bluuebunny/crossref_metadata_2025 huggingface dataset:
Oculocardiac Reflex as a Late Presentation of Orbital Floor Fracture
Authors: Başağaoğlu Berkay , Steinberg Ashley , Tung Irene T. , Olorunnipa Shola , Maricevich Renata S.
Published: September 2018

Delayed repair of orbital trapdoor fractures can jeopardize the viability of entrapped contents and prolong recovery. Variation in presentations, both clinically and radiographically, complicate prompt diagnosis. The oculocardiac reflex may be the only indication of fracture with entrapped orbital contents, but, unfortunately, the reflex has variable onset patterns and can mimic common diagnoses. Therefore, the authors present the case of a 14-year-old male with a right orbital floor fracture, who presented with delayed symptoms secondary to an oculocardiac reflex. The vagal sequelae of the reflex, including gastric hyperactivity and headache, were experienced approximately 1 week after the injury and caused the patient to be misdiagnosed with gastroenteritis and status migrainosus, on 2 separate hospital visits. After admission to the hospital due to progressive symptoms, a CT scan showed concerns for a subacute orbital blowout fracture. The patient underwent orbital floor exploration with findings of scarred orbital fat herniating into a healing fracture site. Repositioning of the fat into the orbit resulted in immediate resolution of the patient's symptoms. Awareness of the presenting characteristics of the oculocardiac reflex can lead to prompt diagnosis and maximize clinical outcomes.
miRBaseConverter: An R/Bioconductor Package for Converting and Retrieving miRNA Name, Accession, Sequence and Family Information in Different Versions of miRBase
Authors: Xu Taosheng , Su Ning , Liu Lin , Zhang Junpeng , Wang Hongqiang , Zhang Weijia , Gui Jie , Yu Kui , Li Jiuyong , Le Thuc Duy
Published: September 2018

Background

miRBase is the primary repository for published miRNA sequence and annotation data, and serves as the “go-to” place for miRNA research. However, the definition and annotation of miRNAs have been changed significantly across different versions of miRBase. The changes cause inconsistency in miRNA related data between different databases and articles published at different times. Several tools have been developed for different purposes of querying and converting the information of miRNAs between different miRBase versions, but none of them individually can provide the comprehensive information about miRNAs in miRBase and users will need to use a number of different tools in their analyses.

Results

We introducemiRBaseConverter,an R package integrating the latest miRBase version 22 available in Bioconductor to provide a suite of functions for converting and retrieving miRNA name (ID), accession, sequence, species, version and family information in different versions of miRBase. The package is implemented in R and available under the GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/miRBaseConverter/). A Shiny-based GUI suitable for non-R users is also available as a standalone application from the package and also as a web application athttp://nugget.unisa.edu.au:3838/miRBaseConverter.miRBaseConverterhas a built-in database for querying miRNA information in all species and for both pre-mature and mature miRNAs defined by miRBase. In addition, it is the first tool for batch querying the miRNA family information. The package aims to provide a comprehensive and easy-to-use tool for miRNA research community where researchers often utilize published miRNA data from different sources.

Conclusions

The Bioconductor packagemiRBaseConverterand the Shiny-based web application are presented to provide a suite of functions for converting and retrieving miRNA name, accession, sequence, species, version and family information in different versions of miRBase. The package will serve a wide range of applications in miRNA research and could provide a full view of the miRNAs of interest.
Deep Learning Based Retrieval System for Gigapixel Histopathology Cases and Open Access Literature
Authors: Otálora Sebastian , Schaer Roger , Jimenez-del-Toro Oscar , Atzori Manfredo , Müller Henning
Published: September 2018

Clinical practice is getting increasingly stressful for pathologists due to increasing complexity and time constraints. Histopathology is slowly shifting to digital pathology, thus creating opportunities to allow pathologists to improve reading quality or save time using Artificial Intelligence (AI)-based applications. We aim to enhance the practice of pathologists through a retrieval system that allows them to simplify their workflow, limit the need for second opinions, while also learning in the process. In this work, an innovative retrieval system for digital pathology is integrated within a Whole Slide Image (WSI) viewer, allowing to define regions of interest in images as queries for finding visually similar areas using deep representations. The back-end similarity computation algorithms are based on a multimodal approach, allowing to exploit both text information and content-based image features. Shallow and deep representations of the images were evaluated, the later showed a better overall retrieval performance in a set of 112 whole slide images from biopsies. The system was also tested by pathologists, highlighting its capabilities and suggesting possible ways to improve it and make it more usable in clinical practice. The retrieval system developed can enhance the practice of pathologists by enabling them to use their experience and knowledge to properly control artificial intelligence tools for navigating repositories of images for decision support purposes.
Taxonomic revision of Leopold and Rudolf Blaschka Glass Models of Invertebrates 1888 Catalogue, with correction of authorities
Authors: Callaghan Eric , Egger Bernhard , Doyle Hazel , Reynaud Emmanuel G.
Published: September 2018

The glass models of invertebrates crafted by Leopold and Rudolf Blaschka were made between 1863 and 1889. Production ceased when the glassmakers turned their attention to what is now known as the Ware Collection of Blaschka Glass Models of Plants, created for the Harvard Museum of Natural History. Nearly 130 years have passed since their last published catalogue of species in 1888 and the nomenclature they applied is now a confusing mix that includes many junior synonyms and unavailable names. This is an issue for many museums and universities which owns Blaschka models as uncertain identifications may compromised interpretation of this rediscovered legacy. Nowadays, many museums and universities hold collections of those glass invertebrates but misspelled, mislabelled or simply apply the century old taxonomy of 1888. Here, we provide a valuable resource for curators and enthusiasts alike. We studied and updated the final catalogue 1888 from the Blaschkas’ Dresden-based workshop. We first focused on major taxonomical changes from taxa to species, as well as on an analysis of the acknowledged authorities. We found that only 35.3% of the models retain their original names, while 3.7% lack any known synonym and their identity remains open to interpretation. Finally, two of the authorities listed in the catalogue, Ernst Haeckel and Philip Henry Gosse, were incorrectly acknowledged for an extensive range of models. This study is the first of its kind on the Blaschka collection, and it will help in the identification and naming of Blaschka models worldwide.
Radiomics Analysis Using Stability Selection Supervised Principal Component Analysis for Right-censored Survival Data
Authors: Yan Kang K. , Wang Xiaofei , Lam Wendy , Vardhanabhuti Varut , Lee Anne W.M. , Pang Herbert
Published: September 2018

Radiomics is a newly emerging field that involves the extraction of a large number of quantitative features from biomedical images through the use of data-characterization algorithms. Radiomics provides a noninvasive approach for personalized therapy decision by identifying distinctive imaging features for predicting prognosis and therapeutic response. So far, many of the published radiomics studies utilize existing out of the box algorithms to identify the prognostic markers from biomedical images that are not specific to radiomics data. T o better utilize biomedical image, we propose a novel machine learning approach, stability selection supervised principal component analysis (SSSuperPCA) that identify a set of stable features from radiomics big data coupled with dimension reduction for right censored survival outcomes. In this paper, we describe stability selection supervised principal component analysis for radiomics data with right-censored survival outcomes. The proposed approach allows us to identify a set of stable features that are highly associated with the survival outcomes, control the per-family error rate, and predict the survival in a simple yet meaningful manner. We evaluate the performance of SSSuperPCA using simulations and real data sets for non-small cell lung cancer and head and neck cancer, and compare it with other machine learning algorithms. The results demonstrate that our method has a competitive edge over other existing methods in identifying the prognostic markers from biomedical big imaging data for the prediction of right-censored survival outcomes. An R package SSSuperPCA is available at the website:http://web.hku.hk/∼herbpang/SSSuperPCA.html
Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved?
Authors: Tiger Li Zheng-Rong , Zarnitsyna Veronika I. , Lowen Anice C. , Weissman Daniel , Koelle Katia , Kohlmeier Jacob E. , Antia Rustom
Published: September 2018

The high-degree conservation of CD8 T cell epitopes of influenza A virus (IAV) may allow T cell-inducing vaccines effective across different strains and subtypes. This conservation is not fully explained by functional constraint, since additional mutation(s) can compensate the replicative fitness loss of IAV escape-variant. Here, we propose three additional mechanisms that contribute to the conservation of CD8 T cell epitopes of IAV. First, influenza-specific CD8 T cells may protect predominantly against severe pathology rather than infection and may only have a modest effect on transmission. Second, polymorphism of human MHC-I gene restricts the advantage of an escape-variant to only a small fraction of human population, who carry the relevant MHC-I alleles. Finally, infection with CD8 T cell-escapevariants may result in compensatory increase in the responses to other epitopes of IAV. A combination of population genetics and epidemiological models is used to examine how the interplay between these mechanisms affects the rate of invasion of IAV escape-variants. We conclude that the invasion of an escape-variant will be very slow with a timescale of decades or longer, even if the escape-variant does not have a replicative fitness loss. Our results suggest T cell-inducing vaccines may not engender the rapid evolution of IAV and serve as a foundation for future modeling works on the long-term effectiveness and impacts of T cell-inducing influenza vaccines. (Word count: 221)

Importance

Universal influenza vaccines against the conserved epitopes of influenza A virus have been proposed to minimize the burden of seasonal outbreaks and prepare for the pandemics. However, it is not clear to which extent the T cell-inducing vaccines will select for viruses that escape the T cell responses. Our mathematical models suggest how the nature of CD8 T cell protection contributes to the conservation of the CD8 T cell epitopes of influenza A virus. Also, it points out the essential biological parameters and questions that need addressing by future experimental works. (Word count: 91)
FUS controls the processing of snoRNAs into smaller RNA fragments that can regulate gene expression
Authors: Plewka Patrycja , Szczesniak Michal Wojciech , Stepien Agata , Zywicki Marek , Pacak Andrzej , Colombo Martino , Makalowska Izabela , Ruepp Marc-David , Raczynska Katarzyna Dorota
Published: September 2018

FUS is a multifunctional protein involved in many steps of RNA metabolism, including transcription, splicing, miRNA processing and replication-dependent histone gene expression. In this paper, we show for the first time that FUS binds and negatively regulates the levels of a subset of snoRNAs in cells. Scanning of available human small RNA databases revealed the existence of smaller RNA fragments that can be processed from FUS-dependent snoRNAs. Therefore, we suggest that FUS mediates the biogenesis of snoRNA-derived small RNAs, called sdRNAs. Furtherin silicoapproaches enabled us to predict putative targets of selected FUS-dependent sdRNAs. Our results indicate that sdRNAs may bind to different regions of target mRNAs as well as to noncoding transcripts and influence the posttranscriptional level or translation of these targets.

SIGNIFICANCE STATEMENT

RNA metabolism is orchestrated by a complex network of RNA-protein interactions and involves various classes of RNA molecules. Small nucleolar RNAs (snoRNAs) are commonly considered essential components of the ribosome biogenesis pathway. However, recent studies have revealed that snoRNAs can also be fragmented into small entities called snoRNA-derived RNAs (sdRNAs), which have been linked to multiple cancer types and thus may serve as next-generation prognostic or diagnostic biomarkers. In this paper, a multifunctional protein, FUS, was shown to be involved in the biogenesis of snoRNA-derived fragments. Furthermore, we combined bioinformatic analyses with complementary experimental approaches to elucidate the role of FUS-dependent sdRNAs in gene expression regulation. Our findings reveal the considerable regulatory potential of this new class of small noncoding RNAs.
Mutation of influenza A virus PA-X decreases pathogenicity in chicken embryos and can increase the yield of reassortant candidate vaccine viruses
Authors: Hussain Saira , Turnbull Matthew L. , Wise Helen M. , Jagger Brett W. , Beard Philippa M. , Kovacikova Kristina , Taubenberger Jeffery K. , Vervelde Lonneke , Engelhardt Othmar G , Digard Paul
Published: September 2018

The PA-X protein of influenza A virus has roles in host cell shut-off and viral pathogenesis. While most strains are predicted to encode PA-X, strain-dependent variations in activity have been noted. We found that PA-X protein from A/PR/8/34 (PR8) strain had significantly lower repressive activity against cellular gene expression compared with PA-Xs from the avian strains A/turkey/England/50-92/91 (H5N1) (T/E) and A/chicken/Rostock/34 (H7N1). Loss of normal PA-X expression, either by mutation of the frameshift site or by truncating the X-ORF, had little effect on the infectious virus titre of PR8 or PR8 7:1 reassortants with T/E segment 3 grown in embryonated hens’ eggs. However, in both virus backgrounds, mutation of PA-X led to decreased embryo mortality and lower overall pathology; effects that were more pronounced in the PR8 strain than the T/E reassortant, despite the low shut-off activity of the PR8 PA-X. Purified PA-X mutant virus particles displayed an increased ratio of HA to NP and M1 compared to their WT counterparts, suggesting altered virion composition. When the PA-X gene was mutated in the background of poorly growing PR8 6:2 vaccine reassortant analogues containing the HA and NA segments from H1N1 2009 pandemic viruses or an avian H7N3 strain, HA yield increased up to 2-fold. This suggests that the PR8 PA-X protein may harbour a function unrelated to host cell shut-off and that disruption of the PA-X gene has the potential to improve the HA yield of vaccine viruses.

IMPORTANCE

Influenza A virus is a widespread pathogen that affects both man and a variety of animal species, causing regular epidemics and sporadic pandemics with major public health and economic consequences. A better understanding of virus biology is therefore important. The primary control measure is vaccination, which for humans, mostly relies on antigens produced in eggs from PR8-based viruses bearing the glycoprotein genes of interest. However, not all reassortants replicate well enough to supply sufficient virus antigen for demand. The significance of our research lies in identifying that mutation of the PA-X gene in the PR8 strain of virus can improve antigen yield, potentially by decreasing the pathogenicity of the virus in embryonated eggs.
Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA-dominated PHAS loci
Authors: Polydore Seth , Lunardon Alice , Axtell Michael J.
Published: September 2018

Small RNAs regulate key physiological functions in land plants. Small RNAs can be divided into two categories: microRNAs (miRNAs) and short interfering RNAs (siRNAs); siRNAs are further sub-divided into transposon/repetitive region-localized heterochromatic siRNAs and phased siRNAs (phasiRNAs). PhasiRNAs are produced from the miRNA-mediated cleavage of a Pol II RNA transcript; the miRNA cleavage site provides a defined starting point from which phasiRNAs are produced in a distinctly phased pattern. 21-22 nucleotide (nt)-dominated phasiRNA-producing loci (PHAS) are well represented in all land plants to date. In contrast, 24 nt-dominated PHAS loci are known to be encoded only in monocots and are generally restricted to male reproductive tissues. Currently, only one miRNA (miR2275) is known to trigger the production of these 24 nt-dominated PHAS loci. In this study, we use stringent methodologies in order to examine whether or not 24 nt-dominated PHAS loci also exist in Arabidopsis thaliana. We find that highly expressed heterochromatic siRNAs were consistently mis-identified as 24 nt-dominated PHAS loci using multiple PHAS-detecting algorithms. We also find that MIR2275 is not found in A. thaliana, and it seems to have been lost in the last common ancestor of Brassicales. Altogether, our research highlights the potential issues with widely used PHAS-detecting algorithms which may lead to false positives when trying to annotate new PHAS, especially 24 nt-dominated loci.
Visualisation and analysis of RNA-Seq assembly graphs
Authors: Nazarie Fahmi W. , Shih Barbara , Angus Tim , Barnett Mark W. , Chen Sz-Hau , Summers Kim M. , Klein Karsten , Faulkner Geoffrey J. , Saini Harpreet K. , Watson Mick , Dongen Stijn van , Enright Anton J. , Freeman Tom C.
Published: September 2018

RNA-sequencing (RNA-Seq) is a powerful transcriptome profiling technology enabling transcript discovery and quantification. RNA-Seq data are large, and most commonly used as a source of genelevel quantification measurements, whilst the underlying assemblies of reads, if inspected, are usually viewed as sequence reads mapped on to a reference genome. Whilst sufficient for many needs, when the underlying transcript assemblies are complex, this visualisation approach can be limiting; errors in assembly can be difficult to spot and interpretation of splicing events is challenging.

Here we report on the development of a graph-based visualisation method as a complementary approach to understanding transcript diversity and read assembly from short-read RNA-Seq data. Following the mapping of reads to the reference genome, read-to-read comparison is performed on all reads mapping to a given gene, producing a matrix of weighted similarity scores between reads. This is used to produce an RNA assembly graph where nodes represent reads derived from a cDNA and edges similarity scores between reads, above a defined threshold. Visualisation of resulting graphs is performed using Graphia Professional. This tool can render the often large and complex graph topologies that result from DNA/RNA sequence assembly in 3D space and supports info rmatio no verlay on to nodes, e.g. transcript models. We have also implemented an analysis pipeline for the creation of RNA assembly graphs with both a command-line and web-based interface that allows users to create and visualise these data. Here we demonstrate the utility of this approach on RNA-Seq data, including the unusual structure of these graphs and how they can be used to identify issues in assembly, repetitive sequences within transcripts and splice variants. We believe this approach has the potential to significantly improve our understanding of transcript complexity.
Automated EEG mega-analysis I: Spectral and amplitude characteristics across studies
Authors: Bigdely-Shamlo Nima , Touryan Jonathan , Ojeda Alejandro , Kothe Christian , Mullen Tim , Robbins Kay
Published: September 2018

Significant achievements have been made in the fMRI field by pooling statistical results from multiple studies (meta-analysis). More recently, fMRI standardization efforts have focused on enabling the joint analysis of raw fMRI data across studies (mega-analysis), with the hope of achieving more detailed insights. However, it has not been clear if such analyses in the EEG field are possible or equally fruitful. Here we present the results of a large-scale EEG mega-analysis using 18 studies from six sites representing several different experimental paradigms. We demonstrate that when meta-data are consistent across studies, both channel-level and source-level EEG mega-analysis are possible and can provide insights unavailable in single studies. The analysis uses a fully-automated processing pipeline to reduce line noise, interpolate noisy channels, perform robust referencing, remove eye-activity, and further identify outlier signals. We define several robust measures based on channel amplitude and dispersion to assess the comparability of data across studies and observe the effect of various processing steps on these measures. Using ICA-based dipolar sources, we also observe consistent differences in overall frequency baseline amplitudes across brain areas. For example, we observe higher alpha in posterior vs anterior regions and higher beta in temporal regions. We also detect consistent differences in the slope of the aperiodic portion of the EEG spectrum across brain areas. In a companion paper, we apply mega-analysis to assess commonalities in event-related EEG features across studies. The continuous raw and preprocessed data used in this analysis are available through the DataCatalog at https://cancta.net.
Flexible backbone assembly and refinement of symmetrical homomeric complexes
Authors: Roy Burman Shourya S. , Yovanno Remy A. , Gray Jeffrey J.
Published: September 2018

Symmetrical homomeric proteins are ubiquitous in every domain of life, and information about their structure is essential to decipher function. The size of these complexes often makes them intractable to high-resolution structure determination experiments. Computational docking algorithms offer a promising alternative for modeling large complexes with arbitrary symmetry. Accuracy of existing algorithms, however, is limited by backbone inaccuracies when using homology-modeled monomers. Here, we present Rosetta SymDock2 with a broad search of symmetrical conformational space using a six-dimensional coarse-grained score function followed by an all-atom flexible-backbone refinement, which we demonstrate to be essential for physically-realistic modeling of tightly packed complexes. In global docking of a benchmark set of complexes of different point symmetries — staring from homology-modeled monomers — we successfully dock (defined as predicting three near-native structures in the five top-scoring models) 19 out of 31 cyclic complexes and 5 out of 12 dihedral complexes.

Highlights

SymDock2 is an algorithm to assemble symmetric protein structures from monomers

Coarse-grained score function discriminates near-native conformations

Flexible backbone refinement is necessary to create realistic all-atom models

Results improve six-fold and outperform other symmetric docking algorithms

Graphical Abstract
Comparison of null models for combination drug therapy reveals Hand model as biochemically most plausible
Authors: Sinzger Mark , Vanhoefer Jakob , Loos Carolin , Hasenauer Jan
Published: September 2018

Null models for the effect of combination therapies are widely used to evaluate synergy and antagonism of drugs. Due to the relevance of null models, their suitability is continuously discussed. Here, we contribute to the discussion by investigating the properties of five null models. Our study includes the model proposed by David J. Hand, which we refer to asHand model. The Hand model has been introduced almost 20 years ago but hardly was used and studied. We show that the Hand model generalizes the principle of dose equivalence compared to the Loewe model and resolves the ambiguity of the Tallarida model. This provides a solution to the persisting conflict about the compatibility of two essential model properties: the sham combination principle and the principle of dose equivalence. By embedding several null models into a common framework, we shed light in their biochemical validity and provide indications that the Hand model is biochemically most plausible. We illustrate the practical implications and differences between null models by examining differences of null models on published data.
A versatile platform strain for high-fidelity multiplex genome editing
Authors: Egbert Robert G. , Rishi Harneet S. , Adler Benjamin A. , McCormick Dylan M. , Toro Esteban , Gill Ryan T. , Arkin Adam P.
Published: September 2018

Precision genome editing accelerates the discovery of the genetic determinants of phenotype and the engineering of novel behaviors in organisms. Advances in DNA synthesis and recombineering have enabled high-throughput engineering of genetic circuits and biosynthetic pathways via directed mutagenesis of bacterial chromosomes. However, the highest recombination efficiencies have to date been reported in persistent mutator strains, which suffer from reduced genomic fidelity. The absence of inducible transcriptional regulators in these strains also prevents concurrent control of genome engineering tools and engineered functions. Here, we introduce a new recombineering platform strain, BioDesignER, which incorporates (1) a refactored λ-Red recombination system that reduces toxicity and accelerates multi-cycle recombination, (2) genetic modifications that boost recombination efficiency, and (3) four independent inducible regulators to control engineered functions. These modifications resulted in single-cycle recombineering efficiencies of up to 25% with a seven-fold increase in recombineering fidelity compared to the widely used recombineering strain EcNR2. To facilitate genome engineering in BioDesignER, we have curated eight context-neutral genomic loci, termed Safe Sites, for stable gene expression and consistent recombination efficiency. BioDesignER is a platform to develop and optimize engineered cellular functions and can serve as a model to implement comparable recombination and regulatory systems in other bacteria.
An essential checkpoint for TLR9 signaling is release from Unc93b1 in endosomes
Authors: Majer Olivia , Woo Brian J , Liu Bo , Dis Erik Van , Barton Gregory M
Published: September 2018

Nucleic acid-sensing Toll-like receptors (TLRs) are subject to complex regulation to facilitate recognition of microbial DNA and RNA while limiting recognition of self-nucleic acids1. Failure to properly regulate nucleic acid-sensing TLRs can lead to autoimmune and autoinflammatory disease2-6. Intracellular localization of these receptors is thought to be critical for self vs. non-self discrimination7, yet the molecular mechanisms that reinforce compartmentalized activation of intracellular TLRs remain poorly understood. Here we describe a new mechanism that prevents TLR9 activation from locations other than endosomes. This control is achieved through the regulated release of TLR9 from its trafficking chaperone Unc93b1, which only occurs within endosomes and is required for ligand binding and signal transduction. Mutations in Unc93b1 that increase affinity for TLR9 impair release and result in defective signaling. The release is specific to TLR9, as TLR7 does not dissociate from Unc93b1 in endosomes. This work defines a novel checkpoint that reinforces self vs. non-self discrimination by TLR9 and provides a mechanism by which TLR9 and TLR7 activation can be distinctly regulated.
Spatial neglect is causally linked to an attention-related area in macaque temporal cortex
Authors: Bogadhi Amarender R. , Bollimunta Anil , Leopold David A. , Krauzlis Richard J.
Published: September 2018

Spatial neglect is a common clinical syndrome involving disruption of the brain’s attention-related circuitry, including the dorsocaudal temporal cortex. While neglect is readily modeled in macaques, the absence of evidence for temporal cortex involvement has suggested a fundamental difference from humans. To map the neurological expression of spatial neglect in macaques, we measured attention-related fMRI activity across the cerebral cortex during experimental induction of neglect through reversible inactivation of the superior colliculus. During inactivation, monkeys exhibited hallmark attentional deficits of neglect in tasks using either moving or static stimuli. The behavioral deficits were accompanied by marked reductions in fMRI attentional modulation that were strongest in a small region on the floor of the superior temporal sulcus. Notably, direct inactivation of this mid-STS cortical region caused similar neglect-like spatial attention deficits. These results identify a putative macaque homolog to temporal cortex structures known to play a central role in human neglect.

Highlights

During neglect the mid-STS cortex shows largest reduction in attentional modulation

The mid-STS cortex is selectively affected with static as well as dynamic stimuli

Mid-STS cortex is affected during neglect caused by SC or FEF inactivation

Inactivation of mid-STS cortex itself causes neglect without eye movement deficits

In Brief

Using fMRI in macaques performing attention tasks combined with reversible inactivations, Bogadhi et al. provide causal evidence that a region on the floor of the superior temporal sulcus is a crucial node in the cortical control of covert selective attention and a putative homolog to temporal cortex regions in humans implicated in spatial neglect.
Microglia limit lesion expansion and promote functional recovery after spinal cord injury in mice
Authors: Brennan Faith H. , Hall Jodie C.E. , Guan Zhen , Popovich Phillip G.
Published: September 2018

Traumatic spinal cord injury (SCI) elicits a robust intraspinal inflammatory reaction that is dominated by at least two major subpopulations of macrophages, i.e., those derived from resident microglia and another from monocytes that infiltrate the injury site from the circulation. Previously, we implicated monocyte-derived macrophages (MDMs) as effectors of acute post-injury pathology after SCI; however, it is still unclear whether microglia also contribute to lesion pathology. Assigning distinct functional roles to microglia and MDMs in vivo has been difficult because these CNS macrophage subsets are morphologically and phenotypically similar. Here, to characterize the role that microglia play in experimental models of thoracic spinal contusion or lumbar crush injury, mice were fed vehicle chow or chow laced with a CSF1R receptor antagonist, PLX5622. Feeding PLX5622 depletes microglia. In both groups, spontaneous recovery of hindlimb motor function was evaluated for up to 8 weeks post-SCI using open-field and horizontal ladder tests. Histopathological assessment of intraspinal pathology was assessed in 8 week post-injury tissues. In both SCI models, microglia depletion exacerbated lesion pathology and impaired spontaneous recovery of hind limb function. Notably, the loss of microglia prevented astroglial encapsulation of the lesion core, which was associated with larger lesions, enhanced demyelination and neuron loss and a larger inflammatory response that was dominated by monocyte-derived macrophages. The neuroprotective and healing properties of microglia become obvious in the subacute phases of recovery; microglia depletion up to 7 days post-injury (dpi) had no apparent effect on recovery while delayed depletion from 8-28dpi exacerbated lesion pathology and significantly impaired functional recovery. These data suggest that microglia have essential tissue repair functions after SCI. Selective enhancement of microglial activities may be a novel strategy to preserve tissue and promote recovery of function after neurotrauma.
Identification of miRNAs and associated pathways regulated by Leukemia Inhibitory Factor in trophoblastic cell lines
Authors: Morales-Prieto Diana M. , Barth Emanuel , Murrieta-Coxca Jose Martín , Favaro Rodolfo R. , Gutiérrez-Samudio Ruby N. , Chaiwangyen Wittaya , Ospina-Prieto Stephanie , Gruhn Bernd , Schleußner Ekkehard , Marz Manja , Markert Udo R.
Published: September 2018

Introduction

Leukemia Inhibitory Factor (LIF) regulates behavior of trophoblast cells and their interaction with immune and endothelial cells.In vitro, trophoblast cell response to LIF may vary depending on the cell model. Reported differences in the miRNA profile of trophoblastic cells may be responsible for these observations. Therefore, miRNA expression was investigated in four trophoblastic cell lines under LIF stimulation followed byin silicoanalysis of altered miRNAs and their associated pathways.

Methods

Low density TaqMan miRNA assays were used to quantify levels of 762 mature miRNAs under LIF stimulation in three choriocarcinoma-derived (JEG-3, ACH-3P and AC1-M59) and a trophoblast immortalized (HTR-8/SVneo) cell lines. Expression of selected miRNAs was confirmed in primary trophoblast cells and cell lines by qPCR. Targets and associated pathways of the differentially expressed miRNAs were inferred from the miRTarBase followed by a KEGG Pathway Enrichment Analysis. HTR-8/SVneo and JEG-3 cells were transfected with miR-21-mimics and expression of miR-21 targets was assessed by qPCR.

Results

A similar number of miRNAs changed in each tested cell line upon LIF stimulation, however, low coincidence of individual miRNA species was observed and occurred more often among choriocarcinoma-derived cells (complete data set athttp://www.ncbi.nlm.nih.gov/geo/under GEO accession number GSE130489). Altered miRNAs were categorized into pathways involved in human diseases, cellular processes and signal transduction. Six cascades were identified as significantly enriched, including JAK/STAT and TGFB-SMAD. Upregulation of miR-21-3p was validated in all cell lines and primary cells and STAT3 was confirmed as its target.

Discussion

Dissimilar miRNA responses may be involved in differences of LIF effects on trophoblastic cell lines.
Glycogen Synthase Kinase 3 induces multilineage maturation of human pluripotent stem cell-derived lung progenitors in 3D culture
Authors: de Carvalho Ana Luisa Rodrigues Toste , Strikoudis Alexandros , Dantas Tiago J. , Chen Ya-Wen , Liu Hsiao-Yun , Vallee Richard B. , Correia-Pinto Jorge , Snoeck Hans-Willem
Published: September 2018

Although strategies for directed differentiation of human pluripotent stem cells (hPSCs) into lung and airway have been established, terminal maturation of the cells remains a vexing problem. We show here that in Collagen I 3D cultures in the absence of glycogen synthase kinase 3 (GSK3) inhibition, hPSC-derived lung progenitors (LPs) undergo multilineage maturation into proximal cells arranged in pseudostratified epithelia, type I alveolar epithelial cells and morphologically mature type II cells. Enhanced cell cycling, one of the signaling outputs of GSK3 inhibition, plays a role in the maturation-inhibiting effect of GSK3 inhibition. Using this model, we show NOTCH signaling induced a distal at the expense of a proximal and ciliated cell fate, while WNT signaling promoted a proximal, club cell fate, thus implicating both signaling pathways in proximodistal specification in human lung development. These findings establish an approach to achieve multilineage maturation of lung and airway cells from hPSCs, demonstrate a pivotal role of GSK3 in the maturation of lung progenitors, and provide novel insight into proximodistal specification during human lung development.
Special interests and inclusive academic learning: an autistic perspective
Authors: Boven Frederik
Published: September 2018

Purpose

Many people with an autistic spectrum condition have one or more “special interests” which is more restricted, and which they pursue with more than average intensity. The purpose of this paper is to offer a first-person perspective on inclusion of special interests in academic learning. The paper describes examples of special interests of university students and offers recommendations for university teachers.

Design/methodology/approach

The author combines the emerging strategy of using his own autobiographical material as research object with the more establish method of conceptual analysis.

Findings

The author finds that special interests can be a source of academic strength, but can also interfere with learning. The paper argues that including special interests in academic learning is an effective way of including students with autism in higher education, but requires some special provisions.

Originality/value

Existing research has focused either on the special interests of persons with autism or on their inclusion in education, but the combination of these two issues has rarely been considered. The paper addresses this neglected topic from the inside perspective of a former student with autism who, after completing a research master’s in philosophy, was diagnosed with Asperger’s syndrome at age 34. The author combines this inside perspective with knowledge of the theory and history of autism.
Effects of different roughness elements on friction and pressure drop of laminar flow in microchannels
Authors: Lalegani Fakhrodin , Saffarian Mohammad Reza , Moradi Ahmadreza , Tavousi Ebrahim
Published: September 2018

Purpose

According to very small dimensions of the microchannels, producing a microchannel with smooth surfaces is approximately impossible. The surface roughness can have a specific effect on microchannel performances. This paper aims to investigate the changes in friction and pressure drop in the microchannels by considering the different roughness elements on microchannel wall and changes in elementary geometry and flow conditions. Results show a significant effect of roughness on the pressure drop and friction.

Design/methodology/approach

Two-dimensional fluid flow in the rough microchannels is analyzed using FLUENT. Microchannels have a height of 50 µm. Water at room temperature (25°C) has been used as working fluid. The Reynolds numbers are considered in laminar flow range and from 50 to 300.

Findings

The results show that the value of friction factor reduces nonlinearly with an increase in Reynolds number. But, the pressure drops and the Poiseuille number in the microchannels increase with an increase in Reynolds number. The values of the pressure drop and the friction factor increase by increasing the height and size of the roughness elements, but these values reduce with an increase in the distance of roughness elements.

Originality/value

The roughness elements types in this research are rectangular, trapezoidal, elliptical, triangular and complex (composed of multiple types of roughness elements). The effects of the Reynolds number, roughness height, roughness distance and roughness size on the pressure drop and friction in the rough microchannels are investigated and discussed. Furthermore, differences between the effects of five types of roughness elements are identified.
New services development: a study in the context of a health organization
Authors: Eberle Luciene , Milan Gabriel Sperandio , De Toni Deonir , Lazzari Fernanda
Published: September 2018

Purpose

The purpose of this study is to highlight the understanding of the consequent factors of new services development (NSD) in the literature owing to the impact on organizational competitiveness, especially in professional services, such as that investigated by health plan operators in the present study.

Design/methodology/approach

The sample (customer of family health plans) consisted of 255 valid cases. For the analysis of the data, multivariate statistical techniques were used through the modeling of structural equations.

Findings

The results found evidence of the significant relationships between the NSD considering the constructs, client orientation, reputation, professional competences and customer retention, as consequences of the NSD, which impact on the success of the new services launched by the health plan operator from the perception of the customer.

Practical implications

This implies that health plan operators need to develop new customer-oriented services by investing in new technologies and having more trained and qualified staff so that they can deliver superior services and, as a consequence, have a more profitable relationship with customers.

Originality/value

The new services may result in greater organizational performance and greater competitiveness for health service providers.
Heritage values: towards a holistic and participatory management approach
Authors: Heras Veronica Cristina , Moscoso Cordero María Soledad , Wijffels Anja , Tenze Alicia , Jaramillo Paredes Diego Esteban
Published: September 2018

Purpose

In other fields, like natural resources, a wide range of participatory methods have been applied, criticized and adapted trough practice. Areas such as anthropology, history or architecture have contributed to the identification of heritage values. Semi-structured interviews and cultural mapping are examples of qualitative and participative methods that have been applied already in the conservation field. Nevertheless, no framework exists to assess the effectiveness of such methods and little experience has been built up in actor’s integration within the heritage value identification process. The purpose of this paper is to develop a framework to recognize heritage values incorporating multidisciplinary and multi-actor perspectives.

Design/methodology/approach

The socio-praxis approach, which is the outcome of an articulation of diverse methodologies that aim to support social processes from a bottom-up approach as a tool for decision making and community planning, was implemented in the present research. In this context, it supported the identification of heritage values incorporating multidisciplinary and multi-actor perspectives of two traditional neighborhoods of the city of Cuenca in Ecuador.

Findings

The results show that the identification of heritage values from multidisciplinary and multi-actor perspectives allows a more comprehensive vision of the existing values and the process reveals a greater involvement of the neighbors in heritage issues. The importance of structuring organized group of neighbors and positioning them as living experts has showed the complexity of cultural heritage conservation process but at the same time the significance for heritage management has been demonstrated. Therefore, this experience can be considered as an invaluable tool for heritage sites managers.

Originality/value

Stakeholder involvement in heritage conservation management has been widely discussed on international forums in the ultimate decades. While the importance of actor perceptions and priorities for sustainable heritage conservation is recognized, little has been said about the ways to reveal – non-expert – heritage values in such a way that people get involved in the heritage value assessment. In this perspective, the present research represents an invaluable tool for heritage sites that aim to implement a long-term management plans.
Impact of continuity of care on quality of life in patients with chronic obstructive pulmonary disease
Authors: Bikmoradi Ali , Jalalinasab Azam , Salvati Mohsen , Ahmadpanah Mohamad , Divani Farshid , Roshanaei Ghodratollah
Published: September 2018

Purpose

Patients with chronic obstructive pulmonary disease (COPD) suffer many physical disabilities which cause many problems in their life. These patients really need to have continuity of care based on cooperation between patient, the family and their care givers in order to achieve an integration of care. The purpose of this paper is to assess the impact of continuous care on quality of life of patients with COPD.

Design/methodology/approach

A before–after quasi-experimental study was carried out with 72 patients with COPD at Beheshti educational hospital of Hamadan University of Medical Sciences. The patients who met inclusion criteria were randomly allocated into an intervention group (n=36) and a control group (n=36). The patients completed the St George’s Respiratory Questionnaire before and after their care. The intervention comprised continuous care with orientation and sensitization sessions (2 weeks), control and evaluation sessions (45 days) for intervention group and with routine care in the control group. Data were analyzed with SPSS, descriptive and inferential statistics were conducted to measure differences between intervention and control group.

Findings

Continuity of care improved significantly the quality of life of COPD patients in general, and in the symptoms, activity and impact domains (P=0.001). In contrast, routine care did not improve quality of life for patients in general, and in the symptoms, activity and impact domains (P=0.05).

Originality/value

Continuity of care has a positive impact on quality of life for COPD patients. Health care system should utilize continuity of care models as an overall plan for patients with COPD. Moreover, managers of health care system could reduce burden of chronic diseases by employing continuity of care models in planning patient care.
Model for the enhancement of learning in higher education through the deployment of emerging technologies
Authors: Isaías Pedro
Published: September 2018

Purpose

Change is the operative word in higher education; as roles shift, classrooms are reinvented, and content becomes increasingly more accessible. At the core of these changes is the pervasiveness of learning technology. This papers aims to propose a model for the selection and adoption of emerging learning technologies to enhance learning within the context of higher education.

Design/methodology/approach

Higher education institutions are resorting to the deployment of learning technologies to address the demands of the twenty-first century learners and to ascertain their competitiveness. This paper draws from the literature to provide a model, composed of five key characteristics of learning, to support the selection and adoption of emerging learning technologies.

Findings

The model posits that the attainment of each of these five characteristics, personalised, ubiquitous, collaborative, lifelong and authentic needs to be supported by corresponding technologies: adaptive learning technologies, artificial intelligence, mobile technology, social technology, massive open online courses, virtual and augmented reality, gamification and the Internet of Things.

Originality/value

Higher education is progressively being displaced from the traditional classroom, and as it progresses towards online settings, it requires the support of technology to facilitate that transference. In examining the potential of future learning technologies, this paper contributes to a growing body of research that focuses on the benefits of technology within higher education and assists educators in the selection and adoption of the most relevant technologies.