bluuebunny/crossref_metadata_2025 huggingface dataset:
A synaptic threshold mechanism for computing escape decisions
Authors: Evans D.A , Stempel A.V. , Vale R. , Ruehle S. , Lefler Y. , Branco T.
Published: February 2018

Escaping from imminent danger is an instinctive behaviour fundamental for survival that requires classifying sensory stimuli as harmless or threatening. The absence of threat allows animals to forage for essential resources, but as the level of threat and potential for harm increases, they have to decide whether or not to seek safety1. Despite previous work on instinctive defensive behaviours in rodents2–13, little is known about how the brain computes the threat level for initiating escape. Here we show that the probability and vigour of escape in mice scale with the intensity of innate threats, and are well described by a theoretical model that computes the distance between threat level and an escape threshold. Calcium imaging and optogenetics in the midbrain of freely behaving mice show that the activity of excitatory VGluT2+ neurons in the deep layers of the medial superior colliculus (mSC) represents the threat stimulus intensity and is predictive of escape, whereas dorsal periaqueductal gray (dPAG) VGluT2+ neurons encode exclusively the escape choice and control escape vigour. We demonstrate a feed-forward monosynaptic excitatory connection from mSC to dPAG neurons that is weak and unreliable, yet necessary for escape behaviour, and which we suggest provides a synaptic threshold for dPAG activation and the initiation of escape. This threshold can be overcome by high mSC network activity because of short-term synaptic facilitation and recurrent excitation within the mSC, which amplifies and sustains synaptic drive to the dPAG. Thus, dPAG VGluT2+ neurons compute escape decisions and vigour using a synaptic mechanism to threshold threat information received from the mSC, and provide a biophysical model of how the brain performs a critical behavioural computation.
Predicting the occurrence of variants in RAG1 and RAG2
Authors: Lawless Dylan , Allen Hana Lango , Thaventhiran James ,   NIHR BioResource-Rare Diseases Consortium, Hodel Flavia , Anwar Rashida , Fellay Jacques , Walter Jolan E. , Savic Sinisa
Published: February 2018

While widespread genome sequencing ushers in a new era of preventive medicine, the tools for predictive genomics are still lacking. Time and resource limitations mean that human diseases remain uncharacterised because of an inability to predict clinically relevant genetic variants. A strategy of targeting highly conserved protein regions is used commonly in functional studies. However, this benefit is lost for rare diseases where the attributable genes are mostly conserved. An immunological disorder exemplifying this challenge occurs through damaging mutations in RAG1 and RAG2 which presents at an early age with a distinct phenotype of life-threatening immunodeficiency or autoimmunity. Many tools exist for variant pathogenicity prediction but these cannot account for the probability of variant occurrence. Here, we present a method that predicts the likelihood of mutation for every amino acid residue in the RAG1 and RAG2 proteins. Population genetics data from approximately 146,000 individuals was used for rare variant analysis. Forty-four known pathogenic variants reported in patients and recombination activity measurements from 110 RAG1/2 mutants were used to validate calculated scores. Probabilities were compared with 98 currently known human cases of disease. A genome sequence dataset of 558 patients who have primary immunodeficiency but that are negative for RAG deficiency were also used as validation controls. We compared the difference between mutation likelihood and pathogenicity prediction. Our method builds a map of most probable mutations allowing pre-emptive functional analysis. This method may be applied to other diseases with hopes of improving preparedness for clinical diagnosis.
Live Zika virus chimeric vaccine candidate based on a yellow fever 17-D attenuated backbone
Authors: Touret Franck , Gilles Magali , Klitting Raphaelle , Aubry Fabien , de-Lamballerie Xavier , Nougairède Antoine
Published: February 2018

Zika virus (ZIKV) recently dispersed throughout the tropics and sub-tropics causing epidemics associated with congenital disease and neurological complications. There is currently no commercial vaccine for ZIKV. Here we describe the initial development of a chimeric virus containing the prM/E proteins of a ZIKV epidemic strain incorporated into a yellow fever 17-D attenuated backbone. Using the versatile and rapid ISA (Infectious Subgenomic Amplicons) reverse genetics method, we compared different constructs and confirmed the need to modify the cleavage site between the pre-peptide and prM protein. Genotypic characterization of the chimeras indicates that emergence of compensatory mutations in the E protein is required to restore virus replicative fitness. Using an immunocompromised mouse model, we demonstrate that mice infected with the chimeric virus produced levels of neutralizing antibodies close to those observed following infection with ZIKV and that pre-immunized mice were protected against viscerotropic and neuroinvasive virus following challenge with a heterologous strain of ZIKV. These data provide a sound basis for the future development of this ZIKV vaccine candidate.
The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies
Authors: Liu Yang , Liu Simin , Yeh Chia-Fen , Zhang Nan , Chen Guoling , Que Pinjia , Dong Lu , Li Shou-hsien
Published: February 2018

Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.
Temporal Multivariate Pattern Analysis (tMVPA): a single trial approach exploring the temporal dynamics of the BOLD signal
Authors: Vizioli Luca , Bratch Alexander , Lao Junpeng , Ugurbil Kamil , Muckli Lars , Yacoub Essa
Published: February 2018

Background

fMRI provides spatial resolution that is unmatched by any non-invasive neuroimaging technique. Its temporal dynamics however are typically neglected due to the sluggishness of the hemodynamic based fMRI signal.

New Methods

We present temporal multivariate pattern analysis (tMVPA), a method for investigating the temporal evolution of neural representations in fMRI data, computed using pairs of single-trial BOLD time-courses, leveraging both spatial and temporal components of the fMRI signal. We implemented an expanding sliding window approach that allows identifying the time-window of an effect.

Results

We demonstrate that tMVPA can successfully detect condition-specific multivariate modulations over time, in the absence of univariate differences. Using Monte Carlo simulations and synthetic data, we quantified family-wise error rate (FWER) and statistical power. Both at the group and at the single subject level, FWER was either at or significantly below 5%. For the group level, we reached the desired power with 18 subjects and 12 trials; for the single subject scenario, 14 trials were required to achieve comparable power.

Comparison with existing methods

tMVPA adds a temporal multivariate dimension to the tools available for fMRI analysis, enabling investigations of the evolution of neural representations over time. Moreover, tMVPA permits performing single subject inferential statistics by considering single-trial distribution.

Conclusion

The growing interest in fMRI temporal dynamics, motivated by recent evidence suggesting that the BOLD signal carries temporal information at a finer scale than previously thought, advocates the need for analytical tools, such as the tMVPA approach proposed here, tailored to investigating BOLD temporal information.
Brain–gut communications via distinct neuroendocrine signals bidirectionally regulate longevity in C. elegans
Authors: Zhang Bi , Gong Jianke , Zhang Wenyuan , Xiao Rui , Liu Jianfeng , Xu X.Z. Shawn
Published: February 2018

Tissue–tissue communications are integral to organismal aging, orchestrating a body-wide aging process. The brain plays a key role in this process by detecting and processing signals from the environment and then communicating them to distal tissues such as the gut to regulate longevity. How this is achieved, however, is poorly understood. Here, using Caenorhabditis elegans as a model, we identified two distinct neuroendocrine signaling circuits by which the worm nervous system senses cool and warm environmental temperatures through cool- and warm-sensitive neurons and then signals the gut to extend and shorten life span, respectively. The prolongevity “cool” circuit uses the small neurotransmitters glutamate and serotonin, whereas the anti-longevity “warm” circuit is mediated by insulin-like neuropeptides. Both types of neuroendocrine signals converge on the gut through their cognate receptors to differentially regulate the transcription factor DAF-16/FOXO, leading to opposing outcomes in longevity. Our study illustrates how the brain detects and processes environmental signals to bidirectionally regulate longevity by signaling the gut.
New 1-(2-pyridinyl)-2-(o-, m-, p-hydroxyphenyl) benzimidazoles as corrosion inhibitors for API 5L X52 steel in acid media
Authors: Rodriguez-Clemente Edelmira , Barrera-Pascual Victoria , Cervantes-Cuevas Humberto , Aldana-González Jorge , Uruchurtu-Chavarin Jorge , Romero-Romo Mario , Palomar-Pardavé Manuel
Published: February 2018

Purpose

This paper aims to evaluate the corrosion inhibition capacities of synthesized compounds 1-(2-pyridinyl)-2-(o,m-,p-hydroxyphenyl) benzimidazoles in API 5L X52 steel/HCl 1M corrosion system.

Design/methodology/approach

Electrochemical impedance spectroscopy technique was used.

Findings

The studies determined that under stagnant conditions, the durability and efficiency were maintained over 80 per cent for up to 500 h of immersion, while the residence time started to decrease after 150 h at the best inhibitor concentration (150 ppm).

Practical implications

This work may help to attenuate corrosion problems in the petroleum industry.

Originality/value

It is the first time that 1-(2-pyridiniy)-2-(o-,m-,p-hydroxyphenyl) benzimidazoles were evaluated as corrosion inhibitors.
Older workers and i-deals: building win-win working arrangements
Authors: Rice Bridget
Published: February 2018

Purpose

The purpose of this paper is to present the importance of i-deals, or idiosyncratic deals, especially for older workers in organizations.

Design/methodology/approach

The paper briefly reviews recent literature relating to the important benefits older workers bring to organizations and the elements of their work that older workers value.

Findings

Keeping older workers in the organization can have important benefits. Enhanced flexibility and autonomy is especially valued by older workers.

Research limitations/implications

As a brief review, this paper summarizes other literature.

Practical implications

I-deals, or flexible work deals, must respond to the specific needs and desires of older workers. Older workers have increasingly diverse wants and needs, and it is important that they be heard in this regard.

Social implications

As society ages, managing these challenges will become both more important and challenging.

Originality/value

This paper will be widely read and may drive practical change in organizations.
A centralized platform of open government data as support to applications in the smart cities context
Authors: Vieira Daniel Ianegitz , Alvaro Alexandre
Published: February 2018

Purpose

The development of smart cities (SCs) is a costly process as it requires the implementation of physical infrastructure to meet the demand for data collection. On the other hand, there are open government data (OGD) that are open and free, and can be a first step from the current city evolution to SCs at a more affordable cost. However, these data are available in a decentralized way, in different formats and granularities. To date, the authors have not found any literature work that performs the centralization of OGDs on a single platform. The purpose of this paper is provide a centralized OGD platform.

Design/methodology/approach

This work investigates the state-of-the-art literature from the OGD, establishes the research question, design and develop the platform for OGD and accomplish the validation of the platform.

Findings

Through the validations of the platform, advantages were observed in relation to productivity gain for the development of solutions, in the SC context, using the proposed platform.

Research limitations/implications

The data have been collected in a manual way but for future works, the authors will use the web-crawler for the collection of data.

Practical implications

One town hall (Sorocaba) is interested in using the platform to analyze the data usage in the simple way and compare with the other nearby towns.

Originality/value

It is a recent work in literature using OGD, and there is no work that centralizes the information about several town halls to provide comparison between them and improve the decision-making.
Student assessment in higher education: embargo or empowerment?
Authors: McPhee Iain , D’Esposito Maria Eugenia Witzler
Published: February 2018

Purpose

This study recruited students who struggled to meet institutional deadlines for summative assessments. Increasing the number of diverse and non-traditional students in higher education (HE) institutions presents challenges in learning and teaching in online, conventional and hybrid contexts, impacting on student academic success. The purpose of this paper is to expand our understanding of student perceptions of the factors involved in academic achievement.

Design/methodology/approach

Using qualitative methods and in-depth semi-structured interviews, 14 participants were interviewed. Using Freire’s concept of empowerment, and Bordieu’s concept of habitus, the authors explore student perceptions of assessment.

Findings

Results presented thematically indicate that student perceptions of the purpose of the assessment and academic qualification are at odds with institutional habitus. Several embargoes impacting on academic achievement were revealed.

Research limitations/implications

Shifting organisational patterns and modes of production within HE institutions have influenced the student experience of academic writing and assessment. Findings highlight the factors that impact on academic success in HE institutions for non-traditional students in particular. Social class and educational background (habitus) are not factors taken into account when students are assessed. This impacts on capacity to achieve academic success.

Practical implications

The paper includes implications for curriculum designers, and self-reflective practitioners on issues related to academic success for non-traditional students.

Social implications

The study uses two case studies from two countries, Scotland and Brazil, both countries have invested heavily to address the twenty-first century learning agenda. Issues of widening access have increased student diversity, however, embargoes on academic achievement remain powerful factors that require further discussion and study.

Originality/value

This paper fulfils an identified need to study how issues of widening access can be mitigated, in particular for non-traditional students.
An empirical investigation of swift trust in humanitarian logistics operations
Authors: Lu Qing , Goh Mark , De Souza Robert
Published: February 2018

Purpose

Trust is essential for any team working together. In humanitarian logistics operations, relief organizations often have to work collaboratively in hastily formed networks. Trust in such a context, termed as “swift trust” in the literature, is an important but less explored topic. The purpose of this paper is to empirically explore the antecedents of swift trust as well as its impact on the coordination among the humanitarian workers.

Design/methodology/approach

The authors choose the humanitarian workers in Southeast Asia as the research sample. An exploratory survey study is conducted in three Southeast Asian countries, namely, Singapore, Indonesia, and the Philippines, with 89 usable responses.

Findings

The empirical results have shown support for most hypotheses. Third-party certification, competency, similarity in procedure standards and organizational values, can all generate swift trust. Moreover, swift trust can lead to greater openness in information sharing for coordination, though not to active assistance. Both coordination activities would lead to greater coordination effectiveness.

Research limitations/implications

Future studies could examine the four antecedent conditions for swift trust with better proxies. The connection between swift trust and coordination effectiveness can be explored in depth.

Practical implications

NGOs and governments could use these means effectively to build swift trust among the humanitarian players. For example, organizing field-oriented training activities would be beneficial for humanitarian workers in both network building and enhancing personal competency.

Originality/value

The findings point to the importance of swift trust in humanitarian operations and identify several means to enhance this trust. It has filled a research gap on the empirical investigation of the antecedents and impact of swift trust on inter-organizational coordination in humanitarian logistics operations.
Beyond deaths in school: education, knowledge production, and the Adivasi experience
Authors: Tukdeo Shivali
Published: February 2018

Purpose

Submergence, dislocation, rehabilitation and reform are the terms that crowd out most discussions on Adivasi/indigenous communities. They also fit in aptly with the Adivasi experiences of education and their relationship with knowledge construction, for them but not necessarily with them. Over the course of the last century, the Adivasi story has been composed and reoriented by a confluence of hegemonic regimes, institutions and epistemic traditions. The paper aims to discuss these issues.

Design/methodology/approach

Tracing the shifts over last few decades and paying attention to the larger politics of indigeneity, schooling and knowledge production, this paper advances a critical reading of the relationship between the marginalised and formal systems of schooling.

Findings

Employing Gayatri Chakravorty Spivak’s (1989) “Can the Subaltern Speak?”, the paper identifies the discourses that have contributed to the construction of Adivasi communities and their relationship with the Indian state.

Originality/value

As schooling continues to occupy a significant place among the communities in India and it gets associated with a number of contradictory logics, the present paper highlights the historicity of the project by which marginalised communities have been defined and their schooling needs have been framed and justified.
Pyric herbivory, scales of heterogeneity and drought
Authors: Bielski Christine H. , Twidwell Dirac , Fuhlendorf Samuel D. , Wonkka Carissa L. , Allred Brady W. , Ochsner Tyson E. , Krueger Erik S. , Carlson J. D. , Engle David M.
Published: February 2018

Understanding how extreme drought alters spatial patterns and temporal stability in grassland biomass will become increasingly important by the end of the century when climate model forecasts suggest drought events will occur more frequently. In grassland landscapes where grazing is driven by fire (termed pyric herbivory), temporal stability in above‐ground plant biomass at landscape scales typically coincides with greater spatial variability across local communities (time‐since‐fire patches), whereas variability within local communities is associated with lower temporal stability.

We assess the robustness of this relationship during one of the most severe droughts on modern record in the southern Great Plains. We use a long‐term pyric herbivory experiment to test whether extreme drought (1) changes patterns of spatial variability in above‐ground plant biomass among or within local communities, (2) changes the temporal stability in above‐ground plant biomass and the relationship between spatial variability and temporal variability and (3) changes the underlying feedback mechanisms associated with pyric herbivory.

Ordination revealed a shift from spatially distinct patches before drought to a convergence of patches during drought in terms of above‐ground plant biomass and crude protein. Permutation tests revealed that within‐patch variability in above‐ground plant biomass significantly increased during drought compared to pre‐drought levels. Temporal stability in above‐ground plant biomass decreased during drought and indeed corresponded with reduced variability in biomass among local communities and increased variability within local communities compared to pre‐drought levels.

The results from this study strongly suggest that both positive and negative feedback loops responsible for pyric herbivory were maintained by scale‐switching during periods of extreme drought and further reinforce the importance of scale in the study of pattern–process relationships.

A plain language summary is available for this article.
Uric acid as an independent predictor of coronary artery disease in essential hypertension: Data from an 8‐year‐follow‐up study
Authors: Andrikou Ioannis , Tsioufis Costas , Dimitriadis Kyriakos , Konstantinidis Dimitrios , Kasiakogias Alexandros , Kouremeti Mairi , Andrikou Eirini , Karapati Ioanna , Kalos Theodoros , Fragoulis Christos , Liatakis Ioannis , Koutra Evaggelia , Kyriazopoulos Konstantinos , Thomopoulos Costas , Tousoulis Dimitrios
Published: February 2018

The role of serum uric acid (SUA) in cardiovascular risk prediction remains to be further determined. We assessed the predictive value of SUA for the incidence of coronary artery disease (CAD) in 2287 essential hypertensive patients who were followed up for a mean period of 8 years. The distribution of SUA levels at baseline was split by the median (5.2 mg/dL) and subjects were classified into those with high and low values. Hypertensives who developed CAD (n = 57) compared to those without CAD at follow‐up (n = 2230) had at baseline higher SUA. In multivariate Cox regression model, among established confounders, high SUA (hazard ratio = 1.216, P = .016) turned out to be independent predictor of CAD. In essential hypertensive patients SUA independently predicts CAD.
The pre‐rRNA processing factor Nop53 regulates fungal development and pathogenesis via mediating production of reactive oxygen species
Authors: Cao Sheng‐Nan , Yuan Ye , Qin Yu (Haity) , Zhang Ming‐Zhe , de Figueiredo Paul , Li Gui‐Hua , Qin Qing‐Ming
Published: February 2018

Botrytis cinerea is a necrotrophic plant fungal pathogen that annually causes enormous economic losses worldwide. The ribosome is an organelle for cellular protein biosynthesis. However, little is known about how the ribosome operates as a machine to mediate microbial pathogenesis. Here, we demonstrate that Nop53, a late‐acting factor for 60S ribosomal subunit maturation, is crucial for the pathogen's development and virulence. BcNop53 is functionally equivalent to yeast nop53p. Complementation of BcNOP53 completely restored the growth defect of the yeast Δnop53 mutant. BcNop53 is located in nuclei and disruption of BcNOP53 also dramatically impaired pathogen growth. Deletion of BcNOP53 blocked infection structure formation and abolished virulence of the pathogen, possibly due to reduced production of reactive oxygen species. Moreover, loss of BcNOP53 impaired pathogen conidiation and stress adaptation, altered conidial and sclerotial morphology, retarded conidium and sclerotium germination as well as reduced the activities of cell‐wall degradation‐associated enzymes. Sclerotium production was, however, increased. Complementation with the wild‐type BcNOP53 allele rescued defects found in the ΔBcnop53 mutant. Our work establishes a systematic elucidation of Nop53 in regulating microbial development and pathogenesis, provides novel insights into ribosomal processes that regulate fungal pathogenesis, and may open up new targets for addressing fungal diseases.
Local Government as Institutional Entrepreneur: Public–Private Collaborative Partnerships in Fostering Regional Entrepreneurship
Authors: Xing Yijun , Liu Yipeng , Cooper Sir Cary L.
Published: February 2018

Due to the intertwined nature of private and public interests, local governments tend to use collaborative partnerships involving entrepreneurs to promote regional entrepreneurship. However, there is still a gap in the theory with regard to the mechanisms underpinning these collaborative partnerships. Drawing on the institutional entrepreneurship literature, we identify the enabling conditions and articulate the role played by local government as an institutional entrepreneur in fostering regional entrepreneurship through entrepreneurial public–private collaborative partnerships. This paper explicates two distinct mechanisms – the establishment of new institutional arrangements by the institutional entrepreneur and the advocation of diffusion by other actors – that underpin entrepreneurial public–private collaborative partnerships. Importantly, we underscore the crucial role played by returnee entrepreneurs who interact collaboratively with the institutional entrepreneur in affecting institutional change and fostering regional entrepreneurship. We conduct in‐depth qualitative interviews with local government officials, entrepreneurs and high‐tech park managers, in conjunction with performing content analysis of policy documents in a peripheral region of China – areas that have largely been neglected in scholarly research. This paper concludes with some theoretical and policy implications for public management and entrepreneurship.
Merit‐based Rewards, Job Satisfaction and Voluntary Turnover: Moderating Effects of Employee Demographic Characteristics
Authors: Froese Fabian Jintae , Peltokorpi Vesa , Varma Arup , Hitotsuyanagi‐Hansel Azusa
Published: February 2018

This paper draws on the reflection theory of compensation (Thierry, H. (1998). ‘Compensating work’. in P. J. D. Drenth, H. Thierry and C. J. de Wolff (eds), Handbook of Work and Organizational Psychology, 2nd edn, pp. 291–315, Psychology Press: Hove; Thierry, H. F. (2001). ‘Job evaluation systems and pay grade structures: do they match’, International Journal of Human Resource Management, 8, pp. 1313–1324) to examine the influence of individual merit‐based rewards on voluntary turnover via job satisfaction. It also tests the moderating effects of employees’ gender, age and education level between merit‐based rewards and job satisfaction. Data were collected from 636 employees in Japan at three points in time over a 12‐month period. The findings show that merit‐based rewards have a direct, positive effect on job satisfaction and an indirect effect on voluntary turnover. The effect of merit‐based rewards on job satisfaction was moderated by gender and education, providing evidence that merit‐based rewards are more important for male and highly educated employees. Practical and theoretical implications are discussed.
The Contingent Effect of TMT International Experience on Firms’ Internationalization Speed
Authors: Mohr Alex , Batsakis Georgios
Published: February 2018

Drawing on upper echelons theory, we argue that there will be an inverted U‐curve‐shaped relationship between the top management team's (TMT's) level of international experience and a firm's internationalization speed. Accounting for the role of executive job demands highlighted in upper echelons theory, we further suggest that competitive pressure, product diversification and geographic scope moderate the relationship between TMT international experience and internationalization speed by increasing the demands of TMT managers’ jobs. Using data on the international expansion of 91 retailers between 2003 and 2012, we find empirical support for the inverted U‐curve‐shaped effect of TMT international experience and the moderating role of competitive pressure. We find no moderating effect of product diversification or geographic scope.
Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains
Authors: Frohnmeyer Esther , Deptula Paulina , Nyman Tuula A. , Laine Pia K. S. , Vihinen Helena , Paulin Lars , Auvinen Petri , Jokitalo Eija , Piironen Vieno , Varmanen Pekka , Savijoki Kirsi
Published: February 2018

This study compared the secretomes (proteins exported out of the cell) of Propionibacterium freudenreichii of different origin to identify plausible adaptation factors. Phylosecretomics indicated strain‐specific variation in secretion of adhesins/invasins (SlpA, InlA), cell‐wall hydrolysing (NlpC60 peptidase, transglycosylase), protective (RpfB) and moonlighting (DnaK, GroEL, GaPDH, IDH, ENO, ClpB) enzymes and/or proteins. Detailed secretome comparison suggested that one of the cereal strains (JS14) released a tip fimbrillin (FimB) in to the extracellular milieu, which was in line with the electron microscopy and genomic analyses, indicating the lack of surface‐associated fimbrial‐like structures, predicting a mutated type‐2 fimbrial gene cluster (fimB‐fimA‐srtC2) and production of anchorless FimB. Instead, the cereal strain produced high amounts of SlpB that tentatively mediated adherent growth on hydrophilic surface and adherence to hydrophobic material. One of the dairy strains (JS22), producing non‐covalently bound surface‐proteins (LspA, ClpB, AraI) and releasing SlpA and InlA into the culture medium, was found to form clumps under physiological conditions. The JS22 strain lacked SlpB and displayed a non‐clumping and biofilm‐forming phenotype only under conditions of increased ionic strength (300 mM NaCl). However, this strain cultured under the same conditions was not adherent to hydrophobic support, which supports the contributory role of SlpB in mediating hydrophobic interactions. Thus, this study reports significant secretome variation in P. freudenreichii and suggests that strain‐specific differences in protein export, modification and protein–protein interactions have been the driving forces behind the adaptation of this bacterial species.
ALK‐rearrangement in non‐small‐cell lung cancer (NSCLC)
Authors: Du Xue , Shao Yun , Qin Hai‐Feng , Tai Yan‐Hong , Gao Hong‐Jun
Published: February 2018

The ALK gene encodes a transmembrane tyrosine kinase receptor. ALK is physiologically expressed in the nervous system during embryogenesis, but its expression decreases postnatally. ALK first emerged in the field of oncology in 1994 when it was identified to fuse to NPM1 in anaplastic large‐cell lymphoma. Since then, ALK has been associated with other types of cancers, including non‐small‐cell lung cancer (NSCLC). More than 19 different ALK fusion partners have been discovered in NSCLC, including EML4, KIF5B, KLC1, and TPR. Most of these ALK fusions in NSCLC patients respond well to the ALK inhibitor, crizotinib. In this paper, we reviewed fusion partner genes with ALK, detection methods for ALK‐rearrangement (ALK‐R), and the ALK‐tyrosine kinase inhibitor, crizotinib, used in NSCLC patients.
Do Analysts' Cash Flow Forecasts Encourage Managers to Improve the Firm's Cash Flows? Evidence from Tax Planning
Authors: Ayers Benjamin C. , Call Andrew C. , Schwab Casey M.
Published: February 2018

Recent research finds that analysts' cash flow forecasts have meaningful financial reporting ramifications, but, to date, the identified effects are unlikely to yield meaningful cash flow benefits. This study examines whether analysts' cash flow forecasts encourage managers to enhance the firm's cash flow position through tax avoidance activities. We evaluate the change in cash tax avoidance after analysts begin issuing cash flow forecasts relative to a propensity score matched control sample of firms without cash flow forecasts. Consistent with analysts' cash flow forecasts encouraging tax avoidance that enhances the firm's cash flow health, we find a negative association between cash tax payments and analysts' cash flow coverage. Additional analysis suggests this association is driven primarily by strategies to permanently avoid rather than to temporarily defer tax payments and that increased cash tax avoidance activity represents a nontrivial component of the overall increase in reported operating cash flows after the initiation of analysts' cash flow coverage.
Business Ties and Information Advantage: Evidence from Mutual Fund Trading
Authors: Duan Ying , Hotchkiss Edith S. , Jiao Yawen
Published: February 2018

This article examines whether ties to portfolio firms’ management via pension business relationships provide mutual funds with an informational advantage. Funds become related to portfolio companies when fund families serve as trustees for firms’ employee pension plans. Selling by related funds is more likely to be motivated by an information advantage than their buying, because the latter is heavily influenced by the desire to secure pension inflows. We find that stocks with larger net sales by related funds experience lower future returns. Information appears related to firm fundamentals, as the return predictability of related funds’ selling concentrates in stocks with negative future earnings surprises. Consistent with an information‐based explanation, the predictive power of related funds’ selling for future returns is more pronounced when information uncertainty about the stock is higher. Our results contribute to a growing literature that shows the sources of informed trading by institutions.
A cycad's non‐saturating response to carbon dioxide enrichment indicates Cenozoic carbon limitation in pre‐historic plants
Authors: Nackley Lloyd L. , Midgley Guy F. , Bösenberg Jacques de Wet , Donaldson John S.
Published: February 2018

Cycads were a dominant plant functional type during the Mesozoic Era when atmospheric carbon dioxide [CO2] greatly exceeded current conditions. Cycads, now rare and endangered, are slow‐growing perennial gymnosperms that develop carbon‐rich structural biomass, such as sclerophyllous leaves, dense stems and massive reproductive cones. Is cycad carbon partitioning to specific organs a constraint of their high [CO2] evolutionary history (CO2 legacy hypothesis, CLH)? To explore changes in cycad growth, carbon partitioning and assimilation responses that could be expected during the CO2 depletion of the Cenozoic Era, individuals of the cycad species Encephalartos villosus plants were grown at four CO2 levels: 400, 550, 750 and 1000 μmol mol−1. The CLH predicts that cycad biomass and growth rates would increase in elevated [CO2] due to increased net assimilation rates, and that carbon‐dense structures would provide sufficient carbohydrate sinks to prevent photosynthetic down‐regulation even under super‐ambient [CO2] of 1000 μmol mol−1. Both hypotheses were confirmed, though the latter less strongly. Plant relative growth rates increased 23% and biomass accumulation increased 65% in 1000 μmol mol−1relative to 400 μmol mol−1 treatment groups. Mean net assimilation rates increased 130% at 1000 μmol mol−1 relative to 400 μmol mol−1 CO2, though there was some down‐regulation of maximum rate of carboxylation (Vcmax). Assimilation rates, relative growth rates, biomass and mean leaf sugar content were linearly related to [CO2] over the entire experimental range. Photosynthesis appears to be regulated by stomata at low CO2 levels and by non‐stomatal (i.e. biochemical limitations) at greater concentrations. In general, our results suggest that growth and physiological performance of cycads have been severely compromised by declining [CO2] during the Cenozoic Era, possibly contributing to the current rare and endangered status of this functional type.
Contract farming: opportunity cost and trade‐offs
Authors: Bellemare Marc F.
Published: February 2018

An important literature has established that participation in contract farming leads to higher incomes and has a number of other beneficial effects on the welfare of participating households. Yet no one has looked at the opportunity cost of and the various trade‐offs involved in participating in contract farming. I look at the relationship between participation in contract farming and income from (i) livestock, (ii) labor markets, (iii) nonfarm businesses, and (iv) agricultural sources other than livestock and contract farming and (v) unearned income. Using data from Madagascar, I find that participation in contract farming is associated with a 79% decrease in how much income per capita the average household derives from labor markets and a 47% decrease in how much income per capita it derives from nonfarm businesses, but also with a 51% increase in how much income per capita the average household derives from agricultural sources other than livestock and contract farming, possibly due to technological spillovers. Thus, even though contract farming has been shown to improve welfare in multiple ways in this context, it looks as though those gains come at the cost of an “agricultural involution” on the part of participating households, who seem to turn away from non‐agricultural activities. This has important implications for structural transformation narratives.
Innovations in Practice: Body dysmorphic disorder in youth – using the Development and Well‐Being Assessment as a tool to improve detection in routine clinical practice
Authors: Buckley Vanessa , Krebs Georgina , Bowyer Laura , Jassi Amita , Goodman Robert , Clark Bruce , Stringaris Argyris
Published: February 2018

Background

Body Dysmorphic Disorder (BDD) is a distressing disorder that is widely underdetected in youth. This study aimed to examine the potential utility of the Development and Well‐Being Assessment (DAWBA) as a tool to improve recognition of BDD in routine clinical practice.

Methods

One hundred and sixty‐one patients assessed across two national and specialist child and adolescent mental health services, one specialising in mood disorders and one specialising in obsessive compulsive disorder and BDD, were included in this study. Results from the DAWBA were compared with clinical diagnosis to examine the utility of the DAWBA in detecting BDD.

Results

Only 27% of participants who received a diagnosis of BDD at assessment had been referred with concerns about appearance anxiety suggesting significant under detection in youth mental health services. Using the single‐screener question on the DAWBA, it was possible to correctly identify 97% of cases with BDD.

Conclusions

Body dysmorphic disorder often goes undetected in routine clinical practice. The DAWBA shows promise as a tool for helping clinicians to accurately detect BDD in routine clinical practice.
Regulatory network analysis of LINC00472, a long noncoding RNA downregulated by DNA hypermethylation in colorectal cancer
Authors: Chen L. , Zhang W. , Li D.Y. , Wang X. , Tao Y. , Zhang Y. , Dong C. , Zhao J. , Zhang L. , Zhang X. , Guo J. , Zhang X. , Liao Q.
Published: February 2018

Colorectal cancer (CRC), one of the common malignant cancers in the world, is caused by accumulated alterations of genetic and epigenetic factors over a long period of time. Along with that protein‐coding genes being identified as oncogenes or tumor suppressors in CRC, a number of lncRNAs have also been found to be associated with CRC. Considering the important regulatory role of lncRNAs, the first goal of this study was to identify CRC‐associated lncRNAs from a public database. One such lncRNA, LINC00472, was verified to be downregulated in CRC cell lines and cancer tissues compared with adjacent tissues. In addition, the down‐regulation of LINC00472 seemed to be caused by DNA hypermethylation at its promoter region. Furthermore, the expression of LINC00472 and DNA methylation of promoter were significantly correlated with clinicopathological features. And DNA hypermethylation of LINC00472 may serve as a better diagnostic biomarker than its expression for CRC. Finally, we predicted the functions of LINC00472 and constructed a regulatory network and found LINC00472 may be involved in cell cycle and cell proliferation processes. Our results may provide a clue to further research into the function and regulatory mechanism of LINC00472 in CRC.
Field‐Aligned Isotropic Surface Remeshing
Authors: Du Xingyi , Liu Xiaohan , Yan Dong‐Ming , Jiang Caigui , Ye Juntao , Zhang Hui
Published: February 2018

We present a novel isotropic surface remeshing algorithm that automatically aligns the mesh edges with an underlying directional field. The alignment is achieved by minimizing an energy function that combines both centroidal Voronoi tessellation (CVT) and the penalty enforced by a six‐way rotational symmetry field. The CVT term ensures uniform distribution of the vertices and high remeshing quality, and the field constraint enforces the directional alignment of the edges. Experimental results show that the proposed approach has the advantages of isotropic and field‐aligned remeshing. Our algorithm is superior to the representative state‐of‐the‐art approaches in various aspects.
Species richness and phylogenetic diversity of native and non‐native species respond differently to area and environmental factors
Authors: Li Daijiang , Monahan William B. , Baiser Benjamin
Published: February 2018

Aim

To test whether native and non‐native species have similar diversity–area relationships (species–area relationships [SARs] and phylogenetic diversity–area relationships [PDARs]) and whether they respond similarly to environmental variables.

Location

United States.

Methods

Using lists of native and non‐native species as well as environmental variables for >250 US national parks, we compared SARs and PDARs of native and non‐native species to test whether they respond similarly to environmental conditions. We then used multiple regressions involving climate, land cover and anthropogenic variables to further explore underlying predictors of diversity for plants and birds in US national parks.

Results

Native and non‐native species had different slopes for SARs and PDARs, with significantly higher slopes for native species. Corroborating this pattern, multiple regressions showed that native and non‐native diversity of plants and birds responded differently to a greater number of environmental variables than expected by chance. For native species richness, park area and longitude were the most important variables while the number of park visitors, temperature and the percentage of natural area were among the most important ones for non‐native species richness. Interestingly, the most important predictor of native and non‐native plant phylogenetic diversity, temperature, had positive effects on non‐native plants but negative effects on natives.

Main conclusions

SARs, PDARs and multiple regressions all suggest that native and non‐native plants and birds responded differently to environmental factors that influence their diversity. The agreement between diversity–area relationships and multiple regressions with environmental variables suggests that SARs and PDARs can be both used as quick proxies of overall responses of species to environmental conditions. However, more importantly, our results suggest that global change will have different effects on native and non‐native species, making it inappropriate to apply the large body of knowledge on native species to understand patterns of community assembly of non‐native species.
Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods
Authors: Nakagawa Hikaru , Yamamoto Satoshi , Sato Yukuto , Sado Tetsuya , Minamoto Toshifumi , Miya Masaki
Published: February 2018

We present a performance evaluation of environmental DNA (eDNA) metabarcoding with MiFish‐U/E primers to investigate local and regional diversities of stream fish species to examine potential effectiveness, limits and future remedies of this technique in large‐scale monitoring. We hypothesised that eDNA inferences are more consistent with fish assemblages observed upstream than downstream due to a directional flow of river water.

River water was sampled at 102 sites in 51 rivers around Lake Biwa in the central part of Honshu Island, Japan, within 10 person‐days, and fish species compositions inferred from eDNA and existing observational data were compared. Observation sites were chosen from the observational data that were within a certain distance (buffer range) of a water‐sampling site along a river trajectory. The hypothesis of the detection bias of eDNA towards upstream assemblage was tested by comparing results with all of the observational data, data from a higher elevation and data from a lower elevation. The Jaccard dissimilarity index was plotted between the observational data and the eDNA estimates against the buffer range; the buffer range with minimum dissimilarity was chosen.

When using existing observational data from within 6 km upstream of the eDNA sampling sites, the eDNA results were the most consistent with the observational data and inferred 86.4% of the species reported (38/44), as well as two additional species. eDNA results also showed patterns consistent with known upstream–downstream turnover of related species and biogeographical assemblage patterns of certain species.

Our 10‐person‐days survey using the metabarcoding technique enabled us to obtain as much regional fish diversity data including the hypothesised pattern of eDNA detection with an upstream bias as the accumulated observational data obtained through greater amounts of time, money and labour. The problems regarding false‐positive/negative detection were suggested in our survey; however, these should be decreased or removed by modifying the sampling methods and experimental procedures in future works. Therefore, we concluded this new tool to enable monitoring that has never been implemented, such as cross‐nation, and even whole‐Earth monitoring with the data at yearly, seasonal or finer temporal scales.