bluuebunny/crossref_metadata_2025 huggingface dataset:
Calling Somatic SNVs and Indels with Mutect2
Authors: Benjamin David , Sato Takuto , Cibulskis Kristian , Getz Gad , Stewart Chip , Lichtenstein Lee
Published: December 2019

Mutect2 is a somatic variant caller that uses local assembly and realignment to detect SNVs and indels. Assembly implies whole haplotypes and read pairs, rather than single bases, as the atomic units of biological variation and sequencing evidence, improving variant calling. Beyond local assembly and alignment, Mutect2 is based on several probabilistic models for genotyping and filtering that work well with and without a matched normal sample and for all sequencing depths.
Characterization of the Purified Recombinant Adenovirus for Viral Genome Structure by Restriction Enzyme Digestions
Authors: Su Qin , Sena-Esteves Miguel , Gao Guangping
Published: December 2019

The easiest way to confirm the structure and identity of genomic DNA isolated from purified adenoviral recombinants is restriction enzyme digestion and gel electrophoresis. This analysis entails comparing the restriction patterns of the adenoviral vector DNA with that plasmid that was used to initiate the entire rescue and expansion process. The integrity of the viral backbone and the presence of both the transgene and viral ITRs are assessed.
Residents vulnerability analysis and explanation of development-induced disasters in a Sub-Saharan African city
Authors: Okunola Olasunkanmi Habeeb
Published: December 2019

Purpose

The purpose of this paper is to identify and analyze indicators for measuring residents’ level of social and physical vulnerability to human-induced disasters in disaster-prone communities of Lagos, Nigeria.

Design/methodology/approach

The study adopted the quantitative research method. Questionnaires were administered to household heads in three disaster-prone communities of Lagos, Nigeria. Using systematic random sampling technique, household heads’ opinions were sampled in 10 per cent of the buildings. This effort culminated in the sampling of 288 household heads in the three communities.

Findings

The study identified flood, fire outbreak and environmental pollution as the most prevalence disasters in the communities. State of infrastructure, housing conditions and residents’ socioeconomic characteristics were identified as the major factors influencing residents’ level of vulnerability to disasters in the communities.

Research limitations/implications

The study could be strengthened by looking at other disaster-prone communities in Nigeria with different cultural and political settings. Hence, the view presented in this paper may not be considered generalizable to other parts of the country with different cultural settings.

Originality/value

To build resilient communities in cities of developing countries, the paper of this nature is important to determine factors influencing residents’ level of vulnerability to disasters. This will aid in strengthening community-disaster preparedness in these countries.
Embracing conflicts for interpersonal competence development in project-based sustainability courses
Authors: Konrad Theres , Wiek Arnim , Barth Matthias
Published: December 2019

Purpose

Advanced skills in communication, teamwork and stakeholder engagement are widely recognized as important success factors for advancing sustainability. While project-based learning formats claim to advance such skills, there is little empirical evidence that demonstrates how interpersonal competence is being developed. This study aims to describe and explains teaching and learning processes of project-based sustainability courses that contribute to the development of interpersonal competence as one of the key competencies in sustainability.

Design/methodology/approach

This study on an international project-based learning course adopted a multi-method case study approach, triangulating observations, semi-structured interviews and focus groups supported by Photovoice method through which students tracked their learning processes. Data collection and analysis followed a grounded theory approach.

Findings

Learning through and from conflicts within a learning community can foster competence development in teamwork, communication and stakeholder engagement. This study identified inner and outer conflicts (within individuals versus between individuals or groups) as potential drivers of learning processes, depending on strategies applied to address these conflicts.

Originality value

The value of this study is fourfold: it demonstrates how conflicts can be leveraged for students’ competence development; it provides in-depth empirical data from multiple perspectives, it discusses the findings in the context of teaching and learning theories, and it demonstrates an application of the Photovoice method to track and improve teaching and learning processes.
The influence of Islamic attributes and religious commitments toward halal wellness services customer satisfaction and loyalty
Authors: Sobari Nurdin , Kurniati Andyan , Usman Hardius
Published: December 2019

Purpose

This study aims to analyze the behavior of Indonesian Muslim consumers toward halal wellness services, especially to determine the effect of Islamic attributes providing halal wellness services and customer religious commitment as a moderating variable on customer satisfaction and loyalty.

Design/methodology/approach

The study was carried out by surveying 260 respondents from 13 Muslim salon outlets in the Jabodetabek area as research samples. Furthermore, a quantitative approach with moderated regression analysis is used as an analytical tool to test the research hypothesis.

Findings

The study found that embedding Islamic attributes in a halal service correlated positively with customer satisfaction. Four of the six dimensions of Islamic attributes that provide halal wellness services have a significant influence on customer satisfaction and loyalty. In addition, it was found that the moderating effect of religious commitment variables was only significant on two Islamic attributes, namely, Muslim goods and services and halal labeled products.

Research limitations/implications

This study was conducted with samples taken from only one brand of muslimah salon in Jabodetabek area. So that generalization needs to be done with caution.

Practical implications

The paper includes implications for the marketing strategy of halal wellness services industry including the importance of experiential marketing strategy, the moderation between fiqh law compliance and customer convenience and the service customization based on customer preferences.

Originality/value

This paper gives an understanding of the behavior of halal wellness service users on how halal service attributes affect user satisfaction and loyalty.
Leadership lessons from the Titanic and Concordia disasters
Authors: Marko Matthew David , Gilman Lorene G. , Vasulingam Senthilkumar , Miliskievic Matthew , Spell Chester S.
Published: December 2019

Purpose

This paper aims to investigate two famous disasters at sea, the Titanic and the Concordia, separated by 100 years, based on a comparison and analysis of those historical events, demonstrating how lessons learned and training methods used in the hazardous marine environments of aircraft carrier operations, as well as the near-solo conditions of technical scuba diving, can be better implemented in managing a large ship at sea.

Design/methodology/approach

This study starts with a historical analysis of these two ship-wrecks, both large, technically advanced ships that sank due to poor leadership, a breakdown in command and panic. Next, the study compares and contrasts scuba with operations aboard an aircraft carrier, two different maritime scenarios, yet similar in that there are many hazards that may require split-second decisions with limited or no communication with others. Both these mind-sets and training approaches have direct application to leadership and disaster planning on a large ship by being focused on minimizing decisions under stress in order to reduce panic.

Findings

This study demonstrates the value and impact of training that minimizes decisions under stress and enable people to make decisions independently in the face of a loss of communications. Focusing on two famous naval accidents, our analysis shows how such training can prevent panic and disaster, and can have direct application to leadership and disaster planning on a large ship.

Originality/value

This study uniquely compares and contrasts many of the planning and decision-making strategies used for both aircraft carrier operations and technical scuba diving, and the need to be able to make split-second decisions without communicating to others, and how these approaches can be used to better train a commercial ship to respond to an unforeseen disaster at sea.
Human resource management in merger and acquisition planning
Authors: Rodríguez-Sánchez José-Luis , Mora-Valentín Eva-María , Ortiz-de-Urbina-Criado Marta
Published: December 2019

Purpose

Many of the papers that analyse human resource management (HRM) in merger and acquisition (M&A) processes focus on the last two stages (integration and implementation). Then, the purpose of this paper is to propose an HRM model for the first stage of the process (planning) with four key factors: the due diligence process, the integration plan, the communication plan and the learning plan.

Design/methodology/approach

From the theoretical model, the authors analyse a case study of a multinational company that operates in the mechanical engineering sector.

Findings

The results show the special importance of HRM in the success of the M&A process. And, the main actions implemented in human resources (HRs) contributing to the success of this process are identified.

Research limitations/implications

Subsequent investigations could conduct similar analyses for the rest of the stages of the M&A process (integration and implementation), with the objective of presenting a complete HRM model in M&A processes.

Practical implications

The case study allows researchers to learn from professionals and business leaders while also offering a theoretical model that can help managers make decisions and improve the management of these processes.

Originality/value

The main contribution of this study has been to observe how HRs are managed in the planning stage of M&As.
Do motives matter? Examining the relationships between motives, SSCM practices and TBL performance
Authors: Kitsis Aleksandr M. , Chen Injazz J.
Published: December 2019

Purpose

Drawing on multi-theoretical lenses and a combination of supply chain and business ethics literature, this study aims to investigate the role of motives in driving sustainable supply chain management (SSCM) practices and sustainable performance.

Design/methodology/approach

Using a sample of 205 supply chain companies in the USA, the authors apply structural equation modeling (SEM) analysis to empirically test the proposed model and seven hypothesized relationships.

Findings

Results of the study underscore the critical role of moral motives, while highlighting that all three types of motives (instrumental, relational and moral) are robust in driving SSCM practices and achieving improvement in all three dimensions of sustainable performance–economic, environmental and social.

Research limitations/implications

This research can help supply chain scholars develop a more robust subfield of motivation-based SSCM research to gain a deeper understanding of how motives may differentially predict sustainable supply chain practices and performance.

Practical implications

The results of this study demonstrate the critical links between moral motivation and the triple bottom line (TBL) performance and suggest that managers pay more attention to moral motives in their decision-making.

Originality/value

This study bridges gaps in the extant literature by incorporating motivation-based antecedents, expanding the scope of SSCM practices, including the social dimension of sustainability and investigating the mediating effects of SSCM practices on the links between motives and the TBL performance.
Managing cyber risk in supply chains: a review and research agenda
Authors: Ghadge Abhijeet , Weiß Maximilian , Caldwell Nigel D. , Wilding Richard
Published: December 2019

Purpose

In spite of growing research interest in cyber security, inter-firm based cyber risk studies are rare. Therefore, this study aims to investigate cyber risk management in supply chain contexts.

Design/methodology/approach

Adapting a systematic literature review process, papers from interdisciplinary areas published between 1990 and 2017 were selected. Different typologies, developed for conducting descriptive and thematic analysis, were established using data mining techniques to conduct a comprehensive, replicable and transparent review.

Findings

The review identifies multiple future research directions for cyber security/resilience in supply chains. A conceptual model is developed, which indicates a strong link between information technology, organisational and supply chain security systems. The human/behavioural elements within cyber security risk are found to be critical; however, behavioural risks have attracted less attention because of a perceived bias towards technical (data, application and network) risks. There is a need for raising risk awareness, standardised policies, collaborative strategies and empirical models for creating supply chain cyber-resilience.

Research limitations/implications

Different types of cyber risks and their points of penetration, propagation levels, consequences and mitigation measures are identified. The conceptual model developed in this study drives an agenda for future research on supply chain cyber security/resilience.

Practical implications

A multi-perspective, systematic study provides a holistic guide for practitioners in understanding cyber-physical systems. The cyber risk challenges and the mitigation strategies identified support supply chain managers in making informed decisions.

Originality/value

To the best of the authors’ knowledge, this is the first systematic literature review on managing cyber risks in supply chains. The review defines supply chain cyber risk and develops a conceptual model for supply chain cyber security systems and an agenda for future studies.
Do Chinese farmers benefit from farmland leasing choices? Evidence from a nationwide survey
Authors: Zou Baoling , Mishra Ashok K. , Luo Biliang
Published: December 2019

Using China Family Panel Studies (CFPS), this study investigates factors associated with the choice of farmland leasing strategies and the impact of leasing options on farm performance. Particular attention is given to off‐farm employment and farm subsidies. Additionally, the study applies a selectivity‐based approach to assess the relationship between farmland leasing choices and farm businesses’ performance. Off‐farm employment, older and educated operators, large farms and old‐age pension plans increase the likelihood of leasing out farmland. Part‐time off‐farm employment, grain subsidies and mechanised farms increase the likelihood of leasing in farmland. Finally, the selectivity correction terms in the value of crop production are significantly negative in the choices of farmland leasing, indicating the presence of sample selection effects. Accounting for selectivity is essential to ensure unbiased and consistent estimates.
Securing Urban Frontiers: A View from Yangon, Myanmar
Authors: Sarma Jasnea , Sidaway James D.
Published: December 2019

This article examines how variegated local and transnational interactions are reconfiguring Myanmar's largest city of Yangon. We do this through an analytical focus on frontiers and an empirical focus on how these are secured, drawing on interviews at two Security Expos and street‐level observations in Yangon conducted over three years. Yangon thereby becomes a site for critical reflections about complex and multiple imbrications of frontiers, security and the urban with implications for how these may be conceptualized elsewhere.
Differential frontal alpha oscillations and mechanisms underlying loss of consciousness: a comparison between slow and fast propofol infusion rates
Authors: Sepúlveda P. , Cortinez L. I. , Irani M. , Egaña J. I. , Contreras V. , Sánchez Corzo A. , Acosta I. , Sitaram R.
Published: December 2019

Mechanisms underlying loss of consciousness following propofol administration remain incompletely understood. The objective of this study was to compare frontal lobe electroencephalography activity and brainstem reflexes during intravenous induction of general anaesthesia, in patients receiving a typical bolus dose (fast infusion) of propofol compared with a slower infusion rate. We sought to determine whether brainstem suppression (‘bottom‐up’) predominates over loss of cortical function (‘top‐down’). Sixteen ASA physical status‐1 patients were randomly assigned to either a fast or slow propofol infusion group. Loss of consciousness and brainstem reflexes were assessed every 30 s by a neurologist blinded to treatment allocation. We performed a multitaper spectral analysis of all electroencephalography data obtained from each participant. Brainstem reflexes were present in all eight patients in the slow infusion group, while being absent in all patients in the fast infusion group, at the moment of loss of consciousness (p = 0.010). An increase in alpha band power was observed before loss of consciousness only in participants allocated to the slow infusion group. Alpha band power emerged several minutes after the loss of consciousness in participants allocated to the fast infusion group. Our results show a predominance of ‘bottom‐up’ mechanisms during fast infusion rates and ‘top‐down’ mechanisms during slow infusion rates. The underlying mechanisms by which propofol induces loss of consciousness are potentially influenced by the speed of infusion.
Sutureless intrascleral fixation using different three‐piece posterior chamber intraocular lenses: a literature review of surgical techniques in cases of insufficient capsular support and a retrospective multicentre study
Authors: Czajka Marcin Piotr , Frajdenberg Agata , Stopa Marcin , Pabin Tomasz , Johansson Björn , Jakobsson Gunnar
Published: December 2019

We present a literature review of surgical techniques of intraocular lens placement in eyes with insufficient capsular support, focusing on the most recent publications, together with a retrospective multicentre consecutive case series analysis of 103 eyes undergoing pars plana vitrectomy and sutureless intrascleral (SIS) fixation of a standard three‐piece PCIOL. Many different approaches appear in the literature without any specific procedure achieving superior outcomes. Advantages and disadvantages vary between techniques. Common complications related to IOL fixation techniques were as follow: anterior chamber IOL: transient/permanent corneal oedema (9–66.6%), uveitis (1.1–39.3%); iris‐fixated IOL: pupil ovalization (16–47.7%); and sutured scleral‐fixated IOL: suture breakage/exposure (6.1–11%), vitreous haemorrhage: (5.5–16.6%). In our retrospective case series, indications for surgery were postoperative aphakia in 50 eyes (49%), IOL dislocation in 38 eyes (37%) and natural lens dislocation in 15 eyes (14%). Scleral tunnels for haptic fixation were created with (28 eyes, 27.2%) or without (75 eyes, 72.8%) 25 gauge trocar cannulas. Complications included transient hypotony (n = 20; 19.4%), corneal decompensation (n = 7; 6.7%), IOL dislocation (n = 6; 5.8%), cystoid macular oedema (n = 5; 4.8%), vitreous haemorrhage (n = 4; 3.8%) and retinal detachment (n = 4; 3.8%). Mean best corrected visual acuity improved from logMAR 0.65 to 0.36 at the final visit (p = 0.001). In conclusion, SIS fixation provides good anatomical and functional outcomes; however, complications can occur. The number of surgical approaches for IOL dislocation described in the literature indicates that optimal treatment remains to be found.
Modeling pediatric medulloblastoma
Authors: Roussel Martine F. , Stripay Jennifer L.
Published: December 2019

Mouse models of medulloblastoma have proven to be instrumental in understanding disease mechanisms, particularly the role of epigenetic and molecular drivers, and establishing appropriate preclinical pipelines. To date, our research community has developed murine models for all four groups of medulloblastoma, each of which will be critical for the identification and development of new therapeutic approaches. Approaches to modeling medulloblastoma range from genetic engineering with CRISPR/Cas9 or in utero electroporation, to orthotopic and patient‐derived orthotopic xenograft systems. Each approach or model presents unique advantages that have ultimately contributed to an appreciation of medulloblastoma heterogeneity and the clinical obstacles that exist for this patient population.
Development and Validation of a Risk Prediction Model of Vancomycin‐Associated Nephrotoxicity in Elderly Patients: A Pilot Study
Authors: Pan Chen , Wen Aiping , Li Xingang , Li Dandan , Zhang Yang , Liao Yin , Ren Yue , Shen Su
Published: December 2019

This exploratory study aimed to develop a risk prediction model of vancomycin‐associated nephrotoxicity (VANT) in elderly patients. Clinical information of elderly patients who received vancomycin therapy from January 2016 to June 2018 was retrieved. A total of 255 patients were included in this study. Univariate analysis and multivariable logistic regression analysis revealed that vancomycin trough concentration ≥ 20 mg/L (odds ratio (OR) = 3.009; 95% confidence interval (CI) 1.345–6.732), surgery (OR = 3.357; 95% CI 1.309–8.605), the Charlson Comorbidities Index ≥ 4 points (OR = 2.604; 95% CI 1.172–5.787), concomitant use of cardiotonic drug (OR = 3.283; 95% CI 1.340–8.042), plasma volume expander (OR = 3.459; 95% CI 1.428–8.382), and piperacillin/tazobactam (OR = 2.547; 95% CI 1.680–6.007) were risk factors for VANT in elderly patients. Furthermore, a VANT risk prediction model was developed, which had good discriminative power and was well‐calibrated.
Use of the Dyskinesia Impairment Scale in non‐ambulatory dyskinetic cerebral palsy
Authors: Haberfehlner Helga , Bonouvrié Laura A , Boeschoten Karin , Fleuren Sabine , Monbaliu Elegast , Becher Jules G , Vermeulen R Jeroen , Buizer Annemieke I
Published: December 2019

Aim

To assess the responsiveness, concurrent validity, and feasibility of the Dyskinesia Impairment Scale (DIS) in non‐ambulatory patients with dyskinetic cerebral palsy (CP).

Method

The study is a secondary analysis of data collected in the IDYS trial, a randomized controlled trial on the effects of intrathecal baclofen (ITB). The DIS and Barry–Albright Dystonia Scale (BADS) were conducted at baseline and after 3 months of ITB or placebo treatment. Responsiveness was assessed by comparing the effect sizes and correlation of change after treatment between the DIS and BADS. Concurrent validity was evaluated by assessing the correlations between scales. Feasibility was evaluated for each DIS item by the number of participants who successfully accomplished the item.

Results

Thirty‐three non‐ambulatory patients (9 females, 24 males) with dyskinetic CP (ITB‐treated: n=17, mean [SD] age: 14y 1mo [4y 1mo]; placebo‐treated: n=16, mean [SD] age: 14y 7mo [4y]) were included in the study. The effect sizes for BADS and DIS were similar in The ITB‐treated group (−0.29 and −0.22 respectively). Changes after treatment on the DIS dystonia subscale correlated with changes on the BADS (r=0.64; p<0.001). The DIS dystonia subscale and BADS correlated at baseline and follow‐up (r=0.78; p<0.001 and r=0.79; p<0.001). Not all DIS activity items could be performed in this sample of patients.

Interpretation

For non‐ambulatory patients with dyskinetic CP, the responsiveness of the DIS equalled the responsiveness of BADS. Concurrent validity was adequate. Feasibility for activity items was restricted in patients with severe dyskinetic CP.

What this paper adds

The Dyskinesia Impairment Scale (DIS) and Barry–Albright Dystonia Scale showed similar responsiveness in non‐ambulatory patients with dyskinetic cerebral palsy (CP).

No floor or ceiling effect was observed for DIS in non‐ambulatory participants.

The concurrent validity of DIS was adequate in non‐ambulatory participants.

Patients with dyskinetic CP in Gross Motor Function Classification System levels IV and V could not perform all DIS activity items.
Long‐term real‐life glycaemic outcomes with a hybrid closed‐loop system compared with sensor‐augmented pump therapy in patients with type 1 diabetes
Authors: Akturk Halis Kaan , Giordano Dominique , Champakanath Anagha , Brackett Scott , Garg Satish , Snell‐Bergeon Janet
Published: December 2019

Aim

To compare glycaemic metrics at 3 and 6 months in patients with type 1 diabetes on a 670G hybrid closed‐loop (HCL) system after using a sensor‐augmented pump (SAP) for at least 3 months.

Materials and Methods

A retrospective study from a centre that has the largest number of 670G users in the United States was conducted. Data from 202 SAP users were reviewed. Sixty‐one patients were excluded (two for steroid use, four for pregnancy, 27 for previous Enlite use, and 28 for non‐continuous use of 670G). Out of 141 patients who met the inclusion criteria, 127 (aged 21–68 years) had complete data.

Results

HbA1c levels decreased by 0.4% at 3 months and were maintained at 6 months (7.6 ± 0.07 vs. 7.2 ± 0.08, P < 0.001) with no weight gain at 6 months. Time‐in‐range (70–180 mg/dL) increased from 59.5% ± 1.1% to 70.2% ± 1.2% and 70.1% ± 1.1% at 3 and 6 months (P < 0.001), respectively. At 6 months, time spent in hypoglycaemia (<70 mg/dL) and time spent in hyperglycaemia (>180 mg/dL) were reduced by 30% (2.2% ± 0.2% vs. 3.2% ± 0.2%; P < 0.05) and 26% (28.3% ± 1.2% vs. 38.1% ± 1.2%; P < 0.001), respectively. More time in auto‐mode was associated with improved continuous glucose monitoring metrics, lower HbA1c and decreased glycaemic variability. Time in auto‐mode declined in men after 3 months, while women maintained similar auto‐mode use throughout the study.

Conclusions

The HCL system improved HbA1c levels and time‐in‐range, and decreased time spent in hypoglycaemia and hyperglycaemia at 6 months. Auto‐mode use was significantly correlated with continuous glucose monitoring metrics and glycaemic outcomes.
Accuracy of left ventricular ejection fraction determined by automated analysis of handheld echocardiograms: A comparison of experienced and novice examiners
Authors: Aldaas Omar M. , Igata Sachiyo , Raisinghani Ajit , Kraushaar Megan , DeMaria Anthony N.
Published: December 2019

Background

Handheld ultrasound devices have been developed that facilitate imaging in new clinical settings. However, quantitative assessment has been difficult. Software algorithms have recently been developed with the aim of providing rapid measurements of left ventricular ejection fraction (LVEF) with minimal operator input.

Methods

We prospectively enrolled a cohort of 70 patients scheduled to undergo echocardiography at the University of California, San Diego. Each patient underwent a standard echocardiography examination by an experienced sonographer as well as a handheld ultrasound with automated software by both the sonographer and an inexperienced resident.

Results

There was a positive correlation between the LVEFs obtained from the standard transthoracic echocardiogram and handheld device in the hands of a novice (r = 0.62; 95% CI 0.45‐0.75) and experienced sonographer (r = 0.69; 95% CI 0.54‐0.80). The sensitivity and specificity to detect a reduced LVEF (<50%) were 69% and 96% for the novice and 64% and 98% for the experienced sonographer. The sensitivity and specificity to detect a severely reduced LVEF (<35%) were 67% and 97% for the novice and 56% and 93% for the experienced sonographer, but when limited to recordings of at least adequate quality, improved to 100% and 100% for the novice and 100% and 98% for the experienced sonographer, respectively.

Conclusion

These data demonstrate that the handheld ultrasound device paired with novel software can provide a clinically useful estimate of LVEF when the images are of adequate quality and yield results by novice examiners that are similar to experienced sonographers.
A refined model of body mass and population density in flightless birds reconciles extreme bimodal population estimates for extinct moa
Authors: Latham A. David M. , Latham M. Cecilia , Wilmshurst Janet M. , Forsyth David M. , Gormley Andrew M. , Pech Roger P. , Perry George L. W. , Wood Jamie R.
Published: December 2019

Flightless birds were once the largest and heaviest terrestrial fauna on many archipelagos around the world. Robust approaches for estimating their population parameters are essential for understanding prehistoric insular ecosystems and extinction processes. Body mass and population density are negatively related for extant flightless bird species, providing a method for quantifying densities and population sizes of extinct flightless species. Here we assemble an updated global data set of body mass and population densities for extant flightless birds and estimate the relationship between these variables. We use generalised least squares models that account for phylogenetic relatedness and incorporate the effects of limiting factors (e.g. habitat suitability) on population density. We demonstrate the applicability of this allometric relationship to extinct species by estimating densities for each of the nine species of moa (Dinornithiformes) and generating a combined spatially explicit map of total moa density across New Zealand. To compare our density estimates with those previously published, we summed individual species' abundances to generate a mean national density of 2.02–9.66 birds km−2 for low‐ and high‐density scenarios, respectively. Our results reconcile the extreme bimodality of previous estimates (< 2 birds km−2 and > 10 birds km−2) and are comparable to contemporary densities of large herbivorous wild mammals introduced into New Zealand about 150 yr ago. The revised moa density has little effect on the harvest rates required to bring about extinction within 150–200 yr, indicating that rapid extinction was an inevitable response to human hunting, irrespective of the initial population of moa.
Gut microbiota–brain axis in depression: The role of neuroinflammation
Authors: Carlessi Anelise S. , Borba Laura A. , Zugno Alexandra I. , Quevedo João , Réus Gislaine Z.
Published: December 2019

Major depressive disorder (MDD) is a psychiatric condition that affects a large number of people in the world, and the treatment existents do not work for all individuals affected. Thus, it is believed that other systems or pathways which regulate brain networks involved in mood regulation and cognition are associated with MDD pathogenesis. Studies in humans and animal models have been shown that in MDD there are increased levels of inflammatory mediators, including cytokines and chemokines in both periphery and central nervous system (CNS). In addition, microglial activation appears to be a key event that triggers changes in signaling cascades and gene expression that would be determinant for the onset of depressive symptoms. Recent researches also point out that changes in the gut microbiota would lead to a systemic inflammation that in different ways would reach the CNS modulating inflammatory pathways and especially the microglia, which could influence responses to treatments. Moreover, pre‐ and probiotics have shown antidepressant responses and anti‐inflammatory effects. This review will focus on studies that show the relationship of inflammation with the gut microbiota–brain axis and its relation with MDD.
Higher‐order discrimination learning by honeybees in a virtual environment
Authors: Buatois Alexis , Laroche Lou , Lafon Gregory , Avarguès‐Weber Aurore , Giurfa Martin
Published: December 2019

Non‐elemental learning constitutes a cognitive challenge because events to be learned are usually ambiguous in terms of reinforcement outcome, contrary to elemental learning, which relies on unambiguous associations. Negative patterning (NP) constitutes a paradigmatic case of non‐elemental learning, as subjects have to learn that single elements are reinforced while their simultaneous presentation is not reinforced (A+, B+ vs. AB−). Solving NP requires treating AB as being different from the linear sum of its components in order to overcome the ambiguity of stimulus reinforcement (i.e. A and B are as often reinforced as not reinforced). The honeybee is currently the only insect mastering NP as shown by studies restricted mainly to the olfactory domain. Here, we tested the bees' capacity to solve a NP discrimination in the visual domain and used to this end a virtual reality (VR) environment in which a tethered bee walking stationary on a spherical treadmill faces visual stimuli projected on a semicircular screen. We show that bees learn a composite grating made of alternated green and blue bars in an elemental way, and generalize their response to both a blue and a green grating. Yet, after NP training, one‐quarter of the bees inhibited elemental processing and responded significantly more to the single‐coloured gratings than to the composite grating. Alternative strategies were used by the other bees, which achieved partial NP learning. These results offer attractive perspectives to study different forms of visual learning in a controlled VR environment, and dissect their underlying mechanisms.
Reweaving river food webs through time
Authors: Bowes Rachel E. , Thorp James H. , Delong Michael D.
Published: December 2019

Our project sought to determine ecological effects of adding low‐head dams and levees to large rivers by examining potential changes to aquatic food webs over a 70‐year period in the Lower Ohio River (LOR) and Upper Mississippi River (UMR).

We employed museum collections of fish and compound specific stable isotope analysis of amino acids to evaluate long‐term changes in primary food sources for multiple species of fish in each river.

Fishes in both rivers depended more on autochthonous than allochthonous carbon sources throughout the 70‐year period (based on measurements of isotopic signatures of algae, C3 plants, C4 plants, cyanobacteria, and fungi), but the relative use of different carbon sources differed between the UMR and LOR. Significant but opposite shifts in trophic positions (TP) between rivers over time (higher TP in the UMR; lower in the LOR) were correlated with major anthropogenic changes to habitat structure (e.g. slight decrease in abundance of side channels in the UMR; increase in pool water depth in the LOR) resulting from low‐head dam construction. They may also have been influenced by likely increased primary productivity in the UMR from agricultural nitrogen inputs and by possible shifts in the importance of phytoplankton versus benthic algae in the LOR from changes in water depth. Shifts in trophic position and reliance on various food sources were not correlated with variation in discharge, gage height, or temperature.

Although these two rivers have contrasting hydrogeomorphic complexity (UMR is an anastomosing river, while the LOR is a constricted channel river) and different discharge patterns (seasonal versus yearly operation in some cases), both differ substantially from rivers having hydrogeomorphic changes resulting from construction of high dams (>15 m). It is not surprising, therefore, that factors controlling trophic position and reliance on different carbon sources vary among different types of dams and river structures.
Rethinking sources of nitrogen to cereal crops
Authors: Yan Ming , Pan Genxing , Lavallee Jocelyn M. , Conant Richard T.
Published: December 2019

Understanding how to manage N inputs to identify the practices that maximize N recovery has been an organizing principle of agronomic research. Because growth in N fertilizer inputs is expected to continue in an ongoing effort to boost crop production over coming decades, understanding how to efficiently manage recovery of fertilizer N will be important going forward. Yet synthesis of published data that has traced the fate of 15N‐labeled fertilizer shows that less than half of the N taken up by crops is derived from current‐year N fertilizer. The source of the majority of N in crops is something other than current‐year fertilizer and the sources are not really known. This is true for maize (only 41% of N in crops was from current‐year N fertilizer), rice (32%), and small grains (37%). Recovery of organic fertilizer N (manure, green manure, compost, etc.) in crops is low (27%), though N recovery in subsequent years (10%) was greater than that for mineral fertilizers. Thus, while research on efficiency of N fertilizer use through improved rate, type, location, and timing is important, this research fails to directly address management of the majority of the N supplied to crops. It seems likely that the majority of non‐fertilizer N found in crops comes from turnover of soil and crop residue N. We encourage the research community to revisit the mental model that fertilizer is a replacement for N supply from turnover of soil organic N (SON) and consider a model in which N fertilizer augments ongoing SON turnover and makes an important longer term contribution to SON maintenance and turnover. Research focused on the efficient recovery of N current‐year fertilizer inputs neglects this potential role for building soil N and managing soil N turnover, which seems likely to be the most important source of crop N.
Similar factors underlie tree abundance in forests in native and alien ranges
Authors: van der Sande Masha T. , Bruelheide Helge , Dawson Wayne , Dengler Jürgen , Essl Franz , Field Richard , Haider Sylvia , van Kleunen Mark , Kreft Holger , Pagel Joern , Pergl Jan , Purschke Oliver , Pyšek Petr , Weigelt Patrick , Winter Marten , Attorre Fabio , Aubin Isabelle , Bergmeier Erwin , Chytrý Milan , Dainese Matteo , De Sanctis Michele , Fagundez Jaime , Golub Valentin , Guerin Greg R. , Gutiérrez Alvaro G. , Jandt Ute , Jansen Florian , Jiménez‐Alfaro Borja , Kattge Jens , Kearsley Elizabeth , Klotz Stefan , Kramer Koen , Moretti Marco , Niinemets Ülo , Peet Robert K. , Penuelas Josep , Petřík Petr , Reich Peter B. , Sandel Brody , Schmidt Marco , Sibikova Maria , Violle Cyrille , Whitfeld Timothy J. S. , Wohlgemuth Thomas , Knight Tiffany M.
Published: December 2019

Aim

Alien plant species can cause severe ecological and economic problems, and therefore attract a lot of research interest in biogeography and related fields. To identify potential future invasive species, we need to better understand the mechanisms underlying the abundances of invasive tree species in their new ranges, and whether these mechanisms differ between their native and alien ranges. Here, we test two hypotheses: that greater relative abundance is promoted by (a) functional difference from locally co‐occurring trees, and (b) higher values than locally co‐occurring trees for traits linked to competitive ability.

Location

Global.

Time period

Recent.

Major taxa studied

Trees.

Methods

We combined three global plant databases: sPlot vegetation‐plot database, TRY plant trait database and Global Naturalized Alien Flora (GloNAF) database. We used a hierarchical Bayesian linear regression model to assess the factors associated with variation in local abundance, and how these relationships vary between native and alien ranges and depend on species’ traits.

Results

In both ranges, species reach highest abundance if they are functionally similar to co‐occurring species, yet are taller and have higher seed mass and wood density than co‐occurring species.

Main conclusions

Our results suggest that light limitation leads to strong environmental and biotic filtering, and that it is advantageous to be taller and have denser wood. The striking similarities in abundance between native and alien ranges imply that information from tree species’ native ranges can be used to predict in which habitats introduced species may become dominant.
Rapid detection of respiratory organisms with FilmArray respiratory panel and its impact on clinical decisions in Shanghai, China, 2016‐2018
Authors: Qian Yiyi , Ai Jingwen , Wu Jing , Yu Shenglei , Cui Peng , Gao Yan , Jin Jialin , Weng Xinhua , Zhang Wenhong
Published: December 2019

Background

In this study, we evaluated the diagnostic potential and clinical impact of an automated multiplex PCR platform (the FilmArray Respiratory Panel; FA‐RP), specially designed for pathogen detection in respiratory tract infections in adults with unexplained pneumonia (UP).

Methods

A total of 112 UP patients in Shanghai, China, were enrolled prospectively and assessed using the FA‐RP from October 2016 to March 2018. We examined the test results and their influence on clinical decisions. Furthermore, as a control group, we retrospectively obtained the clinical data of 70 UP patients between October 2014 and March 2016 (before the FA‐RP was available). The two patient groups were compared with respect to factors, including general antimicrobial use and defined daily dose (DDD) numbers.

Results

Between October 2016 and March 2018, the positive rate obtained using FA‐RP for UP was 76.8%. The primary pathogens in adults with UP were Influenza A/B (47.3%, 53/112). Compared with the patients before FA‐RP was available, patients who underwent FA‐RP testing had higher rates of antiviral drug use and antibiotic de‐escalation during clinical treatment. FA‐RP significantly decreased the total DDDs of antibiotic or antifungal drugs DDDs by 7 days after admission (10.6 ± 2.5 vs 14.1 ± 8.8, P < .01).

Conclusions

The FA‐RP is a rapid and sensitive nucleic acid amplification test method for UP diagnosis in adults. The application of FA‐RP may lead to a more accurately targeted antimicrobial treatment and reduced use of antibiotic/antifungal drugs.
Factors associated with death in people with intellectual disability
Authors: Reppermund Simone , Srasuebkul Preeyaporn , Dean Kimberlie , Trollor Julian N
Published: December 2019

Background

People with intellectual disability (ID) experience higher mortality than the general population. This study examines factors contributing to deaths in people with intellectual disability.

Method

Linked administrative data spanning ten years for 49,947 people with intellectual disability receiving disability services were analysed to assess the impact of demographic variables, comorbidities and health service utilization on the risk of death using Cox proportional hazard models.

Results

People admitted for cancer were 8 times more likely to die within the study period compared to people not admitted for cancer. Down syndrome, cerebral palsy and heart disease also increased the risk of death. Emergency department presentations and/or mental health admissions increased the risk of death 4 times.

Conclusions

Our findings provide a basis for policy changes and public health interventions. Cancer screening, mental health interventions, inclusion of people with intellectual disability in health policy and improved health care are needed to meet the needs of this population.
The role of exposome in acne: results from an international patient survey
Authors: Dreno B. , Shourick J. , Kerob D. , Bouloc A. , Taïeb C.
Published: December 2019

Background

Acne severity and its response to treatment may be influenced by internal and external factors: the exposome.

Objectives

The aim of this international real‐life survey was to assess the most involved exposome factors in acne.

Methods

Eleven thousand individuals, aged between 15 and 39 years, with clinically confirmed acne or without acne, defined by age, gender and prevalence, were invited to participate in an Internet survey of 63 questions in order to assess the frequency of identified acne exposome factors.

Results

Data from 6679 questionnaires were used for statistical analysis purposes: 2826 from the acne group and 3853 from the control group. Nibbling, consumption of dairy products, sweets, alcohol or whey proteins, as well as exposure to pollution, stress, certain mechanical factors and humid or hot weather or sun exposure, were significantly (all P ≤ 0.05) more frequently reported for the acne group than for the control group. This was not the case for tobacco consumption. Data regarding the impact of cannabis consumption were insufficient for drawing any conclusions.

Conclusions

Data from this international, anonymized Internet questionnaire conducted with more than almost 6700 participants add new arguments to assumptions made that certain exposome factors have an impact on acne. Nutrition, pollution, stress and harsh skincare, as well as climate and sun exposure may be considered the most frequent factors related to acne.
Cutaneous metastases from solid neoplasms in the 21st century: a retrospective study from a Portuguese tertiary care center
Authors: Queirós C.S. , Filipe P.L. , Soares de Almeida L.
Published: December 2019

Introduction

Cutaneous metastases account for 2% of all skin cancers and are usually associated with widespread disease. The main of this retrospective study was to describe and illustrate clinicopathological features of cutaneous metastases diagnosed in our centre since the beginning of this century.

Methods

All cases of cutaneous metastases from solid neoplasms diagnosed in our Dermatopathology Department from January 2000 to December 2018 were included. Statistical analysis was performed with SPSS.

Results

A total of 164 patients were included, with a female to male ratio of 3:2. Malignancies that most commonly metastasized to the skin were melanoma (N = 58), breast cancer (N = 54) and lung cancer (N = 13). Immunohistochemical study was performed in 99 patients (60.4%). Time diagnosis of the primary tumour and appearance of cutaneous metastases was significantly higher in breast cancer, followed by melanoma and then by lung cancer (P < 0.05). Median survival after diagnosis of cutaneous metastases was 8 months. Survival after diagnosis of cutaneous metastases was also influenced by age of the patient, both at diagnosis of the primary tumour and at diagnosis of the cutaneous metastasis.

Discussion

Clinical presentation of cutaneous metastases is highly variable and non‐specific, being easily mistaken for other dermatological conditions. Histopathological examination is essential in this setting, and the judicious use of an immunohistochemistry panel considered the appropriate morphologic and clinical context. Survival after the diagnosis of cutaneous metastases is influenced not only by the location of the tumour but also by the age of the patient. Dermatologists should therefore be to these clinical pictures, and a high degree of suspicion is, along with a careful clinical history and physical examination. Although being limited by its retrospective nature, we describe one of the largest European series of cutaneous metastases, with findings with most of the available literature.