bluuebunny/crossref_metadata_2025 huggingface dataset:
PastView: a user-friendly interface to explore evolutionary scenarios
Authors: Chevenet François , Castel Guillaume , Jousselin Emmanuelle , Gascuel Olivier
Published: May 2019

Background

Ancestral character states computed from the combination of phylogenetic trees with extrinsic traits are used to decipher evolutionary scenarios in various research fields such as phylogeography, epidemiology, and ecology. Despite the existence of powerful methods and software in ancestral character state inference, difficulties may arise when interpreting the outputs of such inferences. The growing complexity of data (trees, annotations), the diversity of optimization criteria for computing trees and ancestral character states, the combinatorial explosion of potential evolutionary scenarios if some ancestral characters states do not stand out clearly from others, requires the design of new methods that operate on tree topologies and extrinsic traits associations to ease the identification of evolutionary scenarios.

Result

We developed a tool, PastView, a user-friendly interface that includes numerical and graphical features to help users to import and/or compute ancestral character states and extract evolutionary scenario as a set of successive transitions of ancestral character states from the tree root to its leaves. PastView offers synthetic views such as transition maps and integrates comparative analysis methods to highlight agreements or discrepancies between methods of ancestral annotations inference.

Conclusion

The main contribution of PastView is to assemble known numerical and graphical methods into a multi-maps graphical user interface dedicated to the computing, searching and viewing of evolutionary scenarios based on phylogenetic trees and ancestral character states. PastView is available publicly as a standalone software on www.pastview.org.
A deep learning-based approach for high-throughput hypocotyl phenotyping
Authors: Dobos Orsolya , Horvath Peter , Nagy Ferenc , Danka Tivadar , Viczián András
Published: May 2019

Hypocotyl length determination is a widely used method to phenotype young seedlings. The measurement itself has been developed from using rulers and millimeter papers to the assessment of digitized images, yet it remained a labour-intensive, monotonous and time consuming procedure. To make high-throughput plant phenotyping possible, we developed a deep learning-based approach to simplify and accelerate this method. Our pipeline does not require a specialized imaging system but works well with low quality images, produced with a simple flatbed scanner or a smartphone camera. Moreover, it is easily adaptable for a diverse range of datasets, not restricted toArabidopsis thaliana. Furthermore, we show that the accuracy of the method reaches human performance. We not only provide the full code athttps://github.com/biomag-lab/hypocotyl-UNet, but also give detailed instructions on how the algorithm can be trained with custom data, tailoring it for the requirements and imaging setup of the user.

One-sentence summary

A deep learning-based algorithm, providing an adaptable tool for determining hypocotyl or coleoptile length of different plant species.
Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski’s scorpion (Scorpiones: Buthidae) in arid Asian inland
Authors: Zhang Xue-Shu , Liu Gao-Ming , Feng Yu , Zhang De-Xing , Shi Cheng-Min
Published: May 2019

Reliable delimitation of venomous scorpions is not only consequential to toxicological studies but also instructive to conservation and exploration of these important medical resources. In the present study, we delimited species boundary for the the Przewalski’s scorpion from arid northwest China through a combined approach employing phylogenetic analysis, ecological niche modeling and morphological comparison. Our results indicate that the the Przewalski’s scorpion represent an independent taxonomic unit and should be recognized as full species rank,Mesobuthus przewalsiistat. n.. This species and the Chinese scorpionM. martensiirepresent the eastern members of theM. caucasicusspecies group which manifests a trans-Central Asia distribution across the Tianshan Mountains range. We also discussed the likely geographic barrier and climatic boundary that demarcate distributional range of the the Przewalski’s scorpion.
Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations
Authors: Choi Yoon-Mi , Choi Dong-Hyuk , Lee Yi Qing , Koduru Lokanand , Lewis Nathan E. , Lakshmanan Meiyappan , Lee Dong-Yup
Published: May 2019

The biomass equation is a critical component in genome-scale metabolic models (GEMs): it is used as the de facto objective function in flux balance analysis (FBA). This equation accounts for the quantities of all known biomass precursors that are required for cell growth based on the macromolecular and monomer compositions measured at certain conditions. However, it is often reported that the macromolecular composition of cells could change across different environmental conditions; the use of the same single biomass equation in FBA, under multiple conditions, is questionable. Thus, we first investigated the qualitative and quantitative variations of macromolecular compositions of three representative host organisms, Escherichia coli, Saccharomyces cerevisiae and Cricetulus griseus, across different environmental/genetic variations. While macromolecular building blocks such as DNA, RNA, protein, and lipid composition vary notably, variations in fundamental biomass monomer units such as nucleotides and amino acids are not appreciable. We further observed that while macromolecular compositions are similar across taxonomically closer species, certain monomers, especially fatty acids, vary substantially. Based on the analysis results, we subsequently propose a new extension to FBA, named “Flux Balance Analysis with Ensemble Biomass (FBAwEB)”, to embrace the natural variation in selected components of the biomass equation. The current study clearly highlights that certain components of the biomass equation are very sensitive to different conditions, and the ensemble representation of biomass equation in the FBA framework enables us to account for such natural variations accurately during GEM-guided in silico simulations.
Thermostability improvement ofAspergillus awamoriglucoamylase via directed evolution of its gene located on episomal expression vector inPichia pastoris
Authors: Schmidt Alexander , Shvetsov Alexey , Soboleva Elena , Kil Yury , Sergeev Vladimir , Surzhik Marina
Published: May 2019

Novel thermostable forms of glucoamylase (GA) from filamentous fungusAspergillus awamoriX100 were constructed using the directed evolution approach based on random mutagenesis by error-prone PCR of the catalytic domain region of glucoamylase gene with its localization on a new episomal expression vector pPEHα inPichia pastoriscells. Of 3000 yeast transformants screened, six new thermostable GA mutants with amino acid substitutions Val301Asp, Thr390Ala, Thr390Ala/Ser436Pro, Leu7Met/His391Tyr, Asp9His/Ile82Phe, Ser8Arg/Gln338Leu were identified and studied. To estimate the effect of every single substitution in the double mutants, we have constructed an appropriate single mutants of GA by site-directed mutagenesis and analyzed their thermal properties. Results of the analysis showed that only Ile82Phe and Ser8Arg mutations caused an increased thermostability. While Leu7Met and Asp9His mutations decreased the thermal stability of GA, and Gln338Leu had little effect, the synergistic effect of double mutant forms Leu7Met/His391Tyr, Asp9His/Ile82Phe and Ser8Arg/Gln338Leu revealed the significant thermostability improvement as compared to wild type GA.
Confounding by indication of the safety of de-escalation in community-acquired pneumonia: a simulation study embedded in a prospective cohort
Authors: van Heijl Inger , Schweitzer Valentijn A. , Boel C.H. Edwin , Oosterheert Jan Jelrik , Huijts Susanne M. , Dorigo-Zetsma Wendelien , van der Linden Paul D. , Bonten Marc J.M. , van Werkhoven Cornelis H.
Published: May 2019

Background

Observational studies have demonstrated that de-escalation of antimicrobial therapy is independently associated with lower mortality. This most probably results from confounding by indication. Reaching clinical stability is associated with the decision to de-escalate and with survival. However, studies rarely adjust for this confounder. We quantified the potential confounding effect of clinical stability on the estimated impact of de-escalation on mortality in patients with community-acquired pneumonia.

Methods

Data were used from the Community-Acquired Pneumonia immunization Trial in Adults (CAPiTA). The primary outcome was 30-day mortality. We performed Cox proportional-hazards regression with de-escalation as time-dependent variable and adjusted for baseline characteristics using propensity scores. The potential impact of unmeasured confounding was quantified through simulating a variable representing clinical stability on day three, using data on prevalence and associations with mortality from the literature.

Results

Of 1,536 included patients, 257 (16.7%) were de-escalated, 123 (8.0%) were escalated and in 1156 (75.3%) the antibiotic spectrum remained unchanged. The adjusted hazard ratio of de-escalation for 30-day mortality (compared to patients with unchanged coverage), without adjustment for clinical stability, was 0.36 (95%CI: 0.18-0.73). If 90% to 100% of de-escalated patients were clinically stable on day three, the fully adjusted hazard ratio would be 0.53 (95%CI: 0.26-1.08) to 0.90 (95%CI: 0.42-1.91), respectively. The simulated confounder was substantially stronger than any of the baseline confounders in our dataset.

Conclusions

With plausible, literature-based assumptions, clinical stability is a very strong confounder for the effects of de-escalation. Quantification of effects of de-escalation on patient outcomes without proper adjustment for clinical stability results in strong negative bias. As a result, the safety of de-escalation remains to be determined.
The polymorphic PolyQ tail protein of the Mediator Complex, Med15, regulates variable response to stress
Authors: Gallagher Jennifer E.G. , Nassif Casey , Pupo Amaury
Published: May 2019

The Mediator is a multi-protein complex composed of subunits called head, body, tail, and CDK that is conserved from yeast to humans and plays a central role in transcription. However, not all the components are required for basal transcription. Components of the tail are not essential but to varying degrees are required for growth in different stresses. While some stresses are familiar such as heat, desiccation, and starvation, others are exotic, yet yeast can elicit a successful stress response. MCHM is a hydrotrope that induces growth arrest in yeast. By exploiting genetic variation, specifically in Med15, between yeast strains, we found that a naturally occurring Med15 allele with polyQ (polyglutamine) expansion conferred MCHM sensitivity. Expansion in polyQ repeat can induce protein aggregation and in humans can cause neurodegenerative diseases. In yeast, the MCHM sensitivity was not from a loss of function as the reciprocal hemizygous hybrids were all sensitive and the homozygous null mutant was less sensitive than the hemizygous hybrids. This suggests that there is an incompatibility between Mediator components from genetic divergent yeast strains. Transcriptomics from yeast expressing the incompatible Med15 (longer polyQ repeats in the strain with fewer repeats) changed gene expression in diverse pathways. Med15 protein existed in multiple isoforms, mostly from likely post-translational modifications and different alleles have different patterns of isoforms. Stability of both alleles of Med15 was dependent on Ydj1, a J-type chaperone. The protein level of the incompatible Med15 allele was lower than the compatible allele and was turned over faster. Med15 is tethered to the rest of the Mediator complex via Med2 and 3. Deletion of either Med2 or Med3 changed the Med15 isoform patterns in a similar manner. Whereas deletion of Med5, a distal component of the Mediator tail, did not change the pattern. Themed2andmed3mutants were similarly sensitive to MCHM whilemed5mutants were not. Differences in the phenotype of yeast carrying different Med15 alleles extend to other stresses. The incompatible allele of Med15 improved growth of yeast to chemicals that produce free radicals and the compatible allele of Med15 improved growth to reducing agents, caffeine, and hydroxyurea. Med15 directly interacts with Gcn4 and other TFs andin vitroform phase-separated droplets. This variation may reflect the positive and negative role that Med15 has in transcription. Genetic variation in transcriptional regulators can magnify differences in response to environmental changes, in contrast, genetic variation in a metabolic enzyme. These polymorphic control genes are master variators.
Tautomeric polymorphism of the neuroactive inhibitor kynurenic acid
Authors: Pogoda Dorota , Janczak Jan , Pawlak Sylwia , Zaworotko Michael , Videnova-Adrabinska Veneta
Published: May 2019

Kynurenic acid (KYN; systematic name: 4-hydroxyquinoline-2-carboxylic acid, C10H7NO3) displays a therapeutic effect in the treatment of some neurological diseases and is used as a broad-spectrum neuroprotective agent. However, it is understudied with respect to its solid-state chemistry and only one crystal form (α-KYN·H2O) has been reported up to now. Therefore, an attempt to synthesize alternative solid-state forms of KYN was undertaken and six new species were obtained: five solvates and one salt. One of them is a new polymorph, β-KYN·H2O, of the already known KYN monohydrate. All crystal species were further studied by single-crystal and powder X-ray diffraction, thermal and spectroscopic methods. In addition to the above methods, differential scanning calorimetry (DSC), in-situ variable-temperature powder X-ray diffraction and Raman microscopy were applied to characterize the phase behaviour of the new forms. All the compounds display a zwitterionic form of KYN and two different enol–keto tautomers are observed depending on the crystallization solvent used.
100 research rules of the game
Authors: Brennan Niamh M.
Published: May 2019

Purpose

There are several basic, and at times minor, pedantic principles required to successfully publish in good-quality international peer-reviewed journals. These are what the author calls the “rules of the game”. Many are so basic, so taken-for-granted, tacit knowledge, that at times supervisors do not tell their students about them. The paper aims to discuss this issue.

Design/methodology/approach

The author has assembled 100 research rules of the game from her work over many years with doctoral students and early career researchers. Each rule is accompanied by short advice. Additional citations are included directing readers to further resources on the 100 research rules of the game.

Findings

The paper documents 100 research rules of the game.

Research limitations/implications

There are many other rules of the game not included in the author’s list of 100 research rules of the game.

Originality/value

This paper is a one-stop-shop brief introduction to the author’s 100 research rules of the game.
Learning @ work: informal learning strategies of German craft workers
Authors: Kortsch Timo , Schulte Eva-Maria , Kauffeld Simone
Published: May 2019

Purpose

In competitive labor markets, promoting employees’ learning becomes a key challenge for companies. However, in small German craft companies, employee development is always connected with worries about employee turnover. This study aims to investigate the current informal learning strategies of craft workers and how they use the strategies, the effect of learning on employees’ internal and external marketability and beneficial workplace characteristics (autonomy, feedback).

Design/methodology/approach

An online prestudy (N = 131) explored current informal learning strategies. In the main study (N = 526), cluster analysis was applied to identify patterns of informal learning strategies. The relations of these patterns to workplace characteristics and marketability were investigated.

Findings

Four informal learning strategies were found (informal learning from oneself, from others, from other sources and from new media). Craft workers used combinations of the strategies (i.e. patterns): three learning patterns (balanced high, person-oriented and balanced low) differed in intensity and combination with the learning strategy use. More intense learning patterns were positively related to internal marketability but were not related to external marketability. Higher autonomy and feedback availability were related to higher learning engagement.

Research limitations/implications

Studies should have a broader view of informal learning strategies concerning different learning patterns. The use of new media is a learning strategy that might increase in the future.

Practical implications

Craft companies could promote different informal learning strategies without worries about employee turnover.

Originality/value

The study reveals how German small- and medium-sized enterprise employees use informal learning strategies in digitalized times and how human resources development can use informal learning strategies.
Board gender diversity and US corporate bonds
Authors: Oyotode-Adebile Renee M. , Raja Zubair Ali
Published: May 2019

Purpose

The purpose of this paper is to examine the impact of board gender diversity on bond terms and bondholders’ returns.

Design/methodology/approach

The authors perform pooled OLS regression, simultaneous regressions and propensity score matching to a panel data set of bond data for 319 US firms from 2007 to 2014.

Findings

The authors find that firms with gender-diverse boards have lower yields, higher ratings, larger issue size and shorter maturity. They also find that bondholders require fewer returns from firms with gender-diverse boards. However, the effect is more pronounced when women, constitutes at least 29.67 percent of the board.

Originality/value

This analysis supplements the findings that board gender diversity is essential for bondholders. It shows that bondholders should look at board gender diversity as a criterion to invest because bonds issued by firms with gender-diverse board have less risk. For practitioners, this study shows that more women participation on boards leads to a reduction in borrowing costs.
A cost minimisation model for system reliability allocation
Authors: Vaidya Omkarprasad S. , Ganapathy L. , Kumar Sushil
Published: May 2019

Purpose

The purpose of this paper is to consider a nonlinear problem of minimizing the cost of providing reliable systems. The authors assume that the system consists of several components in series, and for each such component, the cost of the component increases exponentially with its reliability.

Design/methodology/approach

In order to solve this nonlinear optimization problem, the authors propose two approaches. The first approach is based on the concept of adjusting the reliability of a pair of components to minimize the cost of the system. The authors call this procedure as reliability adjustment routine (RAR). Proofs of optimality and convergence for the proposed model are also provided. The second approach solves the problem by using a Lagrangian multiplier. A procedure is developed to obtain the maximum step size to achieve the desired optimal solution in minimum iterations. Proposed approaches are efficient and give exact solutions.

Findings

Proposed methods enable a decision maker to allocate reliability to the components in series while minimizing the total cost of the system. The developed procedures are illustrated using a numerical example. Although an exponential relationship between the component cost and reliability is assumed, this can be extended to various other nonlinear distributions.

Originality/value

This cost optimization problem, subject to system component reliability values, assumes the near practical nonlinear pattern of cost vs reliability. Such problems are complex to solve. The authors provide a unique approach called RAR to solve such convoluted problems. The authors also provide an approach to solve such problems by using a Lagrangian multiplier method. Various proofs have been worked out to substantiate the work.
Preparedness for ASEAN Economic Community (AEC): a case study of Malaysian SME manufacturing sector
Authors: Ho Shelen W.H.
Published: May 2019

Purpose

The ASEAN Economic Community (AEC) initiative poses both significant opportunities and difficult challenges to the Malaysian SME communities. This study aims to investigate the preparedness of the local SMEs to compete and exploit opportunities in a post-AEC era. The aim is to contribute to existing literature and knowledge base on SMEs’ practices in the ASEAN region. The manufacturing sector has been selected for study, and the research efforts focus on procurement competencies. SME procurement practices in the two largest manufacturing sub-sectors in Malaysia – resource-based (RB) and electrical and electronics (E&E) – are explored.

Design/methodology/approach

Preparedness for AEC is gauged from four key performance areas summarized from literature review. Six key research activities are also identified for each performance area from the findings of previous works. Data were collected using a survey instrument and face-to-face interviews. Research methodology is primarily qualitative with quantitative data for robustness check.

Findings

The findings reveal peculiar procurement practices in Malaysian SME manufacturers that have significant implications on their preparedness to compete effectively post-AEC. The findings also highlighted the key influences that have contributed to variations in Malaysian SMEs’ attitude toward trade liberalization challenges and business process improvements in comparison with practices in foreign firms and more advanced economies.

Originality/value

Theoretical models have been adopted across business settings and environments by managers. This study reveals managerial practices in Malaysian SME manufacturers run counter to developed theories. The peculiarities and business attitudes of this resilient economic sector can be an important input to managerial decision-making when analyzing business activities in the region.
New product performance advantages for extending large, established fast moving consumer goods (FMCG) brands
Authors: Hoskins Jake David , Griffin Abbie
Published: May 2019

Purpose

This paper aims to investigate how the current size and structure of a branded product portfolio impacts new product performance for fast-moving consumer goods (FMCG), testing the long-standing proposition that extending a firm’s brand and product portfolio too far is a dangerous proposition that may damage the market performance of the firm’s new product launches.

Design/methodology/approach

Aspects associated with brand size and structure that may impact new product performance are operationalized along two key dimensions: within-category (scale) and cross-category (scope). The impact of the brand’s scale and scope on the sales performance of newly commercialized products by the brand is empirically investigated in the context of FMCG. Over 2,000 new products launched in 2009 and 2010 across 31 food and non-food FMCG product categories in the USA are included in the regression-based analysis.

Findings

The authors find strong evidence that brands with broader within-category scale and cross-category scope overall are associated with more successful new product introductions, and that these influences generally are driven more by increased product trial than by repeat or persistence. The authors argue that the higher new product performance observed for more established and proliferated brands may be attributed to advantages of firm product development abilities and product acceptance by the marketplace.

Originality/value

The current results serve to temper the strong cautions set forth in much of the marketing literature about the dangers of overextending the firm’s brand and product portfolio. These results also suggest that future research should be conducted to further understand more nuanced implications of how best to grow the scale and scope of the firm’s brand and product portfolio.
Like a chameleon: the polychromatic virtue of dynamic brands
Authors: Lelis Catarina
Published: May 2019

Purpose

The purpose of this paper is to identify the chromatic approaches in dynamic brand identities, describing and analysing new trends, patterns or shared strategies which seem to be taking place and renunciating the consistent use of corporate colours in some brands.

Design/methodology/approach

The research consisted of a qualitative visual content analysis, based on the comparison and scrutiny of 50 dynamic visual identities, verifying the changes that their colours would undergo in their numerous forms of representation and the symbolic associations these would carry. This analysis was performed using three different studies.

Findings

The results show that colour in dynamic brands does not follow any consistent pattern regarding its application and none of the most common colour harmonies seem to be an obvious strategic preference.

Practical implications

This research provides insights for brand managers to look at how this dynamic positioning can be successfully implemented without affecting recognition whilst establishing or maintaining customer loyalty, and for brand designers and marketers to clarify how brand guidelines will explain the usage of such colourful approaches.

Originality/value

This paper is a contribution to the knowledge of how a traditional visual element such as colour is being combined, deconstructed and reassembled in the context of modern visual identities. Three patterns are identified, and two of them draw attention to the apparent unnecessity of colour consistency and the way this may affect the relevance of colour in transmitting certain meanings.
Elevational cline in herbivore abundance driven by a monotonic increase in trophic‐level sensitivity to aridity
Authors: Nelson Annika S. , Symanski Cole T. , Hecking Matthew J. , Mooney Kailen A.
Published: May 2019

The abiotic environment drives species abundances and distributions both directly and indirectly through effects on multi‐trophic species interactions. However, few studies have documented the individual and combined consequences of these direct and indirect effects.

We studied an ant‐tended aphid along an elevational gradient, where lower elevations were more arid. Hypotheses of stronger species interactions at lower elevations and a greater sensitivity of higher trophic levels to climate led us to predict increased top‐down control of aphids by natural enemies (third trophic level) but even stronger protection from mutualist ants (fourth trophic level) with increasing aridity. As a result, we predicted that mutualism strength and aphid abundance would increase with aridity.

We documented patterns of aphid abundance and tested for both the direct and multi‐trophic indirect effects of aridity on aphid performance. To do so, we used both observational and manipulative methods across two years in replicate high‐ and low‐elevation valleys, where summer temperatures decreased by 3.7°C and precipitation increased by 27 mm/mo from low to high elevations.

Aphid colonies were 75% larger in the most (vs. least) arid sites, and this was best explained by changes in interactions with predators and ants. Aphids were unaffected by the direct effects of the abiotic environment or its indirect effects via host plant quality. In contrast, natural enemy effects increased with aridity; under ant exclusion, natural enemies had no effect on aphids in the least arid sites but depressed colony growth by 252% in the most arid sites. Ant activity also increased with aridity, with ants discovering more aphid colonies and experimental baits and allocating more foragers per aphid, although there was no effect of aridity on ant abundance or community composition. Correspondingly, the mutualist services provided by ants increased with aridity; ants provided no benefits to aphids in the least arid sites but doubled colony growth in the most arid sites.

In summary, an elevational cline in herbivore abundance was driven by a monotonic increase in trophic‐level sensitivity to aridity. These findings illustrate that predicting species responses to climate change will require a multi‐trophic perspective.
Interactive effects of grazing and global change factors on soil and ecosystem respiration in grassland ecosystems: A global synthesis
Authors: Zhou Guiyao , Luo Qin , Chen Yajie , Hu Jiaqi , He Miao , Gao Jing , Zhou Lingyan , Liu Huiying , Zhou Xuhui
Published: May 2019

As the key carbon (C) fluxes between biosphere and atmosphere, soil respiration (Rs) and ecosystem respiration (Re) play vital roles in regulating global C balance and climate‐biosphere feedback in the Earth system. Despite the fact that numerous manipulative studies and a few meta‐analyses have been conducted to examine the responses ofRsand its components (i.e. autotrophic [Ra] and heterotrophic respiration [Rh]) as well asReto grazing (G) or global change factors, the interactive effects between grazing and global change factors remain poorly understood.

Here, we performed a comprehensive meta‐analysis of manipulative experiments with both grazing and global change factors to quantify their individual and interactive effects onRsand its components as well asRe.

Our results showed that grazing and drought significantly decreasedRsby 12.35% and 20.95%, respectively, whereas warming (W), nitrogen addition (N) and increased precipitation (P) stimulated it by 2.12%, 5.49% and 13.44%, respectively. Similarly, grazing, warming, nitrogen addition and increased precipitation increasedReby 7.21%, 4.94%, 48.45% and 21.57%, respectively, while drought decreased it by 16.86%. However, the combinations of grazing with warming (GW), nitrogen addition (GN) and increased precipitation (GP) exhibited non‐significant effects onRs.More importantly, additive interactions between grazing and global change factors exhibited a substantial predominance onRs,Ra,RhandRerather than synergistic and antagonistic ones.

Synthesis and applications. Our findings highlight the crucial importance of the interactive effects between grazing and global change factors on soil respiration (Rs) and ecosystem respiration (Re). Therefore, incorporating this key influence on ecosystem processes into Earth system models (ESMs) could better improve the prediction of climate‐biosphere feedbacks and develop sustainable strategies for grassland management in the Anthropocene.
Bacterial predation under changing viscosities
Authors: Sathyamoorthy Rajesh , Maoz Anat , Pasternak Zohar , Im Hansol , Huppert Amit , Kadouri Daniel , Jurkevitch Edouard
Published: May 2019

Bdellovibrio and like organisms (BALOs) are largely distributed in soils and in water bodies obligate predators of gram‐negative bacteria that can affect bacterial communities. Potential applications of BALOs include biomass reduction, their use against pathogenic bacteria in agriculture, and in medicine as an alternative against antibiotic‐resistant pathogens. Such different environments and uses mean that BALOs should be active under a range of viscosities. In this study, the predatory behaviour of two strains of the periplasmic predator B. bacteriovorus and of the epibiotic predator Micavibrio aeruginosavorus was examined in viscous polyvinylpyrrolidone (PVP) solutions at 28 and at 37°C, using fluorescent markers and plate counts to track predator growth and prey decay. We found that at high viscosities, although swimming speed was largely decreased, the three predators reduced prey to levels similar to those of non‐viscous suspensions, albeit with short delays. Prey motility and clumping did not affect the outcome. Strikingly, under low initial predator concentrations, predation dynamics were faster with increasing viscosity, an effect that dissipated with increasing predator concentrations. Changes in swimming patterns and in futile predator–predator encounters with viscosity, as revealed by path analysis under changing viscosities, along with possible PVP‐mediated crowding effects, may explain the observed phenomena.
Radiology teaching for interns: Experiences, current practice and suggestions for improvement
Authors: Glenn‐Cox Sophie , Hird Kathryn , Sweetman Greg , Furness Erin
Published: May 2019

Introduction

Junior doctors are typically responsible for requesting and interpreting diagnostic imaging studies. European studies have highlighted the paucity of radiology teaching leading to junior doctors feeling underprepared for clinical practice involving radiology. There is a lack of published data on the experiences of Australian medical students and junior doctors. This study aimed to describe the experiences of interns in Western Australia to establish whether they felt prepared for clinical practice by the radiology teaching they received at medical school and beyond.

Methods

This cross‐sectional observational study involved a needs analysis questionnaire. The study population included all interns currently employed by Fiona Stanley Hospital (n = 121).

Results

Radiology teaching at medical school was reportedly mostly informal and infrequent. More than half felt this was inadequate (52%). Current teaching was also reportedly infrequent and 31% reported receiving no radiology teaching in their current rotation. The interns reported requesting high volumes of diagnostic imaging with 66% reporting requesting imaging once a day or more frequently. The overwhelming majority stated their clinical practice would benefit from additional teaching in radiology (98%).

Conclusion

This study has demonstrated a paucity of radiology teaching provided to interns in a large Australian teaching hospital. As they request and interpret high volumes of diagnostic imaging, skills in this domain are paramount in the provision of safe, effective and timely patient care. The results are being used in the design and implementation of a high‐quality radiology teaching programme to improve junior doctors’ skill and develop the radiologist–clinical referrer interface.
SME Stock Markets in Tropical Economies: Evolving Efficiency and Dual Long Memory
Authors: Nguyen Trang , Chaiechi Taha , Eagle Lynne , Low David
Published: May 2019

This paper examines the evolving efficiency and the joint effects of thin trading, structural breaks and inflation on dual long memory in Small and Medium Enterprise stock markets in Hong Kong, Singapore, Thailand and Malaysia. The state‐space GARCH‐M, ARFIMA‐FIGARCH, ARFIMA‐FIAPARCH and ARFIMA‐HYGARCH models are adopted. The results determine that the Hong Kong and Singapore markets exhibit potential tendencies towards efficiency, implying the efficacy of several institutional reforms. The three aforementioned factors jointly have reducing effects on the magnitude and/or statistical significance of long‐memory estimates. The Thailand and Malaysia markets show a smaller degree of volatility persistence, indicating a good hedge for portfolio risk management.
Organizing pneumonia after thoracic radiotherapy followed by anti‐PD‐1 antibody treatment for patients with lung cancer: Three case reports
Authors: Sakaguchi Masakuni , Maebayashi Toshiya , Aizawa Takuya , Ishibashi Naoya , Okada Masahiro
Published: May 2019

Anti‐PD‐1 antibodies and thoracic radiation therapy (TRT) generate adverse events, including pneumonitis. However, there is limited information about potential overlapping toxicity of anti‐PD‐1 antibodies administered after TRT. Herein, we report three cases. The first case was of a man in his 80s with squamous cell lung cancer (cT2aN0M0 stage IB). Twelve months after TRT, tumor regrowth was observed, and the patient was administered nivolumab. Twenty‐four months after TRT, computed tomography (CT) showed organizing pneumonia (OP). The second case was of a man in his 70s with squamous cell lung cancer. He underwent surgery for pT3N1M0 stage IIIA; however, mediastinum lymph node metastasis developed. Therefore, he received TRT for the mediastinum lymph node metastasis. One month after the completion of TRT, nivolumab was administered. Two months after TRT, an OP diagnosis was made. The third case was of a man in his 60s with an unknown type of lung cancer. He received TRT for cT4N2M0 stage IIIB. Fourteen months after TRT, tumor regrowth was observed, thus, nivolumab was administered. Twenty‐seven months after TRT, an OP diagnosis was made. These case reports draw attention to OP after TRT and anti‐PD‐1 antibody administration despite low V20. Careful follow‐up of such patients is advised considering synergistic adverse events.
Modelling the three‐dimensional space use of aquatic animals combining topography and Eulerian telemetry data
Authors: Aspillaga Eneko , Safi Kamran , Hereu Bernat , Bartumeus Frederic
Published: May 2019

Passive acoustic telemetry provides the opportunity to monitor and contextualize the movements of diverse aquatic animals. Despite depth being an essential dimension along which many processes are organized, the Eulerian structure of the acoustic telemetry data (movements perceived from fixed locations) and the consequences of sound propagation in water hinders the incorporation of the vertical dimension into animal’s space use analyses.

Here, we propose a new data‐driven quantitative method to estimate 3D space use from telemetry networks. The methodology is based on simulating large numbers of stochastic synthetic paths, accommodating the detection probability around receivers and the depth information from transmitters and integrating the local topography.

The methodological protocol is explained in detail and tested with acoustic telemetry data from the common dentex Dentex dentex in a Mediterranean marine protected area. We present 3D space use estimations for the tagged individuals and compare them with other 3D and 2D estimations derived with existing probabilistic methods.

3D space use estimations that incorporate topography provided a more comprehensive view of the movement ecology of tracked individuals, with relevant pieces being missed by 2D representations. Our method generated realistic representations of the actual spatial co‐occurrence of individuals, including the spatio‐temporal identification of relevant aggregation areas.
Soil, Striga, or subsidies? Determinants of maize productivity in northern Ghana
Authors: Scheiterle Lilli , Häring Volker , Birner Regina , Bosch Christine
Published: May 2019

High yield gaps persist in sub‐Saharan Africa and increased fertilizer use is considered among the crucial measures to increase productivity. Despite high government investments, particularly in fertilizer subsidy programs (FSPs), overwhelming evidence has revealed their inefficiency. This study employs a multidisciplinary approach to identify the determinants of low maize yields in the Guinea savanna zone of Ghana. We conducted a socioeconomic household survey and analyzed plot‐specific soil samples. Econometric models were estimated based on both socioeconomic and soil variables. The results show that a common parasitic weed, Striga, and labile soil structure have significant effects on yield in the study region. Plot sizes were recorded both from farmers’ direct elicitation and using GPS devices. Considerable discrepancies were detected between self‐reported and GPS‐measured plot sizes. Fertilizer samples from randomly selected agro‐input shops were analyzed to control for adulterated or fake inputs. The measured nutrient contents of the samples reflected the composition indicated on the package labels. Findings underline the need of site‐specific data collection, supported by laboratory‐based soil test results, to efficiently address low productivity. Although there are no signs of fertilizer adulteration, governance challenges persist in targeting, timing, and elite capture in the distribution system of the subsidy program. The study shows that the FSP has not been an effective standalone measure. Rather, the government needs to invest in capacity building and extension services to address the site‐specific problems through comprehensive soil fertility management techniques and weed control. Promoting soil carbon management, minimum mechanical stress, crop rotation, and permanent soil cover should be further investigated as options for the region.
Vaginal microbiome profiles of pregnant women in Korea using a 16S metagenomics approach
Authors: You Young‐Ah , Kwon Eun Jin , Choi Suk‐Joo , Hwang Han‐Sung , Choi Sae‐Kyung , Lee Seung Mi , Kim Young Ju
Published: May 2019

Problem

The stability and dominance of Lactobacillus spp. in vaginal fluid are important for reproductive health. However, the characterization of the vaginal microbiota of women with preterm labor (PTL) or preterm premature rupture of membranes (P‐PROM), and its association with preterm birth (PTB) are poorly understood.

Method of study

We collected vaginal fluid from women at risk of PTB (n = 58) in five university hospitals in Korea. We performed a hierarchical clustering analysis and classification according to the Lactobacillus spp. and Lactobacillus abundance using Illumina MiSeq sequencing of 16S rRNA gene amplicons.

Results

Women at risk for PTB caused by P‐PROM had greater bacterial richness and diversity at the time of admission than those with PTL (P < 0.05). However, they were not significantly different between term and preterm samples. In the classification by Lactobacillus spp., the community commonly dominated by Bacteroides and Lactobacillus crispatus was found for the first time in pregnant women in Korea, and all women with this community delivered preterm. Intriguingly, women with an abundance of Weissella in a Bacteroides‐dominant community delivered at term. Moreover, in the classification by Lactobacillus proportion, the abundances of Weissella and Rickettsiales were associated with term deliveries, but the abundances of Bacteroides and Escherichia‐Shigella were associated with PTBs (P < 0.05).

Conclusion

This result suggests that Lactobacillus abundance‐based classification of vaginal fluid may reveal the microbiome associated with PTB. Further studies are needed to investigate the mechanism underlying the link between the microbiome and PTB.
The Distortion of Related Beliefs
Authors: Little Andrew T.
Published: May 2019

When forming beliefs about themselves, politics, and how the world works more generally, people often face a tension between conclusions they inherently wish to reach and those which are plausible. And the likelihood of beliefs about one variable (e.g., the performance of a favored politician) depends on beliefs about other, related variables (e.g., the quality and bias of newspapers reporting on the politician). I propose a formal approach to combine these two forces, creating a tractable way to study the distortion of related beliefs. The approach unifies several central ideas from psychology (e.g., motivated reasoning, attribution) that have been applied heavily to political science. Concrete applications shed light on why successful individuals sometimes attribute their performance to luck (“imposter syndrome”), why those from advantaged groups believe they in fact face high levels of discrimination (the “persecution complex”), and why partisans disagree about the accuracy and bias of news sources.
Quality‐of‐life research in adult patients with congenital heart disease: current status and the way forward
Authors: Moons Philip , Luyckx Koen
Published: May 2019

Over the past four decades, the number of papers on quality of life (QoL) in congenital heart disease (CHD) has grown exponentially. However, firm conclusions have been hard to draw, because conceptual issues occurred and methodological differences prevented direct comparisons of studies. In general, QoL in CHD patients is good and it can be even better than in healthy peers when measured as life satisfaction. When QoL is measured as physical functioning, patients with complex CHD do worse than patients with moderate or mild defects or healthy individuals. APPROACH‐IS was a large‐scale international project that confirmed international variations in QoL, with Australian patients reporting the best QoL. Poor QoL was predicted by older age, being a job seeker, unemployed or disabled, never having married and those with worse functional status. Perceived illness and religion and spirituality were also significant predictors for QoL. On the other hand, country‐specific characteristics and healthcare system factors did not play a significant role in explaining variances in QoL of patients with CHD around the globe. Future studies should rely on a sound conceptual basis, use longitudinal research designs, be conducted in international, multi‐centre settings and evaluate interventions that promote patients’ QoL.
High risk of clinical events in untreated HBeAg‐negative chronic hepatitis B patients with high viral load and no significant ALT elevation
Authors: Choi Gwang Hyeon , Kim Gi‐Ae , Choi Jonggi , Han Seungbong , Lim Young‐Suk
Published: May 2019

Background

It remains unknown whether antiviral treatment for HBeAg‐negative chronic hepatitis B (CHB) patients having high viral loads without significant elevation of alanine aminotransferase (ALT) levels would reduce the risks of clinical events.

Aim

To compare clinical outcomes of high viral load CHB patients untreated for normal or mildly elevated ALT vs those treated for ALT ≥ 2 upper limit of normal (ULN).

Methods

This historical cohort study included 5414 HBeAg‐negative CHB patients without cirrhosis at a tertiary hospital in Korea from 2000 to 2013. Inactive phase was defined as serum hepatitis B virus [HBV] DNA < 2000 IU/mL and persistently normal ALT (n = 3572). High viral load (HBV DNA ≥ 2000 IU/mL) patients were classified into three phases by ALT levels: Replicative (persistently normal ALT, n = 900); Mildly active (ALT 1‐2ULN, n = 396); and Active (ALT ≥ 2ULN, n = 546) phases. All Active phase patients were treated with nucleos(t)ide analogues.

Results

The mean age of the patients was 47 years without a significant difference among the groups. Compared with the treated Active phase group, the untreated Replicative phase group showed a significantly higher risk of hepatocellular carcinoma (HCC; HR 1.76; 95% CI 1.00 ‐ 3.10, P = 0.05) and death/transplantation (HR 2.14; 5% CI 1.09 ‐ 4.21, P = 0.03) by propensity score‐matched analysis. The untreated mildly active phase patients had further increase in risk of HCC and death/transplantation compared with the treated Active phase group by unadjusted, PS‐matched, competing risks, and multivariable‐adjusted analyses.

Conclusions

Untreated high viral load HBeAg‐negative CHB patients without significant ALT elevation had higher risks of clinical events than treated Active phase patients with elevated ALT.