bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential Gene Expression Analysis of a Small Colony Variant ofEscherichia coliK-12
Authors: Paratore Anthony W. , Santos Victors , Bibis Stergios , Hirshfield Irvin N.
Published: September 2018

As persistent residents of planktonic bacterial cultures, small colony variants (SCVs) constitute a slow-growing subpopulation with atypical colony morphology and unusual biochemical characteristics that, in the case of clinical isolates, cause latent and recurrent infections. We propose a novel blueprint for the formation ofE. coliSCVs through DNA microarray analysis, coupled with complete genome sequencing and verification by qRT-PCR. While others have used DNA microarrays to study quorum sensing inE. coliSCVs, our work represents the first proposal for a combination of novel mutations, amplified by a differential shift in expression of select gene groups that work in concert to establish and maintain the SCV phenotype. This combination of genetic and expression events fall under selective pressure, leading to unequal fitness in our strain, SCV IH9 versus its parental strain, BW7261 (a MG1655 descendant). We hypothesize that this combination of events would ordinarily be lethal for bacteria, but instead confers a survival advantage to SCV IH9 due to its slow growth and resistance to acidic and oxidative stress challenges.
Template-free detection and classification of heterogeneous membrane-bound complexes in cryo-electron tomograms
Authors: Martinez-Sanchez Antonio , Kochovski Zdravko , Laugks Ulrike , Borgloh Johannes Meyer zum Alten , Chakraborty Saikat , Pfeffer Stefan , Baumeister Wolfgang , Lucic Vladan
Published: September 2018

With faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography (cryo-ET) provides an accurate representation of molecular architecture of cells. However, detection and precise localization of macromolecular complexes within cellular environments is aggravated by the presence of many molecular species and molecular crowding. We developed a template-free image processing procedure for accurate tracing of complex networks of densities in cryo-electron tomograms, a comprehensive and automated detection of heterogeneous membrane-bound complexes and an unsupervised classification. Applying this procedure to tomograms of intact cells and isolated endoplasmic reticulum (ER), we detected and classified small protein complexes like the ER protein translocons, which were not detected by other methods before. This classification provided sufficiently homogeneous particle sets and initial references to allow subsequent de novo subtomogram averaging. Therefore the procedure presented allows a comprehensive detection and a structural analysis of complexes in their native state. In addition, we present structural evidence that different ribosome-free translocon species are present at the ER membrane, determine their 3D structure, and show that they have different localization patterns forming nanodomains.
Optogenetics enables real-time spatiotemporal control over spiral wave dynamics in an excitable cardiac system
Authors: Majumder Rupamanjari , Feola Iolanda , Teplenin Alexander S. , de Vries Antoine A. F. , Panfilov Alexander V. , Pijnappels Daniël A.
Published: September 2018

Propagation of non-linear waves is key to the functioning of diverse biological systems. Such waves can organize into spirals, rotating around a core, whose properties determine the overall wave dynamics. Theoretically, manipulation of a spiral wave core should lead to full spatiotemporal control over its dynamics. However, this theory lacks supportive evidence (even at a conceptual level), making it thus a long-standing hypothesis. Here, we propose a new phenomenological concept that involves artificially dragging spiral waves by their cores, to prove the afore-mentioned hypothesis in silico, with subsequent in vitro validation in optogenetically-modified monolayers of rat atrial cardiomyocytes. We thereby connect previously established, but unrelated concepts of spiral wave attraction, anchoring and unpinning to demonstrate that core manipulation, through controlled displacement of heterogeneities in excitable media, allows forced movement of spiral waves along pre-defined trajectories. Consequently, we impose real-time spatiotemporal control over spiral wave dynamics in a biological system.
Lessons learned when looking for non-neutral ecological processes in the built environment: the bacterial and fungal microbiota of shower tiles
Authors: Adams Rachel I. , Lymperopoulou Despoina L.
Published: September 2018

With periodic pulses of water, bathroom showers represent a habitat in the built environment with a high potential for microbial growth. We set out to apply a neutral model of microbial community assembly and to identify deviations from the model that would indicate non-neutral dynamics, such as selective pressures for individual taxa, in this particular indoor habitat. Following a cleaning event, the bacterial and fungal microbiota of the shower stalls in two residences in the San Francisco Bay Area were observed over a four-week period. We observed strong differences in composition between houses, preventing us from combining samples and thus limiting our statistical power. We also identified different aspects of the sampling scheme that could be improved, including increasing the sampling area (to ensure sufficient biomass) and increasing the number of replicates within an individual shower. The data from this pilot study indicate that immigrants to the built environment arising from human shedding dominate the shower ecosystem and that growth conditions are relatively unfavorable despite the water availability. We offer suggestions on how to improve the studying and sampling of microbes in indoor environments.
Genetic differences between Coccidioides spp. and closely related nonpathogenic Onygenales
Authors: Kirkland Theo N.
Published: September 2018

Coccidioides spp. are dimorphic, pathogenic fungi that can cause severe human and animal disease. Like the other primary fungal pathogens, animal infection results in a morphologic transformation from the environmental mycelial phase to a tissue phase, known as a spherule. The sequencing and annotation of Coccidioides spp. and the genomes of several nonpathogenic Onygenales species allows comparisons that provide clues about the Coccidioides spp. genes that might be involved in pathogenesis. The analysis in this study is a gene by gene orthology comparison. Although there were few differences in the size of genes families in the Coccidioides spp.-specific group compared to the genes shared by Coccidioides spp. and nonpathogenic Onygenales, there were a number of differences in the characterization of the two types of genes. Many more Coccidioides spp.-specific genes are up-regulated expression in spherules. Coccidioides spp.-specific genes more often lacked functional annotation and were more often classified as orphan genes. Analysis by random forest machine learning confirmed that high numbers of orthologs and high levels of expression in hyphae were predictive of common genes, while high levels of expression in spherules and more nonsynonymous predicted Coccidioides spp.-specific genes. Review of individual genes in the Coccidioides spp.-specific group identified a histidine kinase, two thioredoxin genes, a calmodulin gene and ureidoglycolate hydrolase. Hopefully, identification of these genes will be useful for pursuing potential Coccidioides spp. virulence genes in the future.
Ultrasensitive molecular controllers for quasi-integral feedback
Authors: Samaniego Christian Cuba , Franco Elisa
Published: September 2018

Feedback control has enabled the success of automated technologies by mitigating the effects of variability, unknown disturbances, and noise. Similarly, feedback loops in biology reduce the impact of noise and help shape kinetic responses, but it is still unclear how to rationally design molecular controllers that approach the performance of controllers in traditional engineering applications, in particular the performance of integral controllers. Here, we describe a strategy to build molecular quasi-integral controllers by following two design principles: (1) a highly ultrasensitive response, which guarantees a small steady-state error, and (2) a tunable ultrasensitivity threshold, which determines the system equilibrium point (reference). We describe a molecular reaction network, which we name Brink motif, that satisfies these requirements by combining sequestration and an activation/deactivation cycle. We show that if ultrasensitivity conditions are satisfied, this motif operates as a quasi-integral controller and promotes homeostatic behavior of the closed-loop system (robust tracking of the input reference while rejecting disturbances). We propose potential biological implementations of Brink controllers and we illustrate different example applications with computational models.
Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro
Authors: Pal Soumitra , Hoinka Jan , Przytycka Teresa M.
Published: September 2018

Understanding the principles of DNA binding by transcription factors (TFs) is of primary importance for studying gene regulation. Recently, several lines of evidence suggested that both DNA sequence and shape contribute to TF binding. However, the question if in the absence of any sequence similarity to the binding motif, DNA shape can still increase probability of binding was yet to be addressed.

To address this challenge, we developed Co-SELECT, a computational approach to analyze the results of in vitro HT-SELEX experiments for TF-DNA binding. Specifically, the presence of motif-free sequences in late HT-SELEX rounds and their enrichment in weak binders allowed us to detect evidence for the role of DNA shape features in TF binding.

Our approach revealed that, even in the absence of the sequence motif, TFs have propensity to weakly bind to DNA molecules enriched in specific shape features. Surprisingly, we also found that some properties of DNA shape contribute to promiscuous binding of all tested TF families. Strikingly, such promiscuously bound shapes correspond to the most frequent shape formed by the DNA. We propose that this promiscuous binding facilitates diffusing of TFs along the DNA molecule before it is locked in its binding site.
Is faster always better? The walking speed-dependency of gait variability in bilateral vestibulopathy
Authors: McCrum Christopher , Lucieer Florence , van de Berg Raymond , Willems Paul , Fornos Angélica Pérez , Guinand Nils , Karamanidis Kiros , Kingma Herman , Meijer Kenneth
Published: September 2018

Study of balance and gait deficits associated with vestibulopathy is important for improving clinical care and is critical to our understanding of the vestibular contributions to gait and balance control. Previous studies report a speed-dependency of the vestibular contributions to gait, so we examined the walking speed effects on gait variability in healthy young and older adults and in adults with bilateral vestibulopathy (BVP). Forty-four people with BVP, 12 healthy young adults and 12 healthy older adults completed walking trials at 0.4m/s to 1.6m/s in 0.2m/s intervals on a dual belt, instrumented treadmill. Using a motion capture system and kinematic data, the means and coefficients of variation for step length, time, width and double support time were calculated. The BVP group also completed a video head impulse test and examinations of ocular and cervical vestibular evoked myogenic potentials and dynamic visual acuity. Walking speed significantly affected all assessed gait parameters. Step length variability at slower speeds and step width variability at faster speeds were the most distinguishing parameters between the healthy participants and people with BVP, and within people with BVP with different locomotor capacities. We observed for step width variability, specifically, an apparent persistent importance of vestibular function at increasing speeds. Gait variability was not associated with the clinical vestibular tests. Our results indicate that gait variability at multiple walking speeds has potential as an assessment tool for vestibular interventions.

New & Noteworthy:

Walking speed significantly but differentially affects gait variability in healthy adults and in adults with bilateral vestibulopathy. Gait variability at different speeds distinguishes between participants with and without bilateral vestibulopathy, but also between more and less able walkers with bilateral vestibulopathy. Specifically, for step width variability, an apparent persistent importance of vestibular function at increasing walking speeds was observed. Gait variability was generally not correlated with clinical tests of vestibular function.
A lysosomal dimmer switch regulates cellular quiescence depth
Authors: Fujimaki Kotaro , Li Ruoyan , Chen Hengyu , Croce Kimiko Della , Zhang Hao Helen , Xing Jianhua , Bai Fan , Yao Guang
Published: September 2018

Numerous physiological and pathological phenomena are associated with the quiescent state of a cell. Cellular quiescence is a heterogeneous resting state; cells in deep than shallow quiescence require stronger growth stimulation to exit quiescence and reenter the cell cycle. Despite the importance of quiescent cells such as stem and progenitor cells to tissue homeostasis and repair, cellular mechanisms controlling the depth of cellular quiescence are poorly understood. Here we began by analyzing transcriptome changes as rat embryonic fibroblasts moved progressively deeper into quiescence under increasingly longer periods of serum starvation. We found that lysosomal gene expression was significantly upregulated in deep than shallow quiescence, which compensated for gradually reduced autophagy flux observed during quiescence deepening. Consistently, we show that inhibiting lysosomal function drove cells deeper into quiescence and eventually into a senescence-like irreversibly arrested state. By contrast, increasing lysosomal function progressively pushed cells into shallower quiescence. That is, lysosomal function modulates quiescence depth continuously like a dimmer switch. Mechanistically, we show that lysosomal function prevents quiescence deepening by reducing oxidative stress in the cell. Lastly, we show that a gene expression signature developed by comparing deep and shallow quiescent cells can correctly classify senescent and aging cells in a wide array of cell lines in vitro and tissues in vivo, suggesting that quiescence deepening, senescence, and aging may share common regulatory mechanisms.
Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish
Authors: Whitesell Thomas R. , Chrystal Paul , Ryu Jae-Ryeon , Munsie Nicole , Grosse Ann , French Curtis , Workentine Matthew L. , Li Rui , Zhu Lihua Julie , Waskiewicz Andrew , Lehmann Ordan J. , Lawson Nathan D. , Childs Sarah J.
Published: September 2018

Despite the critical role of vascular mural cells (smooth muscle cells and pericytes) in supporting the endothelium of blood vessels, we know little of their early morphogenesis and differentiation.foxc1b:EGFPexpressing cells in zebrafish associate with the vascular endothelium (kdrl) and co-express a smooth muscle marker (acta2), but not a pericyte marker (pdgfrβ). The expression offoxc1bin early peri-endothelial mesenchymal cells allows us to follow the morphogenesis of mesenchyme intoacta2expressing vascular smooth muscle cells. We show that mural cells expressing different markers associate with vessels of different diameters, depending on their embryonic location and developmental timing, suggesting marker expression is predictive of functional differences. We identify gene expression signatures for an enriched vascular smooth muscle cell population (foxc1b + acta2)and all smooth muscle(acta2)using fluorescence-activated cell sorting and RNA-Seq. Finally, we demonstrate that progressive loss offoxc1a/foxc1bresults in decreased smooth muscle cell coverage. Together, our data highlight the early cellular dynamics and transcriptome profiles of smooth muscle cellsin vivo,usingfoxc1bas a unique tool to probe vascular smooth muscle cell differentiation.

Summary Statement

Tracing the morphogenesis and transcriptome of early vascular smooth muscle cells using foxc1b
NUCOME: A Comprehensive Database of Nucleosome Organizations in Mammalian Genomes
Authors: Chen Xiaolan , Yang Hui , Zhang Yong
Published: September 2018

Nucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organizations in mammalian genomes are very limited mainly due to the lack of comprehensive data management. Here, we presentNUCOME, which is the first database to organize publicly available MNase-seq data resource and manage unified processed datasets covering various cell types in human and mouse. TheNUCOMEprovides standard, qualified and informative nucleosome organization data at the genome scale and at any genomic regions for users’ downstream analyses.NUCOMEis freely available athttp://compbio.tongji.edu.cn/NUCOME/.
Ligand modulation of allosteric networks in an ancestral steroid receptor
Authors: Okafor C. Denise , Ortlund Eric A.
Published: September 2018

Understanding the evolution of binding specificity, a heavily studied area of research, is key for determining how protein sequence changes alter function. Ligand-activation in the steroid receptor subfamily of transcription factors operates via a common allosteric mechanism which permits extant receptors to respond specifically to their cognate hormones. Here, we combine atomistic simulations with graph theory-based modeling of the inter-residue interactions within protein complexes to gain insight into how allostery drove selectivity in an ancestral receptor. An inactive ligand complex displays weakened allosteric communication, as quantified by suboptimal paths linking two functional surfaces. When function-switching mutations are incorporated, responses in allosteric networks are consistent with ligand activation status. Further analysis reveals residues that modulate features distinguishing active and inactive complexes, identifying a key, conserved residue that is crucial for activation in steroid receptors. We have identified a computational method using dynamic network analysis to probe the allosteric mechanisms driving the evolution of ligand specificity in hormone receptors, determining how residue substitutions altered allosteric networks to permit gain or loss of ligand response. These results may have general utility in elucidating how modern steroid receptors are activated by endogenous and xenobiotic molecules.

Author summary

Proteins interact with a host of biological partners to mediate their function. These binding partners are able to alter structural properties of the protein to send signals dictating downstream biological activity. This mode of regulation is described as allostery. Here, we perform a computational investigation of allostery in steroid receptors, a family of proteins that regulate a host of important biological processes in response to binding and activation by a steroidal ligand. We leverage a defined evolutionary system where known historical amino acid substitutions within the receptor drive a switch in ligand preference and receptor activation. We show that activating ligands induce stronger allosteric signaling between the ligand and the functional surface on the receptor. In addition, we incorporate evolutionary mutations that are known to alter ligand preference and show that this effect may be explained by allostery. This work provides insight into how amino acid substitutions over evolution affect allostery in proteins, permitting the loss and gain of function.
ATM is activated by ATP depletion and modulates mitochondrial function through NRF1
Authors: Chow Hei-Man , Cheng Aifang , Song Xuan , Swerdel Mavis R. , Hart Ronald P. , Herrup Karl
Published: September 2018

We have uncovered new insights into the symptoms of ataxia-telangiectasia (A-T). Neurons with high physiological activity, particularly cerebellar Purkinje cells, have large and dynamic ATP demands. Depletion of ATP generates reactive oxygen species that activate ATM (the A-T Mutated gene product). Activated in this way, but not by DNA damage, ATM phosphorylates nuclear respiratory factor-1 (NRF1). This leads to NRF1 dimerization, nuclear translocation and the upregulation of nuclear-encoded mitochondrial genes, thus enhancing the capacity of the electron transport chain (ETC) and restoring mitochondrial function. In cells with ATM deficiency, resting ATP levels are normal, but cells replenish ATP poorly following surges in energy demand and chronic ATP insufficiency endangers cell survival. This is a particular problem for energy-intensive cells such as Purkinje cells, which degenerate in A-T. Our findings thus identify ATM as a guardian of mitochondrial output as well as genomic integrity, and suggest that alternate fuel sources may ameliorate A-T disease symptoms.

Oxidative stress, resulting from neuronal activity and depleted ATP levels, activates ATM, which phosphorylates NRF1, causing nuclear translocation and upregulation of mitochondrial gene expression. In ATM deficiency, ATP levels recover more slowly, particularly in active neurons with high energy demands.
Axonal tree morphology and signal propagation dynamics improve interneuron classification
Authors: Ofer Netanel , Shefi Orit , Yaari Gur
Published: September 2018

Neurons are diverse and can be differentiated by their morphological, electrophysiological, and molecular properties. Current morphology-based classification approaches largely rely on the dendritic tree structure or on the overall axonal projection layout. Here, we use data from public databases of neuronal reconstructions and membrane properties to study the characteristics of the axonal and dendritic trees for interneuron classification. We show that combining signal propagation patterns observed by biophysical simulations of the activity along ramified axonal trees with morphological parameters of the axonal and dendritic trees, significantly improve classification results compared to previous approaches. The classification schemes introduced here can be utilized to robustly classify neuronal subtypes in a functionally relevant manner. Our work paves the way for understanding and utilizing form-function principles in realistic neuronal reconstructions.
Precursor microRNA Identification Using Deep Convolutional Neural Networks
Authors: Do Binh Thanh , Golkov Vladimir , Gürel Göktuğ Erce , Cremers Daniel
Published: September 2018

Precursor microRNA (pre-miRNA) identification is the basis for identifying microRNAs (miRNAs), which have important roles in post-transcriptional regulation of gene expression. In this paper, we propose a deep learning method to identify whether a small non-coding RNA sequence is a pre-miRNA or not. We outperform state-of-the-art methods on three benchmark datasets, namely the human, cross-species, and new datasets. The key of our method is to use a matrix representation of predicted secondary structure as input to a 2D convolutional network. The neural network extracts optimized features automatically instead of using a large number of handcrafted features as most existing methods do. Code and results are available at https://github.com/peace195/miRNA-identification-conv2D.
The biochemical basis of microRNA targeting efficacy
Authors: McGeary Sean E. , Lin Kathy S. , Shi Charlie Y. , Bisaria Namita , Bartel David P.
Published: September 2018

MicroRNAs (miRNAs) act within Argonaute proteins to guide repression of mRNA targets. Although various approaches have provided insight into target recognition, the sparsity of miRNA–target affinity measurements has limited understanding and prediction of targeting efficacy. Here, we adapted RNA bind-n-seq to enable measurement of relative binding affinities between Argonaute–miRNA complexes and all ≤12-nucleotide sequences. This approach revealed noncanonical target sites unique to each miRNA, miRNA-specific differences in canonical target-site affinities, and a 100-fold impact of dinucleotides flanking each site. These data enabled construction of a biochemical model of miRNA-mediated repression, which was extended to all miRNA sequences using a convolutional neural network. This model substantially improved prediction of cellular repression, thereby providing a biochemical basis for quantitatively integrating miRNAs into gene-regulatory networks.
Structures of substituted pyridine N-oxide with manganese(II) acetate
Authors: Lynch Will , Lynch Genevieve , Sheriff Kirk , Padgett Clifford
Published: September 2018

Manganese(II) acetate coordination polymers have been prepared with three derivatives of pyridine N-oxide. The compounds are catena-poly[manganese(II)-μ3-acetato-di-μ2-acetato-[aquamanganese(II)]-μ2-acetato-μ-(pyridine N-oxide)-manganese(II)-μ3-acetato-μ2-acetato-μ-(pyridine N-oxide)-[aquamanganese(II)]-di-μ2-acetato], [Mn4(CH3COO)8(C5H5NO)2(H2O)2]
n
, (I), catena-poly[[manganese(II)]-μ3-acetato-μ2-acetato-μ-(2-methylpyridine N-oxide)-[aquamanganese(II)]-di-μ2-acetato-manganese(II)-di-μ2-acetato-μ3-acetato-[aquamanganese(II)]-μ2-acetato-μ-(2-methylpyridine N-oxide)], [Mn4(CH3COO)8(C6H7NO)2(H2O)2]
n
, (II), and catena-poly[[manganese(II)-di-μ2-acetato-μ-(4-methylpyridine N-oxide)] monohydrate], {[Mn(CH3COO)2(C6H7NO)]·H2O}
n
, (III). Compounds (I) and (II) both have three unique Mn atoms; in both compounds two of them sit on a crystallographic inversion center while the third is on a general position. In compound (III), the single unique Mn atom sits on a general position. Pseudo-octahedral six-coordinate manganese(II) centers are found in all compounds. All of the compounds form chains of Mn atoms bridged by acetate ions and the oxygen atom of the N-oxide in pyridine N-oxide (PNO), 2-methylpyridine N-oxide (2MePNO), or 4-methylpyridine N-oxide (4MePNO). Compound (I) and (II) both exhibit a bound water of solvation. In (I), the water hydrogen bonds to a nearby acetate whereas in (II) the water molecule forms bridging hydrogen bonds between two neighboring acetates. In compound (III) a water molecule of solvation is found in the lattice, not bound to the metal ion but hydrogen bonding to a bridging acetate.
A model of an e-customized co-design system on garment design
Authors: Li Pei , Chen Jian-Hui
Published: September 2018

Purpose

To improve the apparel e-customized system and meet consumers’ personalized requirement in the e-customization, the purpose of this paper is to develop an e-customized co-design system on garment design (ECS-GD) that enables users to co-design garment and communicate with stakeholders.

Design/methodology/approach

The e-customized co-design system mainly consists of function and modular structure, communication and evaluation modular. Based on the evolutionary algorithm and fuzzy theory, the e-customized system model is proposed with a presentation of garment interface. Based on the parameters of skirts, technical sketches, fabrics, color, patterns, comments and scores, the decision is made by consumers.

Findings

For the system to be effective, the system was conducted by multi-individuals co-work (consumers, designers, manufacturers and experts). The data flow was congruent to the design knowledge. The expert evaluation and communication were involved in the proposed system.

Research limitations/implications

The limitation of this study is that the system is not tested in experiments. The model, main function and data flow are proposed in this study, which is important in the e-customized co-design system development.

Originality/value

Compared to the e-shopping and garment recommendation, the proposed ECS-GD is a good approach to improve the existing e-customized system and a well solution to help consumers with design knowledge recommending, professional suggestions and evaluations. Besides, the sketches and knowledge recommendation are provided to consumers which is a learning process.
Higher education: exploring productivity over time
Authors: Miles Patti Collett , Peterson Michael , Miles Grant , Bement Danuse
Published: September 2018

Purpose

Higher education plays a critical role in the health of the US national economy. At the same time, there are increasing concerns regarding the cost of higher education and the effectiveness with which universities are using their money. Accordingly, the purpose of this paper is to examine changes in higher education productivity over the past 15 years across a sample of more than 500 public universities spanning multiple Carnegie classifications. By utilizing measures generated by a commission of the National Education Council, however, attention is more finely focused on the specific costs and outputs related to instructional activity than previous studies.

Design/methodology/approach

This research utilizes the recommendations of the National Education Center committee to examine productivity changes in higher education over the past 14 years. To that end, the hypotheses put forth in this research utilize 15 years data of Institutional Primary Education Data, 549 institutions and 3 productivity measures to assess how productivity in higher education has changed between 2002 and 2015.

Findings

The results of the present research suggest that instructional activity (measured as multifactor productivity) has increased in all Carnegie classifications between 2002 and 2016.

Research limitations/implications

The present study, organized by Carnegie classification, does not specify the cost of increased instructional productivity. As noted, there are concerns regarding whether at least some of the choices a university might make to increase instructional productivity – such as increased class size and/or an increased use of non-tenure track faculty – could adversely influence the quality of instruction and/or diminish student learning. Further, this research does not examine the relationship between research productivity and increasing instructional productivity.

Practical implications

The present study does not address the bigger question of whether the increasing costs of higher education are justified, because universities produce much more than student credit hours. While, in an ideal world, these various outputs will complement one another and utilize at least some of the same resources, each has its own unique inputs and associated expenses. Given this, an overall assessment of the value or productivity of a university as a whole is a very difficult thing to determine and is well beyond the scope of a single study.

Social implications

The present study explicitly focuses on the instructional component of universities and relationship between output and inputs. Ultimately, providing a clearer picture of how instructional productivity in higher education has been increasing over the past 14 years.

Originality/value

This research is the only research of its kind to the best knowledge of the researchers.
Leadership as a driver of entrepreneurship: an international exploratory study
Authors: Felix Claudia , Aparicio Sebastian , Urbano David
Published: September 2018

Purpose

The purpose of this paper is to examine the influence of cultural leadership factors (charismatic/value-based, team oriented, participative, humane, autonomous and self-protective) on the rates of opportunity and necessity entrepreneurship.

Design/methodology/approach

The study integrates insights from institutional and cultural leadership theories to provide a fresh perspective to advance comparative entrepreneurship research. To test the hypotheses, the authors conduct a multiple regression analysis with observations from 34 countries, using data (from the year 2013) from the Global Entrepreneurship Monitor for the dependent variable and from Global Leadership and Organizational Behavior Effectiveness to create leadership factors as independent variables.

Findings

The results show that all the types of leadership considered in the study have a relevant effect on entrepreneurial activity. However, charismatic leadership has a greater effect on entrepreneurial activity, particularly on opportunity entrepreneurship. The research also shows that autonomous leadership has a negative impact on entrepreneurial activity, although, when it is moderated by the humane dimension, this relationship changes.

Practical implications

Since the alternative dimensions facilitate or inhibit the generation of new firm creation, it is critical for researchers, teachers and leaders to learn about and to foster such leadership types.

Originality/value

This research covers a gap in the cross-cultural evidence presented in the literature and suggests the integration of the concepts leadership and entrepreneurship.
Product recalls, lobbying, and firm value
Authors: Rayfield Blake , Unsal Omer
Published: September 2018

Purpose

The purpose of this paper is to use a unique, hand-collected data set of Food and Drug Administration (FDA)-approved products to understand the effect of lobbying on the product market. The authors gather total 86,462 FDA labels including drug patents, drugs, pre-market approvals and medical devices and test the relationship between lobbying and future firms’ product submissions.

Design/methodology/approach

Using a sample of 86,462 FDA labels including drug patents, drugs, pre-market approvals and medical devices, the authors test the effect of lobbying on a firm’s future product submissions using survival analysis, logit, difference-in-differences and propensity score matching techniques.

Findings

The authors find lobbying firms experience an increase in the number of medical products approved. However, increased number of FDA labeling comes at the cost of product failure. The authors document that lobbying increases product recalls when responsible firms are associated with higher market withdrawals.

Originality/value

This study contributes to both the management literature on corporate lobbying and product recalls. Additionally, the study reveals the connection between pharmaceutical lobbying and firm value.
Managing open innovation
Authors: Naqshbandi M. Muzamil , Tabche Ibrahim , Choudhary Neetu
Published: September 2018

Purpose

The purpose of this paper is to examine the relationships between empowering leadership style and two types of open innovation: inbound and outbound. The intervening mechanism of employee involvement climate in these relationships is also investigated.

Design/methodology/approach

The paper uses data collected using a questionnaire survey from middle and top managers working in various firms in northern India.

Findings

Results reveal that empowering leadership positively affects both types of open innovation. Thus empowering leadership supports followers to seek, integrate and diffuse new ideas and knowledge to improve open innovation outcomes. Further, the mediating role of employee involvement climate is established for empowering leadership-inbound open innovation link. This suggests that an empowering leadership style creates an employee involvement climate that empowers employees and involves them in relevant decision-making which consequently enhances a firms inbound open innovation performance.

Research limitations/implications

This study used a cross-sectional research design and a relatively small sample size. These limitations can affect generalizability of the findings.

Originality/value

The paper contributes to leadership and open innovation literatures and provides insights into how the practitioners can use an appropriate leadership style to maximize success in the open innovation paradigm. The study is one of the first to empirically shed light on this strand of open innovation research.
A building’s design quality: measuring the esoteric
Authors: Zemke Dina Marie , Zhong Yun Ying , Raab Carola
Published: September 2018

Purpose

Firms that serve customers in the service environment rely on a well-designed servicescape. This is particularly true in the hotel industry, where the hotel’s design is an important part of the product mix. However, despite design’s importance, there is no common instrument available to measure hotel design quality. The purpose of this paper is to present a quantitative method, the Design Quality Indicator, to measure guests’ evaluations of hotel design quality.

Design/methodology/approach

Nearly 5,000 guests of two full-service hotel brands were surveyed soon after a hotel stay (within two weeks of check-out). The DQI’s factor structure is tested using principle components analysis and confirmatory factor analysis to improve the reliability, validity and parsimony of the instrument.

Findings

The study yields a DQI instrument that is reduced from 92 to 41 measurement items, with good reliability and validity, enabling more efficient data collection and analysis.

Research limitations/implications

This study only examines guests’ assessments of two full-service hotel brands. The instrument can be used to explore design’s relationship with numerous outcome variables, such as satisfaction, loyalty, and repatronage intentions, as well as property performance outcomes.

Practical implications

The methods demonstrated can be used by hotel owners and operators to inform resource allocation decisions, particularly when planning for renovations.

Originality/value

This study provides a reliable, validated quantitative assessment of hotel design quality. It is also one of the few studies that elicits feedback about a guest’s actual hotel stay, rather than a hypothesized or simulated stay.
Design and 3D printing customized guides for orthopaedic surgery – lessons learned
Authors: Popescu Diana , Laptoiu Dan , Marinescu Rodica , Botezatu Iozefina
Published: September 2018

Purpose

This paper aims to fill a research gap by presenting design and 3D printing guidelines and considerations which apply to the development process of patient-specific osteotomy guides for orthopaedic surgery.

Design/methodology/approach

Analysis of specific constraints related to patient-specific surgical guides design and 3D printing, lessons learned during the development process of osteotomy guides for orthopaedic surgery, literature review of recent studies in the field and data gathered from questioning a group of surgeons for capturing their preferences in terms of surgical guides design corresponding to precise functionality (materializing cutting trajectories, ensuring unique positioning and stable fixation during surgery), were all used to extract design recommendations.

Findings

General design rules for patient-specific osteotomy guides were inferred from examining each step of the design process applied in several case studies in relation to how these guides should be designed to fulfill medical and manufacturing (fused deposition modelling process) constraints. Literature was also investigated for finding other information than the simple reference that the surgical guide is modelled as negative of the bone. It was noticed that literature is focussed more on presenting and discussing medical issues and on assessing surgical outcomes, but hardly at all on guides’ design and design for additive manufacturing aspects. Moreover, surgeons’ opinion was investigated to collect data on different design aspects, as well as interest and willingness to use such 3D-printed surgical guides in training and surgery.

Practical implications

The study contains useful rules and recommendations for engineers involved in designing and 3D printing patient-specific osteotomy guides.

Originality/value

A synergetic approach to identify general rules and recommendations for the patient-specific surgical guides design is presented. Specific constraints are identified and analysed using three case studies of wrist, femur and foot osteotomies. Recent literature is reviewed and surgeons’ opinion is investigated.
Pseudovascular squamous cell carcinoma: A review of the published work and reassessment of prognosis
Authors: Kiyohara Takahiro , Miyamoto Mari , Shijimaya Takako , Nagano Naoko , Nakamaru Sei , Makimura Kaoru , Tanimura Hirotsugu
Published: September 2018

A 90‐year‐old Japanese woman presented with a dome‐shaped, dark‐red, ulcerated nodule measuring 23 mm × 19 mm × 9 mm on the right side of the nasal root. Histologically, anastomosing cord‐like arrays of atypical polygonal keratinocytes exhibiting internal pseudolumina containing detached cells and erythrocytes were observed. Although acantholytic and cohesive areas overlapped, cancer pearls were not detected. The lower epidermis partially demonstrated scattered dyskeratotic and acantholytic keratinocytes with loss of polarity, continuous with an underlying tumor mass. The tumor cells were positive for a variety of cytokeratins, p40 and vimentin. The Ki‐67 proliferation index was 50–60%. Both CD31 and CD34 were expressed in reactive blood vessels of the tumor. A local excision margined by 1 mm was performed, followed by X rays and electron beam irradiation. Neither lymph node nor distant metastasis has appeared over the 14 months since the excision. We performed a review of the published work and identified 24 previously reported patients with pseudovascular squamous cell carcinoma of the skin, oral mucosa and vulva to reassess the prognosis of this tumor. In 12 of these patients (50%), sites other than the head and neck were involved. Eight (33%) tumor‐associated deaths occurred. It is believed that pseudovascular squamous cell carcinoma has a tendency to develop at morbid skin and mucous membranes sites in organs other than the face and neck and to possess an aggressive clinical behavior.
Predation risk for reptiles is highest at remnant edges in agricultural landscapes
Authors: Hansen Nicole A. , Sato Chloe F. , Michael Damian R. , Lindenmayer David B. , Driscoll Don A.
Published: September 2018

Preventing biodiversity loss in fragmented agricultural landscapes is a global problem. The persistence of biodiversity within remnant vegetation can be influenced by an animal's ability to move through the farmland matrix between habitat patches. Yet, many of the mechanisms driving species occurrence within these landscapes are poorly understood, particularly for reptiles.

We used scented and unscented plasticine lizard models and wildlife cameras to (a) estimate predation risk of reptiles in four farmland types (crop field, pasture paddock, restoration tree planting and areas with applied woody mulch) relative to the patch edge and remnant vegetation, and (b) examine how predation risk was influenced by temporal change in the matrix (crop harvesting).

Birds (55.1%), mammals (41.1%), reptiles (3.4%), and invertebrates (0.5%) attacked models, of which 87% were native species. Mammalian predators were 60.2% more likely to attack scented models then unscented models. Bird predators were not influenced by scent.

We found predator attacks on models were highest at edges (49%, irrespective of adjacent farmland type, with a reduced risk within farmland (29%) and remnant patches (33%) (p < 0.01). Both mammal and bird predators contributed to high numbers of predation attempts at edges.

Removal of crops did not increase predation attempts in crop fields or other farmland types, although predation attempts were significantly lower along the crop transect after harvesting, compared to the woody debris transect. However, numbers of predation attempts were higher in edge habitats, particularly prior to harvesting.

Synthesis and applications. Reptiles are at risk of predation by birds and mammals in both remnant patches and the farmland matrix, particularly in edge habitat. Our results demonstrate that edge habitats are potentially riskier for lizards than the farmland. Vulnerability to predation may be increased by a lack of shelter within edge habitats such as by increasing visibility of reptiles to predators. Therefore, to benefit reptiles, land managers could provide shelter (rocks, logs, and grasses), particularly between remnants and linear plantings which could improve landscape connectivity.
Information Asymmetry, Regulations and Equilibrium Outcomes: Theory and Evidence from the Housing Rental Market
Authors: Ambrose Brent W. , Diop Moussa
Published: September 2018

We explore the role of information asymmetry and regulations on equilibrium outcomes in rental markets to show that while landlords price the cost of regulations into rent, they also invest in tenant screening to alleviate information asymmetry, thus restricting access to rental housing. We are the first to document this additional tenant screening in response to regulations.
Transcriptomic analysis of epigenetic modification genes in the termite Reticulitermes speratus
Authors: Mitaka Yuki , Tasaki Eisuke , Nozaki Tomonari , Fuchikawa Taro , Kobayashi Kazuya , Matsuura Kenji
Published: September 2018

Eusocial insects display a caste system in which different castes are morphologically and physiologically specialized for different tasks. Recent studies have revealed that epigenetic modifications, including DNA methylation and histone modification, mediate caste determination and differentiation, longevity, and polyethism in eusocial insects. Although there has been a growing interest in the relationship between epigenetic mechanisms and phenotypic plasticity in termites, there is little information about differential expression levels among castes and expression sites for these genes in termites. Here we show royal‐tissue‐specific expression of epigenetic modification genes in the termite Reticulitermes speratus. Using RNA‐seq, we identified 74 genes, including three DNA methyltransferases, seven sirtuins, 48 Trithorax group proteins, and 16 Polycomb group proteins. Among these genes, 15 showed king‐specific expression, and 52 showed age‐dependent differential expression in kings and queens. Quantitative real‐time PCR revealed that DNA methyltransferase 3 is expressed specifically in the king's testis and fat body, whereas some histone modification genes are remarkably expressed in the king's testis and queen's ovary. These findings imply that epigenetic modification plays important roles in the gamete production process in termite kings and queens.
Effects of preoperative hepatitis B virus infection, hepatitis C virus infection, and coinfection on the development of new‐onset diabetes after kidney transplantation
Authors: Liang Jing , Lv Chaoyang , Chen Minling , Xu Ming , Zhao Chenhe , Yang Yinqiu , Wang Jina , Zhu Dong , Gao Jian , Rong Ruiming , Zhu Tongyu , Yu Mingxiang
Published: September 2018

Background

The effects of preoperative hepatitis B virus (HBV) infection, hepatitis C virus (HCV) infection, and HBV plus HCV coinfection on the development of new‐onset diabetes after transplantation (NODAT) remain unexplored in kidney transplant recipients (KTRs). This study examined the association between preoperative viral status (i.e., HBV, HCV, and HBC + HCV infection) and incident NODAT in a large population of Chinese KTRs.

Methods

This population‐based retrospective cohort study enrolled 557 subjects who underwent kidney transplantation between 1993 and 2014 at Zhongshan Hospital. Pre‐, peri‐, and postoperative data were extracted and analyzed. Viral status was defined by serological results for hepatitis B surface antigen and anti‐HCV antibody. The cumulative incidence of NODAT was compared across four groups of KTRs with different viral status. Multivariate Cox regression models were used to estimate the effects of HBV, HCV, and HBC + HCV infection on incident NODAT after adjusting for important confounders.

Results

Patients seropositive for HCV (both HCV monoinfection and HBC + HCV coinfection) had a significantly higher cumulative incidence of NODAT than KTRs who were not infected with HCV (P < 0.05 for both). However, only HCV infection alone was found to be a risk factor for NODAT, increasing the NODAT risk 3.03‐fold (95% confidence interval 1.77‐5.18; P < 0.001). There was no independent correlation between HBV infection (alone or combined with HCV) and incident NODAT in KTRs.

Conclusions

Preoperative HCV infection significantly increased the risk of NODAT in Chinese KTRs, whereas HBV infection and HBC + HCV coinfection were not correlated with NODAT development.