bluuebunny/crossref_metadata_2025 huggingface dataset:
Higher-level pattern features provide additional information to birds when recognizing and rejecting parasitic eggs
Authors: Stoddard Mary Caswell , Hogan Benedict G. , Stevens Martin , Spottiswoode Claire N.
Published: February 2019

Despite a recent explosion of research on pattern recognition, in both neuroscience and computer vision, we lack a basic understanding of how most animals perceive and respond to patterns in the wild. Avian brood parasites and their hosts provide an ideal study system for investigating the mechanisms of pattern recognition. The cuckoo finch,
Anomalospiza imberbis
, and its host the tawny-flanked prinia,
Prinia subflava
, lay highly polymorphic eggs with a great deal of variation in colour and patterning, with the cuckoo finch capable of close egg mimicry. Behavioural experiments in Zambia have previously shown that prinias use colour and multiple ‘low-level’ (occurring in early stages of visual processing) pattern attributes, derived from spatial frequency analysis, when rejecting foreign eggs. Here, we explore the extent to which host birds might also use ‘higher-level’ pattern attributes, derived from a feature detection algorithm, to make rejection decisions. Using a SIFT-based pattern recognition algorithm,

N
ature
P
attern
M
atch

, we show that hosts are more likely to reject a foreign egg if its higher-level pattern features—which capture information about the shape and orientation of markings—differ from those of the host eggs. A revised statistical model explains about 37% variance in egg rejection behaviour, and differences in colour, low-level and higher-level pattern features all predict rejection, accounting for 42, 44 and 14% of the explained variance, respectively. Thus, higher-level pattern features provide a small but measurable improvement to the original model and may be especially useful when colour and low-level pattern features provide hosts with little information. Understanding the relative importance of low- and higher-level pattern features is a valuable goal for future work on animal coloration, especially in the contexts of mimicry, camouflage and individual recognition.

This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Egg retrieval versus egg rejection in cuckoo hosts
Authors: Yang Canchao , Liang Wei , Møller Anders P.
Published: February 2019

Before complex nests evolved, birds laid eggs on the ground, and egg retrieval evolved as an adaptation against accidental displacement of eggs outside the nest. Therefore, egg retrieval is an ancient, and likely ancestral, widespread behaviour in birds. However, it has received little attention in studies of avian brood parasitism, perhaps because most parasitism occurs in species with complex nests, a context in which egg retrieval seems irrelevant. However, for cavity-nesting hosts of avian brood parasites, egg retrieval may still play an important role in the coevolutionary interactions between obligate brood parasites and hosts, because egg retrieval can be considered to be antagonistic to egg rejection behaviour in hosts, yet both may involve cognition to recognize eggs. We hypothesized that (1) cavity-nesting hosts should retrieve misplaced eggs from outside the nest cup, (2) brood parasitism has modulated egg retrieval behaviour in cavity-nesting hosts and (3) hosts use the same visual cues for decision-making during egg recognition in both egg retrieval and egg rejection actions. To test these hypotheses, we performed a series of experiments in a cavity-nesting host, the green-backed tit (Parus monticolus). Foreign eggs with different levels of mimicry were placed within or outside nest cups of hosts to test their responses. We found that host decisions about whether to retrieve or reject an egg both depended on the degree of mimicry. However, hosts sometimes first retrieved poorly mimetic foreign eggs and then rejected them. Alternatively, hosts sometimes failed to retrieve highly mimetic conspecific eggs. We suggest that egg retrieval in hosts is likely to be a result of the interaction between ancient retrieval behaviour and subsequent adaptation against brood parasitism.

This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Does data cleaning improve brain state classification?
Authors: Meisler Steven L. , Ezzyat Youssef , Kahana Michael J.
Published: February 2019

Background

Neuroscientists routinely seek to identify and remove noisy or artifactual observations from their data. They do so guided by the belief that including such data would reduce power to detect effects of interest. Whereas standard methods can exclude certain well defined noise sources (e.g., line noise), most forms of noise do not easily separate from signals of interest. Here we ask how well methods routinely used to “clean” human electrophysiological recordings actually boost power to detect brain-behavior correlations.

New Method

This, to the authors’ knowledge, is the first large-scale study of the impact of intracranial EEG preprocessing on brain state classification.

Results

We find that several commonly used data cleaning methods (automated methods based on statistical properties of the signal and manual methods based on expert review) reduce statistical power for both univariate and multivariate classification of successful memory encoding, a behavioral state with very well-characterized electrophysiological biomarkers.

Comparison with Existing Methods

By reallocating resources towards collecting more within-patient data instead of attempting to “clean” data, neuroscientists may see increases in the statistical power to detect physiological phenomena.

Conclusions

These findings highlight the challenge of partitioning signal and noise in the analysis of brain-behavior relations. They also prescribe increases in sample size and numbers of observations, rather than data cleaning, as the best approach to improving statistical power.
Multiplex immunofluorescence methods in neurodegenerative diseases
Authors: Ehrenberg Alexander J. , Morales Dulce Ovando , Tejedor Jorge Santos , Mulder Jan , Grinberg Lea T.
Published: February 2019

The application of multiplex immunofluorescence to human post-mortem tissue would drive observational studies of selective vulnerability in neurodegenerative proteinopathies. Efficient elution of antibodies is critical for flexibility of antibody combinations and the ability to utilize a sample in multiple rounds of immunostaining. Here, we test two elution strategies for antibodies relevant to the study of selective vulnerability in neurodegenerative diseases in post-mortem human samples from both long-fixed and short-fixed tissue. Both 2-Mercaptoethanol/SDS-based and Urea/SDS/Glycine-based elution strategies work well with the antibodies selected, confirming observations from previous studies with other antibody types.
When expectations are not met: unraveling the computational mechanisms underlying the effect of expectation on perceptual thresholds
Authors: Urgen Buse M. , Boyaci Huseyin
Published: February 2019

Expectations and prior knowledge strongly affect and even shape our visual perception. Specifically, valid expectations speed up perceptual decisions, and determine what we see in a noisy stimulus. Bayesian models have been remarkably successful to capture the behavioral effects of expectation. On the other hand several more mechanistic neural models have also been put forward, which will be referred as “predictive computation models” here. Both Bayesian and predictive computation models treat perception as a probabilistic inference process, and combine prior information and sensory input. Despite the well-established effects of expectation on recognition or decision-making, its effects on low-level visual processing, and the computational mechanisms underlying those effects remain elusive. Here we investigate how expectations affect early visual processing at the threshold level. Specifically, we measured temporal thresholds (shortest duration of presentation to achieve a certain success level) for detecting the spatial location of an intact image, which could be either a house or a face image. Task-irrelevant cues provided prior information, thus forming an expectation, about the category of the upcoming intact image. The validity of the cue was set to 100, 75 and 50% in different experimental sessions. In a separate session the cue was neutral and provided no information about the category of the upcoming intact image. Our behavioral results showed that valid expectations do not reduce temporal thresholds, rather violation of expectation increases the thresholds specifically when the expectation validity is high. Next, we implemented a recursive Bayesian model, in which the prior is first set using the validity of the specific experimental condition, but in subsequent iterations it is updated using the posterior of the previous iteration. Simulations using the model showed that the observed increase of the temporal thresholds in the unexpected trials is not due to a change in the internal parameters of the system (e.g. decision threshold or internal uncertainty). Rather, further processing is required for a successful detection when the expectation and actual input disagree. These results reveal some surprising behavioral effects of expectation at the threshold level, and show that a simple parsimonious computational model can successfully predict those effects.
Metabolome-Wide Mendelian Randomization Analysis of Emotional and Behavioral Responses to Traumatic Stress
Authors: Carvalho Carolina Muniz , Wendt Frank R. , Stein Dan J. , Stein Murray B. , Gelernter Joel , Belangero Sintia I. , Polimanti Renato
Published: February 2019

Trauma exposure is an important risk factor for several psychiatric disorders; however, the mechanisms that underlie emotional and behavioral responses to traumatic stress are unclear. To understand these mechanisms, this study investigated the genetic overlap and causal relationship between blood metabolites and traits related to trauma response using genome-wide data. Five traits related to trauma response “in the past month” ascertained in the UK Biobank (52 816<N<117 900 individuals) were considered: i) “Avoided activities or situations because of previous stressful experience” (Avoidance); ii) “Felt distant from other people” (Distant); iii) “Felt irritable or had angry outbursts” (Irritable); iv) “Felt very upset when reminded of stressful experience” (Upset); v) “Repeated disturbing thoughts of stressful experience” (Repeated Thoughts). These were investigated with respect to 52 metabolites assessed using nuclear magnetic resonance metabolomics in a previous genome-wide association study (up to 24,925 individuals of European descent). Applying linkage disequilibrium score regression (LDSC), polygenic risk scoring (PRS), and Mendelian randomization (MR), we observed that 14 metabolites were significantly correlated with trauma response traits (p<0.05); PRS of 4 metabolites (citrate (CIT); glycoprotein acetyls (GP); concentration of large very-low-density lipoproteins (VLDL) particles (LVLDLP); total cholesterol in medium particles of VLDL (MVLDLC)) were associated with traits related to trauma response (false discovery rate Q<10%). These associations were partially due to causal relationships (CIT→Upset β=-0.058, p=9.1×10−4; GP→Avoidance β=0.008, p=0.003; LVLDLP→Distant β=0.008, p=0.022; MVLDLC→Avoidance β=0.019, p=3×10−4). No reverse associations were observed. In conclusion, the genetics of certain blood-metabolites are potentially implicated in the response to traumatic experience.
Distinct cytoskeletal proteins define zones of enhanced cell wall synthesis inHelicobacter pylori
Authors: Taylor Jennifer A. , Bratton Benjamin P. , Sichel Sophie R. , Blair Kris M. , Jacobs Holly M. , DeMeester Kristen E. , Kuru Erkin , Gray Joe , Biboy Jacob , VanNieuwenhze Michael S. , Vollmer Waldemar , Grimes Catherine L. , Shaevitz Joshua W. , Salama Nina R.
Published: February 2019

Helical cell shape is necessary for efficient stomach colonization byHelicobacter pylori, but the molecular mechanisms for generating helical shape remain unclear. We show that the helical centerline pitch and radius of wild-typeH. pyloricells dictate surface curvatures of considerably higher positive and negative Gaussian curvatures than those present in straight- or curved-rod bacteria. Quantitative 3D microscopy analysis of short pulses with eitherN-acetylmuramic acid or D-alanine metabolic probes showed that cell wall growth is enhanced at both sidewall curvature extremes. Immunofluorescence revealed MreB is most abundant at negative Gaussian curvature, while the bactofilin CcmA is most abundant at positive Gaussian curvature. Strains expressing CcmA variants with altered polymerization properties lose helical shape and associated positive Gaussian curvatures. We thus propose a model where CcmA and MreB promote PG synthesis at positive and negative Gaussian curvatures, respectively, and that this patterning is one mechanism necessary for maintaining helical shape.
Cryptochromes-mediated Inhibition of the CRL4Cop1-Complex Assembly Defines an Evolutionary Conserved Signaling Mechanism
Authors: Rizzini Luca , Levine Daniel C. , Perelis Mark , Bass Joseph , Peek Clara B. , Pagano Michele
Published: February 2019

In plants, Cryptochromes are photoreceptors that negatively regulate CRL4Cop1(Cul4-RING ubiquitin ligase and its substrate receptor Cop1). In mammals, Cryptochromes are core components of the circadian clock and repressors of the glucocorticoid receptor (GR). Moreover, mammalian Cryptochromes lost their ability to interact with Cop1, suggesting that they are unable to inhibit CRL4Cop1. Contrary to this assumption, we found that mammalian Cryptochromes are also negative regulators of CRL4Cop1and through this mechanism they repress the GR transcriptional network both in cultured cells and in mouse liver. Mechanistically, Cryptochromes inactivate Cop1 by interacting with Det1, a specific subunit of the mammalian CRL4Cop1complex. Through this interaction, the ability of Cop1 to join the CRL4 complex is inhibited; therefore, its substrates accumulate. Thus, the interaction between Cryptochromes and Det1 in mammals mirrors the interaction between Cryptochromes and Cop1in planta,pointing to a common ancestor in which the cryptochrome-Cop1 axis originated.
Habitat type and interannual variation shape unique fungal pathogen communities on a California native bunchgrass
Authors: Farner Johannah E. , Spear Erin R. , Mordecai Erin A.
Published: February 2019

The role of infectious disease in regulating host populations is increasingly recognized, but how environmental conditions affect pathogen communities and infection levels remains poorly understood. Over three years, we compared foliar disease burden, fungal pathogen community composition, and foliar chemistry in the perennial bunchgrassStipa pulchraoccurring in adjacent serpentine and nonserpentine grassland habitats with distinct soil types and plant communities. We found that serpentine and nonserpentineS. pulchraexperienced consistent, low disease pressure associated with distinct fungal pathogen communities with high interannual species turnover. Additionally, plant chemistry differed with habitat type. The results indicate that this species experiences minimal foliar disease associated with diverse fungal communities that are structured across landscapes by spatially and temporally variable conditions. Distinct fungal communities associated with different growing conditions may shieldS. pulchrafrom large disease outbreaks, contributing to the low disease burden observed on this and other Mediterranean grassland species.
Measuring phenotypic heterogeneity in isogenic bacterial populations using flow cytometry and Raman spectroscopy
Authors: García-Timermans Cristina , Rubbens Peter , Heyse Jasmine , Kerckhof Frederiek-Maarten , Props Ruben , Skirtach Andre G. , Waegeman Willem , Boon Nico
Published: February 2019

Investigating phenotypic heterogeneity can help to better understand and manage microbial communities. However, characterizing phenotypic heterogeneity remains a challenge, as there is no standardized analysis framework. Several optical tools are available, which often describe properties of the individual cell. In this work, we compare Raman spectroscopy and flow cytometry to study phenotypic heterogeneity in bacterial populations. The growth phase ofE. colipopulations was characterized using both technologies. Our findings show that flow cytometry detects and quantifies shifts in phenotypic heterogeneity at the population level due to its high-throughput nature. Raman spectroscopy, on the other hand, offers a much higher resolution at the single-cell level (i.e. more biochemical information is recorded). Therefore, it is capable of identifying distinct phenotypic populations when coupled with standardized data analysis. In addition, it provides information about biomolecules that are present, which can be linked to cell functionality. We propose an automated workflow to distinguish between bacterial phenotypic populations using Raman spectroscopy and validated this approach with an external dataset. We recommend to apply flow cytometry to characterize phenotypic heterogeneity at the population level, and Raman spectroscopy to perform a more in-depth analysis of heterogeneity at the single-cell level.

Importance

Single-cell techniques are frequently applied tools to study phenotypic characteristics of bacterial populations. As flow cytometry and Raman spectroscopy gain popularity in the field, there is a need to understand their advantages and limitations, as well as to create a more standardized data analysis framework. Our work shows that flow cytometry allows to study and quantify shifts at the bacterial population level, but since its resolution is limited for microbial purposes, distinct phenotypic populations cannot be distinguished at the single-cell level. Raman spectroscopy, combined with appropriate data analysis, has sufficient resolving power at the single-cell level, enabling the identification of distinct phenotypic populations. As regions in a Raman spectrum are associated with specific (bio)molecules, it is possible to link these to the cell state and/or its function.
Characterization of Intellectual disability and Autism comorbidity through gene panel sequencing
Authors: Aspromonte Maria Cristina , Bellini Mariagrazia , Gasparini Alessandra , Carraro Marco , Bettella Elisa , Polli Roberta , Cesca Federica , Bigoni Stefania , Boni Stefania , Carlet Ombretta , Negrin Susanna , Mammi Isabella , Milani Donatella , Peron Angela , Sartori Stefano , Toldo Irene , Soli Fiorenza , Turolla Licia , Stanzial Franco , Benedicenti Francesco , Marino-Buslje Cristina , Tosatto Silvio C.E. , Murgia Alessandra , Leonardi Emanuela
Published: February 2019

Intellectual disability (ID) and autism spectrum disorder (ASD) are clinically and genetically heterogeneous diseases. Recent whole exome sequencing studies indicated that genes associated with different neurological diseases are shared across disorders and converge on common functional pathways. Using the Ion Torrent platform, we developed a low-cost next generation sequencing (NGS) gene panel that has been transferred into clinical practice, replacing single disease gene analyses for the early diagnosis of individuals with ID/ASD. The gene panel was designed using an innovativein silicoapproach based on disease networks and mining data from public resources to score disease-gene associations. We analyzed 150 unrelated individuals with ID and/or ASD and a confident diagnosis has been reached in 26 cases (17%). Likely pathogenic mutations have been identified in another 15 patients, reaching a total diagnostic yield of 27%. Our data also support the pathogenic role of genes recently proposed to be involved in ASD. Although many of the identified variants need further investigation to be considered disease-causing, our results indicate the efficiency of the targeted gene panel on the identification of novel and rare variants in patients with ID and ASD.
A large self-transmissible plasmid from Nigeria confers resistance to multiple antibacterials without a carrying cost
Authors: Monárrez Rubén , Braun Molly , Coburn-Flynn Olivia , Botelho João , Odeotyin Babatunde W. , Otero-Vera Jose I. , Quartey Naa Kwarley , Peixe Luísa , Aboderin A. Oladipo , Okeke Iruka N.
Published: February 2019

Antimicrobial resistance is rapidly expanding, in a large part due to mobile genetic elements. We screened 94 fecal fluoroquinolone-resistantEscherichia coliisolates from Nigeria for six plasmid-mediated quinolone resistance (PMQR) genes. Sixteen isolates harbored at least one of the PMQR genes and four were positive foraac-6-Ib-cr. In one strain,aac-6-Ib-crwas mapped to a 125 Kb self-transmissible IncFII plasmid, pMB2, which also bearsblaCTX-M-15, seven other functional resistance genes and multiple resistance pseudogenes. We hypothesized that pMB2 had been selected by antimicrobials and that its large size would confer a growth disadvantage. However, laboratory strains carrying pMB2 grew at least as fast as isogenic strains lacking the plasmid in both rich and minimal media. We excised a 32 Kb fragment containing thesitABCDand another putative transporter,pefB, apapBhomolog, and several open-reading frames of unknown function. The resulting 93 Kb mini-plasmid conferred slower growth rates and lower fitness than wildtype pMB2. Trans-complementing the deletion with the clonedsitABCDgenes confirmed that they accounted for the growth advantage conferred by pMB2 in iron-depleted media. The mini-plasmid additionally conferred autoaggregation and was less transmissible and both phenotypes could be complemented with apefBclone. pMB2 is a large plasmid with a flexible resistance region that contains multiple loci that can account for evolutionary success in the absence of antimicrobials. Ancillary functions conferred by resistance plasmids can mediate their retention and transmissibility, worsening the trajectory for antimicrobial resistance and potentially circumventing efforts to contain resistance through restricted use.
Mutation of the ATPase domain of MutS homolog-5 (MSH5) reveals a requirement for a functional MutSγ complex for all crossovers in mammalian meiosis
Authors: Milano Carolyn R. , Holloway J. Kim , Zhang Yongwei , Jin Bo , Bergman Aviv , Edelmann Winfried , Cohen Paula E.
Published: February 2019

During meiosis, induction of DNA double strand breaks (DSB) leads to recombination between homologous chromosomes, resulting in crossovers (CO) and non-crossovers (NCO). Only 10% DSBs resolve as COs, mostly through a class I pathway dependent on MutSγ (MSH4/ MSH5). Class II CO events represent a minor proportion of the total CO count and also arise from DSBs, but are not thought to involve MutSγ. However, loading of MutSγ occurs very early in prophase I at a frequency that far exceeds the final number of class I COs found in late prophase I. Moreover, loss of MutSγ in mouse results in apoptosis before CO formation, preventing analysis of its CO function. We generated a mutation in the ATP binding domain ofMsh5(Msh5GA). While this mutation was not expected to affect MutSγ complex formation, MutSγ foci do not accumulate during prophase I. Nevertheless, while some spermatocytes fromMsh5-/-animals progress into pachynema, most spermatocytes fromMsh5GA/GAmice progress to late pachynema and beyond. Some spermatocytes fromMsh5GA/GAmice complete prophase I entirely, allowing for the first time an assessment of MSH5 function in CO formation. At pachynema,Msh5GA/GAspermatocytes show persistent DSBs, incomplete homolog pairing, and fail to accumulate MutLγ (MLH1/MLH3). Unexpectedly,Msh5GA/GAdiakinesis-staged spermatocytes have no chiasmata at all from any CO pathway, indicating that a functional MutSγ complex in early prophase I is a pre-requisite for all COs.

ARTICLE SUMMARY

MSH4/MSH5 are critical components of the class I crossover (CO) machinery, which is responsible for >90% of the COs that arise in mammalian meiosis. We generated a point mutation in the ATP binding motif ofMsh5, and found that mutant spermatocytes lose all COs, not just those arising from the class I pathway.
The genomic landscape of metastatic castration-resistant prostate cancers using whole genome sequencing reveals multiple distinct genotypes with potential clinical impact
Authors: van Dessel Lisanne F. , van Riet Job , Smits Minke , Zhu Yanyun , Hamberg Paul , van der Heijden Michiel S. , Bergman Andries M. , van Oort Inge M. , de Wit Ronald , Voest Emile E. , Steeghs Neeltje , Martens John W.M. , Sleijfer Stefan , Cuppen Edwin , Zwart Wilbert , van de Werken Harmen J.G. , Mehra Niven , Lolkema Martijn P.
Published: February 2019

Here we present whole-genome sequencing (WGS) analysis of fresh-frozen metastatic biopsies from 197 castration-resistant prostate cancer patients. Using hierarchical unsupervised clustering based on genomic aberrations only, we defined eight different clusters. We detected four distinct and potentially clinically relevant genotypes harboring unique genomic features, including: 1) Microsatellite Instability; 2) Homologous Recombination Deficiency (HRD) with enriched genomic deletions and BRCA2 aberrations; 3) tandem duplication phenotype associated with biallelic CDK12 mutations; and 4) a subgroup enriched for chromothripsis events. Our data suggest that classifying patients using WGS characteristics may improve classification of HRD patients. Moreover, we confirmed that important regulators of AR-mediated signaling are located in non-coding regions. Using ChIP sequencing data, we showed that the amplified AR and MYC promoter regions contain open chromatin and bind AR, suggesting a role in AR mediated biology. Thus, high-resolution WGS may be used to improve patient stratification.
The Molecular Mass and Isoelectric Point of Plant Proteomes
Authors: Mohanta Tapan Kumar , Khan Abdullatif , Hashem Abeer , Abd_Allah Elsayed Fathi , Al-Harrasi Ahmed
Published: February 2019

A proteomic analysis of proteomes from 145 plant species revealed apIrange of 1.99 (epsin) to 13.96 (hypothetical protein). The molecular mass of the plant proteins ranged from 0.54 to 2236.8 kDa. A putative Type-I polyketide synthase (22244 amino acids) inVolvox carteriwas found to be the largest protein in the plant kingdom and was not found in higher plant species. Titin (806.46 kDa) and misin/midasin (730.02 kDa) were the largest proteins identified in higher plant species. ThepIand molecular weight of the plant proteome exhibited a trimodal distribution. An acidicpI(56.44% of proteins) was found to be predominant over a basicpI(43.34% of proteins) and the abundance of acidicpIproteins was higher in unicellular algae species relative to multicellular higher plants. In contrast, the seaweed,Porphyra umbilicalis, possesses a higher proportion of basicpIproteins (70.09%). Plant proteomes were also found to contain the amino acid, selenocysteine (Sec), which is the first report of the presence of this amino acid in plants. Additionally, plant proteomes also possess ambiguous amino acids Xaa (unknown), Asx (asparagine or aspartic acid), Glx (glutamine or glutamic acid), and Xle (leucine or isoleucine) as well.
Inter-thinker consistency of language activations during abstract thoughts
Authors: Berkovich-Ohana Aviva , Noy Niv , Harel Michal , Furman-Haran Edna , Arieli Amos , Malach Rafael
Published: February 2019

Human brain imaging typically employs structured and controlled tasks to avoid variable and inconsistent activation patterns. Here we argue against this assumption by showing that an extremely open-ended, high level cognitive task-loosely defined as “abstract thinking” leads to a precise, and highly consistent activation maps. Thus we show that activation maps generated during such cognitive process were precisely located relative to borders of well-known networks such as internal speech, visual and motor imagery.The activation patterns allowed decoding the thought condition at >95%.Surprisingly, the activated networks remained the same regardless of changes in thought content. Finally, we found a remarkably consistent activation map across individuals engaged in abstract thinking. The activation to abstract thinking bordered, but strictly avoided visual and motor networks. On the other hand, it partly overlapped with left lateralized language networks. These observations were supported by a quantitative neuronal distance metric analysis. Our results reveal that despite its high level, and varied content nature-abstract thinking activates surprisingly precise and consistent networks in the participants’ brains.

’Thinker’ refers to: The agent of thought; Intellectual, one who tries to use his or her intellect to work, study, reflect, speculate on, or ask and answer questions with regard to a variety of different ideas” (Wikipedia).
An alternatively spliced zebrafishjnk1atranscript has an essential and non-redundant role in development of the first heart field derived proximal ventricular chamber
Authors: Santos-Ledo A , Washer S , Dhanaseelan T , Chrystal P , Papoutsi T , Henderson DJ , Chaudhry B
Published: February 2019

Alternative splicing is a ubiquitous mechanism for producing different mRNA species from a single gene, resulting in proteomic diversity. Despite potential for regulating embryogenesis, its developmental role remains under-investigated. TheJun kinase(Jnk) genes, considered downstream effectors of the non-canonical Wnt planar cell polarity pathway, utilise extensive and evolutionarily-conserved alternative splicing. Although many PCP members are associated with heart malformation, the role ofJnkgenes in cardiac development, and specifically which alternatively spliced transcripts orchestrate these processes, remain unknown. In this study we exploit thejnk1duplication and subspecialisation found in zebrafish to reveal an essential and non-redundant requirement forjnk1ain cardiac development. We characterise alternatively splicedjnk1a/jnk1btranscripts and demonstrate that hypoplasia of the proximal ventricular component, which corresponds to human hypoplastic left ventricle, can only be rescued by thejnk1a Ex7 Lgtranscript. These studies highlight the importance of Jnk signalling and alternative splicing in heart development
Assessment of knowledge, attitudes and practices about antibiotic resistance among medical students in India
Authors: Gupta Manoj Kumar , Vohra Chirag , Raghav Pankaja
Published: February 2019

Background

To reduce the magnitude of antimicrobial resistance, there is a need to change the knowledge and behavior of future prescribers regarding use and prescription of antibiotics. This can be ensured through the appropriate training of next generation doctors and medical students. But, before planning or strengthening any teaching or training program for any group, it is required to have a conclusive evidence about knowledge, attitude and practices of that group. With this background this study was conducted to assess the knowledge, attitudes and the practices of medical students in India with respect to antibiotic resistance and usage

Methods

It was a cross-sectional study which was done online through google forms. A semi-structured questionnaire containing a five point Likert scale was used for the data collection. The questionnaire was sent to medical students across India by sharing link through contacts of Medical Students Association of India. Respondent-driven sampling technique was also adopted for the study. Data was analyzed using SPSS v.25 and Microsoft Excel 2016.

Results

The overall mean score of awareness for the students was 4.36 + 0.39. As compared to first year students, mean score of awareness was significantly higher among students of all the years. A significantly better awareness was also observed among pre final year students as compared to other years. Variable practices have been observed regarding use of antibiotics among medical students.

Conclusion

The awareness level of medical students regarding antibiotics and its resistance was quite satisfactory. As far as attitude and practices are concerned, there is a significant need for improvements.
Efficient callus induction and completion of regeneration in kenaf Hibiscus cannabinus
Authors: Odahara Masaki , Horii Yoko , Kimura Mitsuhiro , Numata Keiji
Published: February 2019

Kenaf, Hibiscus cannabinus, is a fiber-enriched plant belonging to Malvaceae and is an important fiber crop. The features of kenaf of being fast-growing and fiber-enriched suggest the potential for the use of kenaf in biomass and materials; however, the complete regeneration procedure, which is essential for genetic modification, is lacking. Here, we report the complete regeneration of kenaf from cotyledon explants achieved by callus induction on an improved callus-inducing medium and shoot induction on a shoot-inducing medium and by seed setting under a regulated growth condition in a chamber. Our complete regeneration method will enable the production of stably transformed kenaf that can improve the properties of kenaf as a material.
A three-domain copper-nitrite reductase with a unique sensing loop
Authors: Opperman Diederik Johannes , Murgida Daniel Horacio , Dalosto Sergio Daniel , Brondino Carlos Dante , Ferroni Felix Martín
Published: February 2019

Dissimilatory nitrite reductases are key enzymes in the denitrification pathway, reducing nitrite and leading to the production of gaseous products (NO, N2O and N2). The reaction is catalysed either by a Cu-containing nitrite reductase (NirK) or by a cytochromecd1nitrite reductase (NirS), as the simultaneous presence of the two enzymes has never been detected in the same microorganism. The thermophilic bacteriumThermus scotoductusSA-01 is an exception to this rule, harbouring both genes within a denitrification cluster, which encodes for an atypical NirK. The crystal structure ofTsNirK has been determined at 1.63 Å resolution.TsNirK is a homotrimer with subunits of 451 residues that contain three copper atoms each. The N-terminal region possesses a type 2 Cu (T2Cu) and a type 1 Cu (T1CuN) while the C-terminus contains an extra type 1 Cu (T1CuC) bound within a cupredoxin motif. T1CuNshows an unusual Cu atom coordination (His2–Cys–Gln) compared with T1Cu observed in NirKs reported so far (His2–Cys–Met). T1CuCis buried at ∼5 Å from the molecular surface and located ∼14.1 Å away from T1CuN; T1CuNand T2Cu are ∼12.6 Å apart. All these distances are compatible with an electron-transfer process T1CuC→ T1CuN→ T2Cu. T1CuNand T2Cu are connected by a typical Cys–His bridge and an unexpected sensing loop which harbours a SerCATresidue close to T2Cu, suggesting an alternative nitrite-reduction mechanism in these enzymes. Biophysicochemical and functional features ofTsNirK are discussed on the basis of X-ray crystallography, electron paramagnetic resonance, resonance Raman and kinetic experiments.
Long-wavelength Mesh&Collect native SAD phasing from microcrystals
Authors: Cianci Michele , Nanao Max , Schneider Thomas R.
Published: February 2019

Harnessing the anomalous signal from macromolecular crystals with volumes of less than 10 000 µm3 for native phasing requires careful experimental planning. The type of anomalous scatterers that are naturally present in the sample, such as sulfur, phosphorus and calcium, will dictate the beam energy required and determine the level of radiation sensitivity, while the crystal size will dictate the beam size and the sample-mounting technique, in turn indicating the specifications of a suitable beamline. On the EMBL beamline P13 at PETRA III, Mesh&Collect data collection from concanavalin A microcrystals with linear dimensions of ∼20 µm or less using an accordingly sized microbeam at a wavelength of 1.892 Å (6.551 keV, close to the Mn edge at 6.549 keV) increases the expected Bijvoet ratio to 2.1% from an expected 0.7% at 12.6 keV (Se K edge), thus allowing experimental phase determination using the anomalous signal from naturally present Mn2+ and Ca2+ ions. Dozens of crystals were harvested and flash-cryocooled in micro-meshes, rapidly screened for diffraction (less than a minute per loop) and then used for serial Mesh&Collect collection of about 298 partial data sets (10° of crystal rotation per sample). The partial data sets were integrated and scaled. A genetic algorithm for combining partial data sets was used to select those to be merged into a single data set. This final data set showed high completeness, high multiplicity and sufficient anomalous signal to locate the anomalous scatterers, and provided phasing information which allowed complete auto-tracing of the polypeptide chain. To allow the complete experiment to run in less than 2 h, a practically acceptable time frame, the diffractometer and detector had to run together with limited manual intervention. The combination of several cutting-edge components allowed accurate anomalous signal to be measured from small crystals.
Competitiveness and managerial discretion: an empirical investigation at the national-level
Authors: Haj Youssef Moustafa Salman , Hussein Hiba Maher , Christodoulou Ioannis
Published: February 2019

Purpose

The purpose of this paper is to examine the national-level predictors of country competitiveness using the concept of managerial discretion. The objective is to empirically link the strategic management discipline particularly the upper echelon theory to the concept of country performance measured by competitiveness.

Design/methodology/approach

This paper tests the proposed relationship between managerial discretion and country competitiveness using a sample of 18 countries from 6 different regional clusters. Discretion scores are generated from survey responses of prominent senior management consultants, while country competitiveness is measured via the Global Competitiveness Index developed by the World Economic Forum. A multi-level regression analysis on the panel data set spanning 10 years of national competitiveness levels is used to empirically demonstrate the association between managerial discretion and country competitiveness.

Findings

The authors show that managerial discretion is a direct predictor of national competitiveness through its ability to provide CEOs with a wider array of actions to innovate and enhance firm performance which will ultimately contribute to country competitiveness.

Practical implications

The positive influence of managerial discretion on country competitiveness provide an interesting framework to examine the influence of firms over public policy-making. Additionally, with businesses becoming increasingly globalized, the profile of countries becomes of a great importance and can become a tool for corporate strategic decisions, such as: market entry strategies.

Originality/value

By linking the well-known term of competitiveness to the concept of managerial discretion, the authors provide a totally new approach to assess country performance. Additionally, this paper contributes to the growing literature of managerial discretion by discovering new national-level consequences.
Export competitiveness with border-sharing countries: an assessment of Pakistan
Authors: Munir Kashif , Sultan Maryam
Published: February 2019

Purpose

The purpose of this study is to analyze the export competitiveness of Pakistan with border-sharing countries, i.e. Afghanistan, China, India and Iran for the year 2014.

Design/methodology/approach

The study uses revealed symmetric comparative advantage (RSCA) index to measure export competitiveness with border-sharing countries. The study has split the results into highest and marginal comparative advantage and disadvantage according to the rank.

Findings

Pakistan is exporting 160, 155, 133 and 60 commodities at three-digit level of Standard International Trade Code (Rev 3) classification to Afghanistan, China, India and Iran, respectively. The results suggest that Pakistan has highest and marginal comparative disadvantage in more than half of these commodities exported to border-sharing countries. Pakistan can improve its market share for rice in Afghanistan, China and Iran. Special measures and productive efforts are required to improve the export competitiveness of cotton, textile yarn and cotton fabric in border-sharing countries.

Practical implications

Pakistan has to adopt special strategies to improve the competitiveness of those commodities that fall in marginal comparative advantage and disadvantage. To increase the volume of cross-border trading, political and diplomatic channels are required among the countries especially the border-sharing countries.

Originality/value

Export competitiveness of Pakistan is analyzed for all the commodities exported to border-sharing countries and categorized into highest and marginal comparative advantage and disadvantage. To avoid the problem of asymmetry in Balassa index revealed comparative advantage, RSCA index is used.
Maximizing expected contractor profit using an integrated model
Authors: Alavipour S.M. Reza , Arditi David
Published: February 2019

Purpose

Planning for increased contractor profits should start at the time the contract is signed because low profits and lack of profitability are the primary causes of contractor failure. The purpose of this paper is to propose an integrated profit maximization model (IPMM) that aims for maximum expected profit by using time-cost tradeoff analysis, adjusted start times of activities, minimized financing cost and minimized extension of work schedule beyond the contract duration. This kind of integrated approach was never researched in the past.

Design/methodology/approach

IPMM is programmed into an automated system using MATLAB 2016a. It generates an optimal work schedule that leads to maximum profit by means of time-cost tradeoff analysis considering different activity acceleration/deceleration methods and adjusting the start/finish times of activities. While doing so, IPMM minimizes the contractor’s financing cost by considering combinations of different financing alternatives such as short-term loans, long-term loans and lines of credit. IPMM also considers the impact of extending the project duration on project profit.

Findings

IPMM is tested for different project durations, for the optimality of the solutions, differing activity start/finish times and project financing alternatives. In all cases, contractors can achieve maximum profit by using IPMM.

Research limitations/implications

IPMM considers a deterministic project schedule, whereas stochastic time-cost tradeoff analysis can improve its performance. Resource allocation and resource leveling are not considered in IPMM, but can be incorporated into the model in future research. Finally, the long computational time is a challenge that needs to be overcome in future research.

Practical implications

IPMM is likely to increase profits and improve the chances of contractors to survive and grow compared to their competitors. The practical value of IPMM is that any contractor can and should use IPMM since all the data required to run IPMM is available to the contractor at the time the contract is signed. The contractor who provides information about network logic, schedule data, cost data, contractual terms, and available financing alternatives and their APRs can use an automated IPMM that adjusts activity start times and durations, minimizes financing cost, eliminates or minimizes time extensions, minimizes total cost and maximizes expected profit.

Originality/value

Unlike any prior study that looks into contractors’ profits by considering the impact of only one or two factors at a time, this study presents an IPMM that considers all major factors that affect profits, namely, time-cost tradeoff analysis, adjusted start times of activities, minimized financing cost and minimized extension of work schedule beyond the contract duration.
WinChannel’s digital gambit to revitalize rural China
Authors: Moran Peter , Chng Daniel Han Ming , Zhao Liman
Published: February 2019

Learning outcomes

Following are the learning outcomes: to understand how the tools and frameworks of strategic analysis can be applied to understand the evolution of value creation and capture in the FMCG industry; to analyze the core competencies of a company and understand their relevance in this fast-changing industry; to understand how to evaluate the pros and cons of a certain strategy and business model; and to develop strategic recommendations.

Case overview/synopsis

The case series traces the developments in China’s FMCG industry from the early 2010s to 2017, in general, and the efforts of Beijing WinChannel Software Technology Co., Ltd. (WinChannel) and its affiliated company, Huixiadan, in their attempt to apply new digital technologies to transform the traditional trade channel, in particular. The decision point of Case A, in early 2015, is how WinChannel can help improve the reach and efficiency of the traditional trade channel and wonders if the emerging online/mobile B2B FMCG platforms are the right solution for the increasingly digitized FMCG retail industry in China. The decision point of Case B, at the end of 2017, is how could Huixiadan’s business model be sustainable and what it should do to withstand the competitive threats even as it tries to exploit opportunities in the traditional FMCG industry in China.

Complexity academic level

It can be used with MBAs, EMBAs and senior executives.

Supplementary materials

Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS: 11: Strategy.
Entrepreneurship education and undergraduate students’ self- and paid-employment intentions
Authors: Otache Innocent
Published: February 2019

Purpose

The purpose of this paper is to conceptually explore the relationship between Entrepreneurship Education (EE) and undergraduate students’ self- and paid-employment intentions. Specifically, the paper aims to examine the effect of paid-employment intention on the relationship between EE and self-employment intention.

Design/methodology/approach

This paper reviewed extensively related literature on EE, entrepreneurial intentions and the theory of planned behaviour (TPB). The detailed literature review undertaken formed the basis for the development of the conceptual framework.

Findings

It is found that undergraduate students have two opposing employment intentions within them, namely, self- and paid-employment intentions. The two employment intentions interact and have a tendency to dominate each other, and consequently lead to different employment behaviours. The dominant employment intention determines whether a graduate will exhibit self- or paid-employment behaviour. This confirms that graduates are faced with two career paths or choices, namely, self- and paid-employment.

Research limitations/implications

It is not an empirical paper. Thus, the conceptual framework needs to be further empirically tested. More specifically, the proposition that undergraduate students’ paid-employment intentions moderate the impact of EE on their self-employment intentions needs to be empirically validated.

Practical implications

This paper provides some insightful and practical implications for the government and the policymakers in the education sector, particularly in tackling the menace of graduate unemployment and its associated problems. It provides an insight into the problem of graduate unemployment. The government and the policymakers should initiate enlightenment programmes that will reorient undergraduate students away from having the mentality of securing paid-jobs after graduation. Equally, undergraduate students should be enlightened about the difficulties in securing paid-jobs and the benefits of being a self-employed graduate.

Originality/value

It is the first to explore the moderating effect of undergraduate students’ paid-employment intentions on the relationship between EE and their self-employment intentions. Therefore, it makes a valuable contribution to the existing literature on EE and entrepreneurial intentions. It further strengthens the TPB by applying it to explain how undergraduate students’ paid-employment intentions could neutralise the impact of EE on their self-employment intentions.