bluuebunny/crossref_metadata_2025 huggingface dataset:
The relationship between spatial configuration and functional connectivity of brain regions revisited
Authors: Bijsterbosch Janine D. , Beckmann Christian F. , Woolrich Mark W. , Smith Stephen M. , Harrison Samuel J.
Published: January 2019

In our previous paper (Bijsterbosch et al., 2018), we showed that network-based modelling of brain connectivity interacts strongly with the shape and exact location of brain regions, such that cross-subject variations in the spatial configuration of functional brain regions are being interpreted as changes in functional connectivity. Here we show that these spatial effects on connectivity estimates actually occur as a result of spatial overlap between brain networks. This is shown to systematically bias connectivity estimates obtained from group spatial ICA followed by dual regression. We introduce an extended method that addresses the bias and achieves more accurate connectivity estimates.

Impact statement

We show that functional connectivity network matrices as estimated from resting state functional MRI are biased by spatially overlapping network structure.
Neuropathological validation of the MDS-PSP criteria with PSP and other frontotemporal lobar degeneration
Authors: Gazzina Stefano , Respondek Gesine , Compta Yaroslau , Allinson Kieren S.J. , Spillantini Maria G. , Molina-Porcel Laura , Guasp-Verdaguer Mar , Moftakhar Shirin , Reich Stephen G. , Hall Deborah , Litvan Irene , Höglinger Günter U. ,   Movement Disorder Society-endorsed PSP Study Group, Rowe James B.
Published: January 2019

Background

Progressive supranuclear palsy (PSP) is clinically heterogeneous. Clinical diagnostic criteria were revised in 2017, to increase sensitivity and operationalize the diagnosis of PSP Richardson’s syndrome (PSP-RS) and “variant” syndromes (vPSP).

Objectives

To determine the (1) sensitivity and specificity of the 1996 NINDS-SPSP and 2017 MDS-PSP criteria; (2) false positive rates in frontotemporal dementia with frontotemporal lobar degeneration (FTLD); and (3) clinical evolution of variant PSP syndromes (vPSP).

Methods

Retrospective multicenter review of 108 neuropathologically-confirmed PSP patients and 81 patients with other forms of FTLD: 38 behavioral variant frontotemporal dementia (bvFTD), 14 non-fluent/agrammatic variant primary progressive aphasia (nfvPPA), and 29 corticobasal degeneration (CBD), Sensitivity and specificity of the MDS-PSP criteria were compared to the NINDS-SPSP criteria at baseline. In a subset of cases, the timing and frequency of clinical features were compared across groups over six years.

Results

Sensitivity for recognition of probable and possible PSP pathology was higher by MDS-PSP criteria (72.2-100%) than NINDS-SPSP criteria (48.1-61.1%). Specificity was higher by NINDS-SPSP criteria (97.5-100%) than MDS-PSP criteria (53.1-95.1%). False positives by MDS-PSP criteria were few for bvFTD (10.5-18.4%) but common for CBD and nfvPPA (fulfilling “suggestive of’ PSP). Most vPSP cases developed PSP-RS-like features within six years, including falls and supranuclear gaze palsy, distinguishing frontal presentations of PSP from bvFTD, and speech/language presentations of PSP from nfvPPA.

Conclusions

The 2017 MDS-PSP criteria successfully identify PSP, including variant phenotypes. This independent validation of the revised clinical diagnostic criteria strengthens the case for novel therapeutic strategies against PSP to include variant presentations.
Chromosome-level assembly of the common lizard (Zootoca vivipara) genome
Authors: Yurchenko Andrey A. , Recknagel Hans , Elmer Kathryn R.
Published: January 2019

Squamate reptiles exhibit high variation in their traits and geographical distribution and are therefore fascinating taxa for evolutionary and ecological research. However, high-quality genomic recourses are very limited for this group of species, which inhibits some research efforts. To address this gap, we assembled a high-quality genome of the common lizard Zootoca vivipara (Lacertidae) using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequence data, with RNAseq data and genetic linkage maps. The 1.46 Gbp genome assembly has scaffold N50 of 11.52 Mbp with N50 contig size of 220.4 Kbp and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total 19,829 gene models were annotated in the genome using a combination of three ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.
TORC2 Affects Endocytosis through Plasma Membrane Tension
Authors: Riggi Margot , Macchione Mariano , Matile Stefan , Loewith Robbie , Roux Aurélien
Published: January 2019

Target Of Rapamycin complex 2 (TORC2) is a conserved protein kinase that regulates multiple plasma membrane (PM)-related processes including endocytosis. Direct, chemical inhibition of TORC2 arrests endocytosis but with kinetics that are relatively slow and therefore inconsistent with signaling being mediated solely through simple phosphorylation cascades. Here, we show that, in addition to regulation of the phosphorylation of endocytic proteins, TORC2 also controls endocytosis by modulating PM tension. Elevated PM tension, upon TORC2 inhibition, impinges on endocytosis at two different levels: first, by severing the bonds between the PM adaptor proteins Sla2 and Ent1 and the actin cytoskeleton; and, second, by hindering recruitment of Rvs167, an N-BAR-containing protein important for vesicle fission, to endocytosis sites. These results underline the importance of biophysical cues in the regulation of cellular and molecular processes.
Coherent coding of spatial position mediated by theta oscillations in hippocampus and prefrontal cortex
Authors: Zielinski Mark C. , Shin Justin D. , Jadhav Shantanu P.
Published: January 2019

Interactions between the hippocampus (area CA1) and prefrontal cortex (PFC) are crucial for memory-guided behavior. Theta oscillations (~8 Hz) underlie a key physiological mechanism for mediating these coordinated interactions, and theta oscillatory coherence and phase-locked spiking in the two regions have been shown to be important for spatial memory. Hippocampal place cell activity associated with theta oscillations encodes spatial position during behavior, and theta-phase associated spiking is known to further mediate a temporal code for space within CA1 place fields. Although prefrontal neurons are prominently phase-locked to hippocampal theta oscillations in spatial memory tasks, whether and how theta oscillations mediate processing of spatial information across these networks remains unclear. Here, we addressed these questions using simultaneous recordings of dorsal CA1 – PFC ensembles and population decoding analyses in male rats performing a continuous spatial working memory task known to require hippocampal-prefrontal interactions. We found that in addition to CA1, population activity in PFC can also encode the animal’s current spatial position on a theta-cycle timescale during memory-guided behavior. Coding of spatial position was coherent for CA1 and PFC ensembles, exhibiting correlated position representations within theta cycles. In addition, incorporating theta-phase information during decoding to account for theta-phase associated spiking resulted in a significant improvement in the accuracy of prefrontal spatial representations, similar to concurrent CA1 representations. These findings indicate a theta-oscillation mediated mechanism of temporal coordination for shared processing and communication of spatial information across the two networks during spatial memory-guided behavior.
Diffusion Tensor Imaging connectivity analysis: detecting structural alterations and their underlying substrates for Optic Ataxia in correlations with “How” stream Visual Pathways
Authors: Elumalai Ganesh , Maiti Panchanan , Vinodhanand Geethanjali , Camoya Brown Valencia Lasandra , Venkata Ghanta Nitya Akarsha Surya , Krishna Kurra Venkata Hari
Published: January 2019

Optic ataxia is a neurological condition that shows clinical manifestations of disturbances in visual guided hand movements on reaching for a target object. Previous studies failed to provide substantial evidences for the neural structural pathway damaged by this condition. Therefore, this study was aimed to identify the neural structural connectivity between “Visual cortex with Superior Parietal Lobule” and to correlate its functional importance, using “Diffusion Imaging fiber Tractography. The fibers were traced, and we confirmed its extension from “Visual cortex (Brodmann’s Areas 18 and 19) to Superior Parietal Lobule (Brodmann’s Area 7)”. This new observation gives an insight to understand the structural existence and functional correlations between “Visual cortex with Superior Parietal Lobule” which is involved in targeting the grasping hand movements towards a visually perceived object, called visuo-motor coordination pathway or “how” stream pathways in visual perception. The observational analysis used thirty-two healthy adults, ultra-high b-value, diffusion MRI datasets from an Open access research platform. The datasets range between 20–49 years, in both sexes, with mean age of 31.1 years. The confirmatory observational analysis process includes, datasets acquisition, pre-processing, processing, reconstruction, fiber tractography and analysis using software tools. All the datasets confirmed that the fiber structural extension between, Visual cortex to superior parietal lobe in both the sexes may be responsible for the visual spatial recognition of objects. These new fiber connectivity evidences justify the structural relevance of visual spatial recognition impairments, such as optic ataxia.
Hip circumduction is not a compensation for reduced knee flexion angle during gait
Authors: Akbas Tunc , Prajapati Sunil , Ziemnicki David , Tamma Poornima , Gross Sarah , Sulzer James
Published: January 2019

It has long been held that hip abduction compensates for reduced swing-phase knee flexion angle, especially in those after stroke. However, there are other compensatory motions such as pelvic obliquity (hip hiking) that could also be used to facilitate foot clearance with greater energy efficiency. Our previous work suggested that hip abduction may not be a compensation for reduced knee flexion after stroke. Previous study applied robotic knee flexion assistance in people with post-stroke Stiff-Knee Gait (SKG) during pre-swing, finding increased abduction despite improved knee flexion and toe clearance. Thus, our hypothesis was that hip abduction is not a compensation for reduced knee flexion. We simulated the kinematics of post-stroke SKG on unimpaired individuals with three factors: a knee orthosis to reduce knee flexion, an ankle-foot orthosis commonly worn by those post-stroke, and matching gait speeds. We compared spatiotemporal measures and kinematics between experimental factors within healthy controls and with a previously recorded cohort of people with post-stroke SKG. We focused on frontal plane motions of hip and pelvis as possible compensatory mechanisms. We observed that regardless of gait speed, knee flexion restriction significantly increased pelvic obliquity (2.79°, p<0.01) compared to unrestricted walking (1.5°, p<0.01), but similar to post-stroke SKG (3.4°). However, those with post-stroke SKG had significantly greater hip abduction (8.2°) compared to unimpaired individuals with restricted knee flexion (4.2°, p<0.05). These results show that pelvic obliquity, not hip abduction, compensates for reduced knee flexion angle. Thus, other factors, possibly neural, facilitate exaggerated hip abduction observed in post-stroke SKG.
Nucleus accumbens cholinergic interneurons oppose cue-motivated behavior
Authors: Collins Anne L. , Aitken Tara J. , Huang I-Wen , Shieh Christine , Greenfield Venuz Y. , Monbouquette Harold G. , Ostlund Sean B. , Wassum Kate. M.
Published: January 2019

Background

Environmental reward-predictive stimuli provide a major source of motivation for adaptive reward pursuit behavior. This cue-motivated behavior is known to be mediated by the nucleus accumbens core (NAc). The cholinergic interneurons in the NAc are tonically active and densely arborized and, thus, well-suited to modulate NAc function. But their causal contribution to adaptive behavior remains unknown. Here we investigated the function of NAc cholinergic interneurons in cue-motivated behavior.

Methods

To do this, we used chemogenetics, optogenetics, pharmacology, and a translationally analogous Pavlovian-to-instrumental transfer behavioral task designed to assess the motivating influence of a reward-predictive cue over reward-seeking actions in male and female rats.

Results

The data show that NAc cholinergic interneuron activity is necessary and sufficient to oppose the motivating influence of appetitive cues. Chemogenetic inhibition of NAc cholinergic interneurons augmented cue-motivated behavior. Optical stimulation of acetylcholine release from NAc cholinergic interneurons prevented cues from invigorating reward-seeking behavior, an effect that was mediated by activation of β2-containing nicotinic acetylcholine receptors.

Conclusions

Thus, NAc cholinergic interneurons provide a critical regulatory influence over adaptive cue-motivated behavior and, therefore, are a potential therapeutic target for the maladaptive cue-motivated behavior that marks many psychiatric conditions, including addiction and depression.
Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life
Authors: Royalty Taylor M. , Steen Andrew D.
Published: January 2019

Widely used microbial taxonomies, such as the NCBI taxonomy, are based on a combination of sequence homology among conserved genes and historically accepted taxonomies, which were developed based on observable traits such as morphology and physiology. A recently-proposed alternative taxonomy, the Genome Taxonomy Database (GTDB), incorporates only sequence homology of conserved genes and attempts to partition taxonomic ranks such that each rank implies the same amount of evolutionary distance, regardless of its position on the phylogenetic tree. This provides the first opportunity to completely separate taxonomy from traits, and therefore to quantify how taxonomic rank corresponds to traits across the microbial tree of life. We quantified the enrichment of clusters of orthologous gene functional categories (COG-FCs) as a proxy for traits within the lineages of 13,735 cultured and uncultured microbial lineages from a custom-curated genome database. On average, 41.4% of the variation in COG-FC enrichment is explained by taxonomic rank, with domain, phylum, class, order, family, and genus explaining, on average, 3.2%, 14.6%, 4.1%, 9.2%, 4.8%, and 5.5% of the variance, respectively (p<0.001 for all). To our knowledge, this is the first work to quantify the variance in metabolic potential contributed by individual taxonomic ranks. A qualitative comparison between the COG-FC enrichments and genus-level phylogenies, generated from published concatenated protein sequence alignments, further supports the idea that metabolic potential is taxonomically coherent at higher taxonomic ranks. The quantitative analyses presented here constrain the integral relationship between diversification of microbial lineages and the metabolisms which they host.

Importance

Recently there has been great progress in defining a complete taxonomy of bacteria and archaea, which has been enabled by improvements in DNA sequencing technology and new bioinformatic techniques. A new, algorithmically-defined microbial tree of life describes those linkages relying solely on genetic data, which raises the question of how microbial traits relate to taxonomy. Here, we adopted cluster of orthologous group functional categories as a scheme to describe the genomic contents of microbes, which can be applied to any microbial lineage for which genomes are available. This simple approach allows quantitative comparisons between microbial genomes with different gene composition from across the microbial tree of life. Our observations demonstrate statistically significant patterns in cluster of orthologous group functional categories at the taxonomic levels spanning from domain to genus.
Circular inference in bistable perception
Authors: Leptourgos Pantelis , Notredame Charles-Edouard , Eck Marion , Jardri Renaud , Denève Sophie
Published: January 2019

When facing fully ambiguous images, the brain cannot commit to a single percept and instead switches between mutually exclusive interpretations every few seconds, a phenomenon known as bistable perception. Despite years of research, there is still no consensus on whether bistability, and perception in general, is driven primarily by bottom-up or top-down mechanisms. Here, we adopted a Bayesian approach in an effort to reconcile these two theories. Fifty-five healthy participants were exposed to an adaptation of the Necker cube paradigm, in which we manipulated sensory evidence (by shadowing the cube) and prior knowledge (e.g., by varying instructions about what participants should expect to see). We found that manipulations of both sensory evidence and priors significantly affected the way participants perceived the Necker cube. However, we observed an interaction between the effect of the cue and the effect of the instructions, a finding incompatible with Bayes-optimal integration. In contrast, the data were well predicted by a circular inference model. In this model, ambiguous sensory evidence is systematically biased in the direction of current expectations, ultimately resulting in a bistable percept.
Why does the zebrafishclochemutant develop lens cataract?
Authors: Posner Mason , McDonald Matthew S. , Murray Kelly L. , Kiss Andor J.
Published: January 2019

The zebrafish has become a valuable model for examining ocular lens development, physiology and disease. The zebrafishclochemutant, first described for its loss of hematopoiesis, also shows reduced eye and lens size, interruption in lens cell differentiation and a cataract likely caused by abnormal protein aggregation. To facilitate the use of theclochemutant for studies on cataract development and prevention we characterized variation in the lens phenotype, quantified changes in gene expression by qRT-PCR and RNA-Seq and compared the ability of two promoters to drive expression of introduced proteins into theclochelens. We found that the severity ofclocheembryo lens cataract varied, while the decrease in lens diameter and retention of nuclei in differentiating lens fiber cells was constant. We found very low expression of both αB-crystallin genes (cryabaandcryabb) at 4 days post fertilization (dpf) by both qRT-PCR and RNA-Seq incloche, clochesibling and wildtype embryos and no significant difference in αA-crystallin (cryaa) expression. RNA-Seq analysis of 4 dpf embryos identified transcripts from 25,281 genes, with 1,329 showing statistically significantly different expression betweenclocheand wildtype samples. Downregulation of eight lens β- and γM-crystallin genes and 22 retinal related genes may reflect a general reduction in eye development and growth. Six stress response genes were upregulated. We did not find misregulation of any known components of lens development gene regulatory networks. These results suggest that theclochelens cataract is not caused by loss of αA-crystallin or changes to lens gene regulatory networks. Instead, we propose that the cataract results from general physiological stress related to loss of hematopoiesis. Our finding that the zebrafish αA-crystallin promoter drove strong GFP expression in theclochelens demonstrates its use as a tool for examining the effects of introduced proteins on lens crystallin aggregation and cataract prevention.
Use of FFPE-Derived DNA in Next Generation Sequencing: DNA extraction methods
Authors: McDonough Samantha J. , Bhagwate Aditya , Sun Zhifu , Wang Chen , Zschunke Michael , Gorman Joshua A. , Kopp Karla J. , Cunningham Julie M.
Published: January 2019

Archival tissues represent a rich resource for clinical genomic studies, particularly when coupled with comprehensive medical records. Use of these in NGS is a priority. Nine formalin-fixed paraffin-embedded (FFPE) DNA extraction methods were evaluated using twelve FFPE samples of varying tissue types. Quality assessment included total yield, percent ds DNA, fragment analysis and multiplex PCR. After assessment, three tissue types from four FFPE DNA methods were selected for NGS downstream evaluation, whole exome (WES) and targeted sequencing. In addition, two low input library protocols were evaluated for WES. Analysis revealed average coverage across the target regions for WES was ~20-30X for all four FFPE DNA methods. For the targeted panels, the highest molecular tag coverage was obtained with the Kingfisher FFPE extraction method. The genotype concordance was 99% for the commonly called variant positions between all four extraction methods with the targeted PCR NGS panel and 96% with WES.
Binding of Filamentous Actin to CaMKII as a Potential Mechanism for the Regulation of Bidirectional Synaptic Plasticity by βCaMKII in Cerebellar Purkinje Cells
Authors: Pinto Thiago M. , Schilstra Maria J. , Roque Antonio C. , Steuber Volker
Published: January 2019

Calcium-calmodulin dependent protein kinase II (CaMKII) regulates many forms of synaptic plasticity, but little is known about its functional role during plasticity induction in the cerebellum. Experiments have indicated that the β isoform of CaMKII controls the bidirectional inversion of plasticity at parallel fibre (PF)-Purkinje cell (PC) synapses in cerebellar cortex. Because the cellular events that underlie these experimental findings are still poorly understood, we developed a simple computational model to investigate how βCaMKII regulates the direction of plasticity in cerebellar PCs. We present the first model of AMPA receptor phosphorylation that simulates the induction of long-term depression (LTD) and potentiation (LTP) at the PF-PC synapse. Our simulation results suggest that the balance of CaMKII-mediated phosphorylation and protein phosphatase 2B (PP2B)-mediated dephosphorylation of AMPA receptors can determine whether LTD or LTP occurs in cerebellar PCs. The model replicates experimental observations that indicate that βCaMKII controls the direction of plasticity at PF-PC synapses, and demonstrates that the binding of filamentous actin to CaMKII can enable the β isoform of the kinase to regulate bidirectional plasticity at these synapses.

Author Summary

Many molecules and the complex interactions between them are involved in synaptic plasticity in the cerebellum. However, the exact relationship between cerebellar plasticity and the different signalling cascades remains unclear. Calcium-calmodulin dependent protein kinase II (CaMKII) is an important component of the signalling network that is responsible for plasticity in cerebellar Purkinje cells (PCs). The CaMKII holoenzyme contains different isoforms such as αCaMKII and βCaMKII. Experiments with Camk2b knockout mice that lack the β isoform of CaMKII demonstrated that βCaMKII regulates the direction of plasticity at parallel fibre (PF)-PC synapses. Stimulation protocols that induce long-term depression in wild-type mice, which contain both α and βCaMKII, lead to long-term potentiation in knockout mice without βCaMKII, and vice versa. We developed a kinetic simulation of the phosphorylation and dephosphorylation of AMPA receptors by CaMKII and protein phosphatase 2B to investigate how βCaMKII can control bidirectional synaptic plasticity in cerebellar PCs. Our simulation results demonstrate that the binding of filamentous actin to βCaMKII can contribute to the regulation of bidirectional plasticity at PF-PC synapses. Our computational model of intracellular signalling significantly advances the understanding of the mechanisms of synaptic plasticity induction in the cerebellum.
Regulation of Parent-of-Origin Allelic Expression inArabidopsis thalianaendosperm
Authors: Hornslien Karina S. , Miller Jason R. , Grini Paul E.
Published: January 2019

Genomic imprinting is an epigenetic phenomenon set in the gametes prior to fertilization that causes differential expression of parental alleles mainly in the endosperm of flowering plants. The overlap between previously identified panels of imprinted genes is limited. In order to achieve high resolution sequencing data we have used sequence capture technology to investigate imprinting. Here, we present a bioinformatics pipeline to assay parent-of-origin allele specific expression and report more than 300 loci with parental expression bias. We find that the level of expression from maternal and paternal alleles in most cases is not binary, instead favouring a differential dosage hypothesis for the evolution of imprinting in plants. To address imprinting regulation, we systematically employed mutations in regulative epigenetic pathways suggested to be major players in the process. We establish the mechanistic mode of imprinting for more than 50 loci regulated by DNA methylation and Polycomb-dependent histone methylation. However, the imprinting patterns of the majority of genes were not affected by these mechanisms. To this end we also demonstrate that the RNA-directed DNA methylation pathway alone does not influence imprinting patterns in a substantial manner, suggesting more complex epigenetic regulation pathways for the majority of identified imprinted genes.

Author summary

Expression of gene copies only from the mother or the father’s genome, also termed imprinting, is a specialized epigenetic phenomenon that is found to be enriched at some genes expressed in the mammalian placenta and in the endosperm of the plant seed. Although several studies have reported on imprinted genes in plants, the identified loci are at large non-overlapping between reports. This motivated us to investigate in detail the expression pattern of imprinted genes in the endosperm and to determine how imprinting patterns are established at various imprinted loci. Although several underlying epigenetic regulation mechanisms have been demonstrated to establish imprinting patterns at certain genes, the majority of imprinted genes have not been linked to such mechanisms. In the present study we systematically investigated the mechanisms that are involved in establishing imprinting, by employing mutants of epigenetic regulators and high-throughput sequencing. In our high resolution study, we report more than 300 imprinted genes and demonstrate that the biological phenomenon imprinting involves gradual expression of parental gene copies rather than switching gene copies on or off. Notably, for the majority of imprinted genes, the mechanisms previously believed to be major to establish their imprinting patterns, are not responsible for mediating imprinting.
100 PhD rules of the game to successfully complete a doctoral dissertation
Authors: Brennan Niamh M.
Published: January 2019

Purpose

A doctoral dissertation is a challenging undertaking requiring determination, persistence and resilience over a long time: four to six years’ study or more. These PhD “rules of the game” are intended to help students successfully navigate this challenge.

Design/methodology/approach

The author has assembled 100 PhD rules of the game from the author’s work over many years with masters and doctoral students. Each rule is accompanied by some further short guidance. Additional citations are included directing readers to resources embellishing the 100 PhD rules of the game.

Findings

The paper documents 100 PhD rules of the game.

Research limitations/implications

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

Originality/value

This paper is a one-stop-shop brief introduction to the author’s 100 PhD rules of the game.
The evolving nature of the marketing–supply chain management interface in contemporary markets
Authors: Noci Giuliano
Published: January 2019

Purpose

The purpose of this paper is to reshape and interpret the essence of marketing–supply chain management (M–SCM) interface in the glance of the dramatic changes occurring in competition and market relationships.

Design/methodology/approach

By reviewing relevant literature and analyzing evolutions in the different phases of the marketing funnel, the author develops an evolutionary pattern for M–SCM interface.

Findings

As the markets evolve to an always-on, service-dominant logic, being market-driving becomes a necessary condition, and as such marketing strategies must be capable of reconfiguring supply chains to reshape the value for customers. This implies a dramatic organizational change, even beyond mere technological issues.

Originality/value

The paper aims at setting some research directions for business process management and organizational patterns to govern M–SCM interface.
Measuring construction for social, economic and environmental assessment
Authors: Ilhan Bahriye , Yobas Banu
Published: January 2019

Purpose

The purpose of this paper is to examine the issues that should be considered for a better gauge of the construction industry and built environment and to propose a set of indicators for measuring the social, economic and environmental value of construction.

Design/methodology/approach

The indicators proposed in this study use Pearce’s schema, which presents a framework to evaluate the socio-economic value of construction and its contribution to sustainable development. After analysing the problems faced by the industry, solutions are raised and finally indicators for each pillar of Pearce’s schema are established through a literature review. Since the proposed indicators can be used for cross-country analysis, these comparisons are also presented as graphs including only those countries for which valid national data could be sourced from OECD databases.

Findings

The issues, suggestions and indicators related to each concern about the main domains of the schema are addressed through the related literature and supported by available statistical data.

Originality/value

Although previous studies have drawn attention to measures for better evaluation of the construction industry and the built environment, this study, distinctively, presents an integrated approach in order to gauge the true value and impacts of construction in a more comprehensive way. The work’s contribution to the body of knowledge is in revealing the hidden input and impact of construction on sustainable development by determining the barriers to this and their solutions, in addition to the proposal of relevant indicators.
Genome‐wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)
Authors: Rogivue Aude , Choudhury Rimjhim R. , Zoller Stefan , Joost Stéphane , Felber François , Kasser Michel , Parisod Christian , Gugerli Felix
Published: January 2019

Advances in high‐throughput sequencing have promoted the collection of reference genomes and genome‐wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single‐nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e., presence/absence of TE insertions at specific loci). We identified 291,396 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic diversity and divergence across populations. Few SNPs were shared among populations and overall showed high population‐specific variation, whereas most polymorphic TEs segregated among populations. The genomic context of these two classes of variants further highlighted candidate adaptive loci having a putative impact on functional genes. In particular, 4.96% of the SNPs were identified as nonsynonymous or affecting start/stop codons. In contrast, 43% of the polymorphic TEs were present next to Arabis genes enriched in functional categories related to the regulation of reproduction and responses to biotic as well as abiotic stresses. This unprecedented data set, mapping variation gained from SNPs and complementary polymorphic TEs within and among populations, will serve as a rich resource for addressing microevolutionary processes shaping genome variation.
Point‐of‐Care Ocular Ultrasound for the Diagnosis of Retinal Detachment: A Systematic Review and Meta‐Analysis
Authors: Gottlieb Michael , Holladay Dallas , Peksa Gary D.
Published: January 2019

Background

Ocular complaints are common presentations to the emergency department (ED). Among these, retinal detachment can cause significant vision loss if not rapidly diagnosed and referred for appropriate treatment. Point‐of‐care ultrasound has been suggested to identify the diagnosis rapidly when the ocular examination is limited or the ophthalmology service is not readily available. However, prior studies were limited by small sample sizes, resulting in wide ranges of potential accuracy. The primary outcome for this review was to determine the test characteristics of point‐of‐care ocular ultrasound for the diagnosis of retinal detachment.

Methods

PubMed, CINAHL, Scopus, LILACS, the Cochrane Database of Systematic Reviews, the Cochrane Central Register of Controlled Trials, and bibliographies of selected articles were assessed for all prospective and randomized controlled trials assessing the accuracy of point‐of‐care ultrasound for identifying retinal detachment. Data were dual extracted into a predefined worksheet and quality analysis was performed using the QUADAS‐2 tool. Data were summarized and a meta‐analysis was performed with planned subgroup analyses by location and provider specialty. This review was registered with PROSPERO CRD42018097288. There was no funding for this review.

Results

Eleven studies (n = 844 patients) were identified. Overall, ultrasound was 94.2% (95% confidence interval [CI] = 78.4% to 98.6%) sensitive and 96.3% (95% CI = 89.2% to 98.8%) specific for the diagnosis of retinal detachment with a positive likelihood ratio of 25.2 (95% CI = 8.1 to 78.0) and a negative likelihood ratio of 0.06 (95% CI = 0.01 to 0.25). Subgroup analysis found that ultrasound was more accurate among ED patients, but was not significantly different when performed by ED or non‐ED providers.

Conclusions

Point‐of‐care ocular ultrasound is sensitive and specific for the diagnosis of retinal detachment. Future studies should determine the ideal training protocol and the influence of color Doppler and contrast‐enhanced ultrasound on diagnostic accuracy.
The Birth of a Return to work Policy for New Resident Parents in Emergency Medicine
Authors: Gordon Alexandra June , Sebok‐Syer Stefanie S. , Dohn Ann M. , Smith‐Coggins Rebecca , Ewen Wang N. , Williams Sarah R. , Gisondi Michael A.
Published: January 2019

Objective

With the rising number of female physicians, there will be more children than ever born in residency, and the current system is inadequate to handle this increase in new resident parents. Residency is stressful and rigorous in isolation, let alone when pregnant or with a new child. Policies that ease these stressful transitions are generally either insufficient or do not exist. Therefore, we created a comprehensive return‐to‐work policy for resident parents and piloted its implementation. Our policy aims to: 1) establish a clear, shared understanding of the regulatory and training requirements as they pertain to parental leave; 2) facilitate a smooth transition for new parents returning to work; and 3) summarize the local and institutional resources available for both males and females during residency training.

Method

In Fall 2017, a task force was convened to draft a return‐to‐work policy for new resident parents. The task force included nine key stakeholders (i.e., residents, faculty, and administration) at our institution and was made up of three graduate medical education (GME) program directors, a vice chair of education, a designated institutional official (DIO), a chief resident, and three members of our academic department's faculty affairs committee. The task force was selected because of individual expertise in gender equity issues, mentorship of resident parents, GME, and departmental administration.

Results

After development, the policy was piloted from November 2017 to June 2018. Our pilot implementation period included seven new resident parents. All of these residents received schedules that met the return‐to‐work scheduling terms of our return‐to‐work policy including no overnight shifts, no sick call, and no more than three shifts in a row. Of equal importance, throughout our pilot, the emergency department schedules at all of our clinical sites remained fully staffed and our sick call pool was unaffected.

Conclusion

Our return‐to‐work policy for new resident parents provides a comprehensive guide to training requirements and family leave policies, an overview of available resources, and a scheduling framework that makes for a smooth transition back to clinical duties.
Gender Differences in Faculty Rank Among Academic Emergency Physicians in the United States
Authors: Bennett Christopher L. , Raja Ali S. , Kapoor Neena , Kass Dara , Blumenthal Daniel M. , Gross Nate , Mills Angela M.
Published: January 2019

Background

The purpose of this study was to complete a comprehensive analysis of gender differences in faculty rank among U.S. emergency physicians that reflected all academic emergency physicians.

Methods

We assembled a comprehensive list of academic emergency medicine (EM) physicians with U.S. medical school faculty appointments from Doximity.com linked to detailed information on physician gender, age, years since residency completion, scientific authorship, National Institutes of Health (NIH) research funding, and participation in clinical trials. To estimate gender differences in faculty rank, multivariable logistic regression models were used that adjusted for these factors.

Results

Our study included 3,600 academic physicians (28%, or 1,016, female). Female emergency physicians were younger than their male colleagues (mean [±SD] age was 43.8 [±8.7] years for females and 47.4 [±9.9] years for males [p < 0.001]), had fewer years since residency completion (12.4 years vs. 15.6 years, p < 0.001), had fewer total and first/last author publications (4.7 vs. 8.6 total publications, p < 0.001; 4.3 vs. 7.1 first or last author publications, p < 0.001), and were less likely to be principal investigators on NIH grants (1.2% vs. 2.9%, p = 0.002) or clinical trials (1.8% vs. 4.4%, p < 0.001). In unadjusted analysis, male physicians were more likely than female physicians to hold the rank of associate or full professor versus assistant professor (13.7 percentage point difference, p < 0.001), a relationship that persisted after multivariable adjustment (5.5 percentage point difference, p = 0.001).

Conclusions

Female academic EM physicians are less likely to hold the rank of associate or full professor compared to male physicians even after detailed adjustment for other factors that may influence faculty rank.
Vaping characteristics and expectancies are associated with smoking cessation propensity among dual users of combustible and electronic cigarettes
Authors: Brandon Karen O. , Simmons Vani N. , Meltzer Lauren R. , Drobes David J. , Martínez Úrsula , Sutton Steven K. , Palmer Amanda M. , Bullen Christopher R. , Harrell Paul T. , Brandon Thomas H.
Published: January 2019

Background and Aims

Most e‐cigarette users who also smoke combustible cigarettes (dual users) begin vaping to quit smoking, yet only a subset succeeds. We hypothesized that reinforcing characteristics of e‐cigarettes (vaping reinforcement) would positively predict smoking cessation propensity (SCP) among dual users.

Design

Secondary analysis of cross‐sectional baseline data from dual users in an ongoing smoking cessation trial. Exploratory and confirmatory factor analysis (EFA and CFA) created latent variables for vaping reinforcement and SCP. A structural equation modeling (SEM) approach was used to test the hypothesis.

Setting

United States.

Participants

A national sample of dual users of combustible and electronic cigarettes who smoke and vape at least once per week (n = 2896) were enrolled (63% male; mean age = 29.9 years) into a randomized controlled trial in which they would receive either smoking cessation materials or no smoking cessation materials.

Measurements

Vaping reinforcement was indexed by vaping frequency (days/week vaping, times/day vaping, puffs/e‐cigarette use), e‐cigarette characteristics [numbers of modifications and tobacco or non‐tobacco flavors, nicotine content (mg) and positive e‐cigarette expectancies]. SCP was measured by items of confidence, commitment to being smoke‐free, cessation motivation (contemplation ladder), change in cigarettes per day since beginning e‐cigarette use and negative smoking expectancies.

Findings

Four factors emerged from the EFA: vaping propensity (vaping frequency, positive expectancies), vaping enthusiasm (e‐cigarette modifications, using non‐tobacco flavors, puffs per use), nicotine/tobacco flavor (nicotine strength, tobacco flavors) and SCP (negative expectancies about smoking, motivation to quit smoking, reduction in smoking). A CFA upheld the exploratory factor structure [root mean square error of approximation (RMSEA) = 0.046, CFI = 0.91]. An SEM with the three vaping latent variables directly predicting SCP had good model fit (RMSEA = 0.030, CFI = 0.97) with a positive relationship of vaping propensity (0.509, P < 0.001), and small negative relationships of vaping enthusiasm (−0.158, P = 0.014) and nicotine/tobacco flavor (−0.230, P < 0.001).

Conclusions

Among e‐cigarette users who also smoke combustible cigarettes, frequent vaping combined with positive e‐cigarette expectancies appears to predict greater smoking cessation propensity. However, vaping enthusiasm (measured by e‐cigarette modifications, using non‐tobacco flavors and puffs per use), higher nicotine content and use of tobacco flavored solution may reduce cessation propensity.
Retracted: Short lipopeptides specifically inhibit the growth of Propionibacterium acnes with dual antibacterial and anti‐inflammatory action
Authors: Yang Guang , Wang Jingyu , Lu Shengsheng , Chen Zhao , Fan Sheng , Chen Daiwei , Xue Huanxin , Shi Wenyuan , He Jian
Published: January 2019

Background and Purpose

Propionibacterium acnes (P. acnes) is a Gram‐positive bacterium associated with the skin disorder acne. In this study, we determined the importance of fatty acids in the life habitat of P. acnes; we tested our lipopeptide library in an attempt to create potent P. acnes‐specific antimicrobial agents.

Experimental Approach

Antimicrobial activity was determined by the minimal inhibitory concentration (MIC). Lipids from P. acnes were used to explore the mode of action. RAW264.7 cells respectively stimulated with LPS and P. acnes were used to measure the anti‐inflammatory activity. Mice ears injected with P. acnes were used to assess the antimicrobial and anti‐inflammatory effects of the peptides tested in vivo.

Key Results

The most potent candidate, C16‐KWKW, was observed to be more active against P. acnes, with an MIC of 2 μg·ml−1, than against other non‐targeted bacterial strains, such as Streptococcus mutans, Staphylococcus aureus, and Escherichia coli. The mode of action of C16‐KWKW was observed to be through interference with the integrity of bacterial membrane, thereby impairing membrane permeability and causing leakage of the inner contents of bacterial cells. In addition, C16‐KWKW inhibited the expression of pro‐inflammatory cytokines, such as IL‐1β, TNF‐α, and inducible NOS, stimulated by both LPS and P. acnes, thus showing potential anti‐inflammatory activity, which was further assessed in animal studies in vivo.

Conclusions and Implications

C16‐KWKW is a lipopeptide displaying both anti‐P. acnes and anti‐inflammatory effects in vitro and in vivo, and exhibits potential as a treatment for acne vulgaris induced by P. acnes.
Questioning cultural narratives of economic development: An investigation of Kitchener‐Waterloo
Authors: Spigel Ben , Bathelt Harald
Published: January 2019

Key Messages

The cultural narrative of how German immigrants have shaped today's technology economy and entrepreneurial culture in Kitchener‐Waterloo appears questionable.

Members of Kitchener‐Waterloo's German community neither have strong professional ties with other members of that community, nor close connections with other regional communities.

Kitchener‐Waterloo's German community has been absorbed into the region's self‐image and creates common reference points for joint initiatives.
Unravelling identities on archaeological borderlands: Late Woodland Western Basin and Ontario Iroquoian Traditions in the Lower Great Lakes region
Authors: St. John Amy , Ferris Neal
Published: January 2019

Borders, boundaries, frontiers, and borderlands are complex things and processes which have become important foci in social sciences over the last two decades. Using archaeological border theory, grounded in anthropological border theory, which focuses on the cultural dimensions of borders, the nature and function of borders and boundaries in the archaeological record of societies indigenous to the Lower Great Lakes can be explored. An archaeological border theory examines how notions of identity, ethnicity, and material culture interplay with borders, allowing for more complex interpretations of archaeological materials and sites. Applying this theory to archaeological evidence from the interaction zones, or borderlands, between archaeologically defined Late Woodland traditions illustrates how these concepts can lead to more complete understandings of the way people lived in the past. Examining borders in the past allows social scientists to recognize their historically situated, fluid nature and will lead to greater consideration of the socially constructed nature of borders in the present.
Does tax competition make mobile firms more footloose?
Authors: Ferrett Ben , Hoefele Andreas , Wooton Ian
Published: January 2019

We examine a two‐period regional model with evolving economic geography, potentially creating incentives for firm relocation between periods. We argue that tax competition makes firms more footloose, but that this increases efficiency relative to the laissez‐faire outcome. We establish that: (i) tax competition leads to efficient investment outcomes and (ii) firm mobility is greater with tax competition than with a laissez‐faire regime. When relocation is costly, there can be too little mobility over time, as firms do not take into account the impact of FDI on social welfare in each country. With lump‐sum taxes or transfers, firms capture these benefits and internalize them, such that tax competition leads to the efficient outcomes. When more time periods are examined, tax competition induces firm relocation sooner than in its absence.