on consumers’ product attitude, and the effect is attenuated when the consumers hold quality beliefs rather than taste beliefs or when the product is a luxury brand.

Practical implications

The current research suggests that managers should develop and adopt AR technology when presenting their products in front of consumers, which can improve consumers’ product attitude. Additionally, emphasizing the taste of target products rather than quality will strengthen the positive effect of AR technology on product attitude. Furthermore, managers of luxury brands should present their products in a traditional way, which induce an exclusive perception rather than using AR technology.

Originality/value

This paper investigates the underlying mechanism of how AR technology improves consumers’ product attitude and shopping experience, to fill the gap in consumers’ unique experience with AR technology. Furthermore, the moderated effect of consumer beliefs and product difference has also been examined in this study, which attributes to the research of product differentiation.
Demand management: the role of cross-functional integration in a context of political turbulence
Authors: Freitas Marlos Rocha de , Pimenta Márcio Lopes , Hilletofth Per , Jugend Daniel , Oprime Pedro Carlos
Published: November 2019

Purpose

The purpose of this study is to investigate how cross-functional integration supports the execution of the demand-side processes and its effects on both the demand and supply-side processes.

Design/methodology/approach

A case study was conducted including a Brazilian multinational manufacturer in the automobile industry and some of its suppliers and dealers. 17 interviews were conducted. A theoretical framework is proposed containing five basic elements, they are: characteristics of the demand/supply processes; involved functions; integration factors; context influencers and impacts of integration on demand and supply processes.

Findings

The findings present three demand-side processes (Product Launch, Marketing and Sales and Demand Planning) that demonstrated a greater need for cross-functional integration in the studied case, mainly through informal integration factors.

Research limitations/implications

The empirical results of this study have methodological limitations due to the use of the case study method. Future research should analyze the effects of other context influencers (e.g. natural catastrophes, civil wars and low level of unemployment) on cross-functional integration.

Practical implications

The results highlight that joint planning, willingness to work together, team spirit, adequate communication and cross-functional meetings helped the studied organizations to achieve competitive advantages and improve their performance.

Originality/value

This study provides a theoretical framework that helped to improve the understanding of the interrelationships between demand management constructs and cross-functional integration factors. There are indications that a political–economic crisis has stimulated the existence of a willingness to work together and group spirit among employees who remain in the organization after mass dismissals. This climate of cooperation helped to increase the agility and resilience of the studied supply chain, which is currently affected by a changing market.
Generalized software release and testing stop time policy
Authors: Shrivastava Avinash Kumar , Sachdeva Nitin
Published: November 2019

Purpose

Almost everything around us is the output of software-driven machines or working with software. Software firms are working hard to meet the user’s requirements. But developing a fault-free software is not possible. Also due to market competition, firms do not want to delay their software release. But early release software comes with the problem of user reporting more failures during operations due to more number of faults lying in it. To overcome the above situation, software firms these days are releasing software with an adequate amount of testing instead of delaying the release to develop reliable software and releasing software patches post release to make the software more reliable. The paper aims to discuss these issues.

Design/methodology/approach

The authors have developed a generalized framework by assuming that testing continues beyond software release to determine the time to release and stop testing of software. As the testing team is always not skilled, hence, the rate of detection correction of faults during testing may change over time. Also, they may commit an error during software development, hence increasing the number of faults. Therefore, the authors have to consider these two factors as well in our proposed model. Further, the authors have done sensitivity analysis based on the cost-modeling parameters to check and analyze their impact on the software testing and release policy.

Findings

From the proposed model, the authors found that it is better to release early and continue testing in the post-release phase. By using this model, firms can get the benefits of early release, and at the same time, users get the benefit of post-release software reliability assurance.

Originality/value

The authors are proposing a generalized model for software scheduling.
Experimental study on the effect of pressure and flow rate on cavitation in a poppet throttle valve
Authors: Zhang Jian , Luo Tingting
Published: November 2019

Purpose

The purpose of this paper is to study the variation of cavitation scale with pressure and flow in poppet throttle valve, to obtain the cavitation scale under pressure and flow conditions and to provide experimental support for the research of suppressing throttle valve cavitation and cavitation theory.

Design/methodology/approach

A hydraulic cavitation platform was set up, a valve was manufactured with highly transparent PMMA material and a high-speed camera was used to observe the change in cavitation scale.

Findings

Through experiments, it is found that the pressure difference between inlet and outlet of throttle valve affects the cavitation scale, and the more the pressure difference is, the easier the cavitation will be formed. Under the condition of small pressure difference, the cavitation is not obvious and reducing the pressure difference can effectively suppress the cavitation; the flow rate also affects the cavitation scale, the smaller the flow rate, the more difficult the cavitation will be formed and the lower the flow rate, the more the cavitation will be suppressed.

Research limitations/implications

Because of the magnification factor of the high-speed camera lens, the morphology of smaller bubbles cannot be observed in this study, and the experimental conditions need to be improved in the follow-up study.

Originality/value

This study can provide experimental support for the study of throttle valve cavitation suppression methods and cavitation theory.
Dynamics of income diversification and bank performance in India
Authors: Vidyarthi Harishankar
Published: November 2019

Purpose

The purpose of this paper is to examine the dynamics between income diversification and performance (cost, profit, revenue, technical, pure technical and scale efficiency) for 38 listed Indian banks within panel data framework during the period 2004-2005 to 2015-16.

Design/methodology/approach

This study computes bank’s cost, profit, revenue, technical, pure technical and scale efficiency within intermediation approach with data envelopment analysis (DEA) as a performance indicator, followed by exploring the association between income diversification and bank performance using truncated Tobit regression within panel data framework.

Findings

Tobit regression results revealed inverted U-shaped relationship between the income diversification and estimated efficiency parameters for the overall panel. Size and bank intermediation ratio seems to be a major factor in exploiting the potential benefits of income diversification. The author reconfirmed the inverted U-shaped relationship with these efficiency parameters for exclusive subsamples consisting of government-owned and private sector banks.

Research limitations/implications

Inverted U-shaped relationship between the income diversification and estimated efficiency parameters suggest that banks should go for limited diversification to improve performance. Thus, regulators and banks should pursue limited diversification strategy for improving banking efficiency.

Originality/value

This study computes bank performance (cost, profit, revenue, technical, pure technical and scale efficiency) based on DEA followed by exploring the association between performance and income diversification for 38 Bombay stock exchange listed banks.
Service recovery satisfaction in offline and online experiences
Authors: Odoom Raphael , Agbemabiese George Cudjoe , Hinson Robert E.
Published: November 2019

Purpose

Given that the peculiar nature of the internet has introduced new dimensions of service delivery as well as new dimensions of service failures and recovery, the purpose of this paper is to investigate and compare the relationships between recovery strategies and recovery satisfaction within offline and online settings.

Design/methodology/approach

Data for the empirical tests of our hypotheses were collected via offline and online (specifically Facebook and Twitter) samples of customers who have experienced some form of service failure and recovery measures from service providers within the past year.

Findings

The results indicate that recovery strategies largely influence recovery satisfaction among aggrieved customers. However, these are conditional and not invariant across the two settings. In the authors’ offline setting, in particular, apology did not show a statistically significant impact on recovery satisfaction, even though, along with compensation and explanation, this relationship was significant among the online sample.

Originality/value

The study offers practical implications for service managers within emerging economies on the various conditions where they can maximise their service recovery efforts (both offline and online) to generate optimum recovery satisfaction.
Incorporating visitors’ preferences into the policy framework of a Rainforest Discovery Centre
Authors: Francis Fiona Jane , Hassan Azman , Mohd Afandi Syamsul Herman , Radam Alias
Published: November 2019

Purpose

This study aims to incorporate visitors’ preferences for sustainable development into the policy framework of Rainforest Discovery Centre (RDC), Sabah, Malaysia.

Design/methodology/approach

A stated preference technique known as choice experiment (CE) method is used in this study. Four management attributes, namely, information provision (IP), protection level (PL), guided tour (GT) and entrance fee (FEE), were identified as the most relevant aspects of the RDC in Sabah. Two econometrics models which are conditional logit and random parameter logit were estimated to achieve the purpose of the study.

Findings

This study finds that visitors support the proposed development of RDC. The alteration of protection level (i.e. improvement of “PL” attribute) is the most concerning matter among visitors. Since the random parameter logit model revealed that PL is specified as random, the individual heterogeneity exists for PL.

Practical implications

The current issues in ecotourism were studied and integrated into the methodology. A unique and comprehensive policy structure was developed, and enables to respond with any contemporary issues linked to protected areas (PA) without neglecting the natural and cultural endowments.

Originality/value

This study presents an in-depth understanding of visitors’ preferences in the ecotourism industry and used CE as a mechanism tool to explore visitors’ preferences. This study incorporates the conceptualisation of visitors’ preferences and sustainable tourism development into the PA framework structure.
Fungal ecological strategies reflected in gene transcription ‐ a case study of two litter decomposers
Authors: Barbi Florian , Kohler Annegret , Barry Kerrie , Baskaran Preetisri , Daum Chris , Fauchery Laure , Ihrmark Katarina , Kuo Alan , LaButti Kurt , Lipzen Anna , Morin Emmanuelle , Grigoriev Igor V. , Henrissat Bernard , Lindahl Björn D. , Martin Francis
Published: November 2019

Microbial communities interplay with their environment through their functional traits that can be a response or an effect on the environment. Here, we explore how a functional trait—the decomposition of organic matter, can be addressed based on genetic markers and how the expression of these markers reflect ecological strategies of two fungal litter decomposer Gymnopus androsaceus and Chalara longipes. We sequenced the genomes of these two fungi, as well as their transcriptomes at different steps of Pinus sylvestris needles decomposition in microcosms. Our results highlighted that if the gene content of the two species could indicate similar potential decomposition abilities, the expression levels of specific gene families belonging to the glycoside hydrolase category reflected contrasting ecological strategies. Actually, C. longipes, the weaker decomposer in this experiment, turned out to have a high content of genes involved in cell wall polysaccharides decomposition but low expression levels, reflecting a versatile ecology compare to the more competitive G. androsaceus with high expression levels of keystone functional genes. Thus, we established that sequential expression of genes coding for different components of the decomposer machinery indicated adaptation to chemical changes in the substrate as decomposition progressed.
Reeling in Newcomers: Urban Competition around Migrant Reception in Brussels
Authors: Swyngedouw Eva
Published: November 2019

The management of ethnic diversity and its various forms of institutional articulation and implementation are increasingly taking place at the urban level. At the same time, urban scholars consider cities to be battlegrounds where competing groups contest the meaning and articulation of citizenship. In this article, I build on these insights to argue that competition over newcomer reception between different, linguistically divided political coalitions in the city of Brussels are mainly battles over establishing their own definition of citizenship and asserting their political influence. Building on an eighteen‐month ethnographic study in three reception offices (two Dutch‐speaking and one francophone) in Brussels, I analyse the different strategies these offices mobilize to recruit and retain newcomers. I argue that recruitment is a deliberate tool used to influence the political‐cultural demographics of the city and destabilize the linguistic power balance in Brussels. In this way, recruitment becomes a means to attract newcomers to the reception offices in the hope that they will develop a deep connection and loyalty to, and eventually identify politically with, the agency's respective political community. Theoretically, this article develops a perspective that regards the city as a field that becomes constituted in and through the contest between different urban institutions to ‘reel in’ newcomers. In this space, these institutions take up positions for and against each other and assemble strategies to influence the urban populations.
Alcohol consumption and alcohol policy in Estonia 2000–2017 in the context of Baltic and Nordic countries
Authors: Pärna Kersti
Published: November 2019

Introduction and Aims

Alcohol consumption has become a global health threat and there is need for an evidence‐based global alcohol policy. This study aimed to describe alcohol consumption in parallel with alcohol policy in 2000–2017 in Estonia in the context of Baltic and Nordic countries.

Design and Methods

A review of routine statistics concerning alcohol consumption and the pertinent legislation in Estonia was performed. The measures used to assess the effects of alcohol policy were adult (15 and older) pure alcohol per capita consumption (APC) in litres, alcohol outlet densities and opening hours, taxes and the price of alcoholic beverages.

Results

Adult domestic APC in Estonia increased from 9.3 to 14.8 in 2000–2007 and thereafter decreased to 10.2 in 2016 (10.3 in 2017). Adult APC in Estonia was lower than that in Latvia and Lithuania but higher than that in Nordic countries. Since 2010, beer has been the most prevalent alcoholic beverage in Estonia. The density and opening hours of alcohol retail shops were much higher in Estonia and other Baltic countries than in Nordic countries. The alcohol retail price increased twice from 2006 to 2017 in Estonia, resulting in a double price difference with Latvia.

Discussion and Conclusions

Evidence‐based comprehensive alcohol policy should continue in Estonia. Based on the example of Nordic countries, more attention should be paid to the physical availability of alcohol in Estonia. In terms of economic availability, it is important to focus on the cross‐border alcohol trade to achieve improvements in public health.
Comparison of endoscopic visibility and miss rate for early gastric cancers after Helicobacter pylori eradication with white‐light imaging versus linked color imaging
Authors: Kitagawa Yoshiyasu , Suzuki Takuto , Nankinzan Rino , Ishigaki Asuka , Furukawa Kiyoto , Sugita Osamu , Hara Taro , Yamaguchi Taketo
Published: November 2019

Background and Aim

We aimed to investigate whether linked color imaging (LCI) improves endoscopic visibility of early gastric cancers (EGC) after Helicobacter pylori eradication, which are often difficult to detect, and reduces the miss rate when compared with white‐light imaging (WLI).

Methods

The visibility study used two images, one each with WLI and LCI, from 84 consecutive EGC after H. pylori eradication. Endoscopic visibility was evaluated using a visibility score and color difference (CD) value. To analyze miss rates, we studied a library of recorded videos using both WLI and LCI for 70 other consecutive patients after H. pylori eradication, among whom 19 had EGC. Endoscopic screening was done using the same protocol to map the entire stomach. Six endoscopists reviewed the videos in a randomized order. Miss rates of EGC were compared among the modalities.

Results

Mean [(±standard deviation) visibility scores with LCI were significantly higher than those with WLI (3.19 ± 0.84 vs 2.52 ± 0.98, P < 0.001), as were mean CD values (26.3 ± 9.1 vs 13.6 ± 6.3, P < 0.001). Miss rates of the six endoscopists were significantly lower with LCI than with WLI (30.7% vs 64.9%, P < 0.001). Both expert and trainee endoscopists had significantly better results with LCI than with WLI.

Conclusions

Linked color imaging significantly improved the visibility of EGC after H. pylori eradication compared with WLI using both subjective and objective criteria. Furthermore, LCI significantly reduced miss rates of these lesions compared with WLI.
The perception of the educational environment in multinational students from a dental medicine faculty in Romania
Authors: Stratulat Sorin I. , Candel Octav S. , Tăbîrţă Alisa , Checheriţă Laura E. , Costan Victor V.
Published: November 2019

Introduction

Dental education comes with important challenges for the faculties as well as for the students. Its evolving nature leads to the constant adoption of new practices and techniques. Thus, the learning environment is in continuous development. This study aimed to describe a sample of senior undergraduate student's perceptions of their learning environment.

Methods

Students (both Romanian and international) enrolled in the 6th year at the Faculty of Dental Medicine from a Romanian University completed the Dundee Ready Education Environment Measure (DREEM). The scale measures students' perceptions of the education environment using five domains: Learning, Teaching, Academic self‐perception, Atmosphere and Social self‐perception. Data were analysed using descriptive statistics, non‐parametric and univariate statistics for group comparison.

Results

Participants (N = 259, Romanian = 111, International = 148) had a good perception of their learning environment, with a total DREEM score of 117.82 out of 200. Still, they had a lower score in the areas of Academic and Social self‐perception. The international students had more negative perceptions of the learning environment compared to the Romanian ones. The French‐speaking students had the lowest scores on most of the areas.

Conclusions

Although the perception of medical dentistry education is generally good, international students are not as satisfied with the learning environment. The students' experiences could be improved by providing them with more social support. Also, it is important to address the needs of international students in order to create a more satisfying environment for them.
Tumor load in patients with multiple myeloma: β₂‐microglobulin levels versus low‐dose whole‐body CT
Authors: Pfahler Vanessa , D'Anastasi Melvin , Dürr Hans‐Roland , Schinner Regina , Ricke Jens , Baur‐Melnyk Andrea
Published: November 2019

Objective

Beta‐2‐microglobulin is a serum marker of tumor burden in multiple myeloma (MM). Our aim was to correlate serum β₂‐microglobulin levels in patients with MM to tumor burden determined by low‐dose whole‐body CT (LDWBCT).

Materials and Methods

A total of 52 patients with newly diagnosed, untreated MM who underwent LDWBCT were included. LDWBCT scans were assessed by two musculoskeletal radiologists in consensus for focal lesions. The Durie and Salmon PLUS staging system was used for staging patients in stages I‐III. β₂‐microglobulin was also subdivided into stages I‐III on the basis of the multiple myeloma International Staging System (ISS).

Results

Using the Durie and Salmon PLUS staging system criteria for image evaluation, we were able to identify stage I MM in 17 patients, stage II MM in nine patients, and stage III MM in 26 patients. Eight of nine patients with stage II MM and 16 of 26 patients with stage III MM had normal β₂‐microglobulin levels. Thus, 24 of 35 patients (68.6%) had 5 or more focal lesions and false‐negative β₂‐microglobulin levels.

Conclusion

Serum β₂‐microglobulin levels alone may not indicate the full extent of tumor burden in a significant subset of myeloma patients.
Dynamics of tumor‐specific cfDNA in response to therapy in multiple myeloma patients
Authors: Vrabel David , Sedlarikova Lenka , Besse Lenka , Rihova Lucie , Bezdekova Renata , Almasi Martina , Kubaczkova Veronika , Brožová Lucie , Jarkovsky Jiri , Plonkova Hana , Jelinek Tomas , Sandecka Viera , Stork Martin , Pour Ludek , Sevcikova Sabina , Hajek Roman
Published: November 2019

Objectives

Progress in multiple myeloma treatment allows patients to achieve deeper responses, for which the assessment of minimal residual disease (MRD) is critical. Typically, bone marrow samples are used for this purpose; however, this approach is site‐limited. Liquid biopsy represents a minimally invasive and more comprehensive technique that is not site‐limited, but equally challenging.

Methods

While majority of current data comes from short‐term studies, we present a long‐term study on blood‐based MRD monitoring using tumor‐specific cell‐free DNA detection by ASO‐qPCR. One hundred and twelve patients were enrolled into the study, but long‐term sampling and analysis were feasible only in 45 patients.

Results

We found a significant correlation of quantity of tumor‐specific cell‐free DNA levels with clinically meaningful events [induction therapy (P = .004); ASCT (P = .012)]. Moreover, length of cfDNA fragments is associated with better treatment response of patients.

Conclusions

These results support the concept of tumor‐specific cell‐free DNA as a prognostic marker.
Human‐induced habitat fragmentation effects on connectivity, diversity, and population persistence of an endemic fish, Percilia irwini, in the Biobío River basin (Chile)
Authors: Valenzuela‐Aguayo Francisca , McCracken Gregory R. , Manosalva Aliro , Habit Evelyn , Ruzzante Daniel E.
Published: November 2019

An understanding of how genetic variability is distributed in space is fundamental for the conservation and maintenance of diversity in spatially fragmented and vulnerable populations. While fragmentation can occur from natural barriers, it can also be exacerbated by anthropogenic activities such as hydroelectric power plant development. Whatever the source, fragmentation can have significant ecological effects, including disruptions of migratory processes and gene flow among populations. In Chile, the Biobío River basin exhibits a high degree of habitat fragmentation due to the numerous hydroelectric power plants in operation, the number of which is expected to increase following new renewable energy use strategies. Here, we assessed the effects of different kinds of barriers on the genetic structure of the endemic freshwater fish Percilia irwini, knowledge that is critically needed to inform conservation strategies in light of current and anticipated further fragmentation initiatives in the system. We identified eight genetic units throughout the entire Biobío system with high effective sizes. A reduced effective size estimate was, however, observed in a single population located between two impassable barriers. Both natural waterfalls and human‐made dams were important drivers of population differentiation in this system; however, dams affect genetic diversity differentially depending on their mode of operation. Evidence of population extirpation was found in two river stretches limited by upstream and downstream dams. Significant gene flow in both directions was found among populations not separated by natural or anthropogenic barriers. Our results suggest a significant vulnerability of P. irwini populations to future dam development and demonstrate the importance of studying basin‐wide data sets with genetic metrics to understand the strength and direction of anthropogenic impacts on fish populations.
Population dynamics of roundjaw bonefish Albula glossodonta at a remote coralline Atoll inform community‐based management in an artisanal fishery
Authors: Filous Alexander , Lennox Robert J. , Eveson Paige , Raveino Raphael , Clua Eric E. G. , Cooke Steven J. , Danylchuk Andy J.
Published: November 2019

Fisheries management requires knowledge on the population dynamics of exploited stocks. To that end, the present study used a mark–recapture approach to characterise the population demographics of roundjaw bonefish Albula glossodonta (Forsskål) and their interaction with a data‐limited fishery on Anaa Atoll in the Tuamotu Archipelago of French Polynesia. Over the course of the study, 2,509 bonefish were tagged and 12.3% were recaptured. The L∞ of bonefish was estimated at 71 cm fork length (FL) with a K of 0.17, based on changes in FL between capture events. Artisanal fish traps located in the migratory corridors of the atoll accounted for 94% of recaptures and these movements occurred during the waning moon. Fishing mortality increased as bonefish reach sexual maturity, recruiting to the trap fishery at age 4 with the onset of spawning behaviour. Bonefish abundance between ages 3 and 5 was estimated to be 29,079 individuals. This case study demonstrated the utility of mark–recapture in filling knowledge gaps that impede the management of data‐limited fisheries. Ultimately, these results supported the creation of an Educational Managed Marine Area and the resurgence of rahui (seasonal closure) to manage this fishery.
Differentiation and adaptation of natural killer cells for anti‐malarial immunity
Authors: Goodier Martin R. , Wolf Asia‐Sophia , Riley Eleanor M.
Published: November 2019

Natural killer cells employ a diverse arsenal of effector mechanisms to target intracellular pathogens. Differentiation of natural killer (NK) cell activation pathways occurs along a continuum from reliance on innate pro‐inflammatory cytokines and stress‐induced host ligands through to interaction with signals derived from acquired immune responses. Importantly, the degree of functional differentiation of the NK cell lineage influences the magnitude and specificity of interactions with host cells infected with viruses, bacteria, fungi, and parasites. Individual humans possess a vast diversity of distinct NK cell clones, each with the capacity to vary along this functional differentiation pathway, which ‐ when combined ‐ results in unique individual responses to different infections. Here we summarize these NK cell differentiation events, review evidence for direct interaction of malaria‐infected host cells with NK cells and assess how innate inflammatory signals induced by malaria parasite‐associated molecular patterns influence the indirect activation and function of NK cells. Finally, we discuss evidence that anti‐malarial immunity develops in parallel with advancing NK differentiation, coincident with a loss of reliance on inflammatory signals, and a refined capacity of NK cells to target malaria parasites more precisely, particularly through antibody‐dependent mechanisms.