bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of air quality using a cloud model method
Authors: Xu Qingwei , Xu Kaili
Published: September 2018

To effectively control air pollution, it is necessary to obtain a preliminary assessment of air quality. The purpose of this study was to introduce a cloud model method in air pollution assessment. First, the standard cloud models of air pollution indicators were obtained, and the calculating process of numerical characteristics employed by the standard cloud model was explained. Second, the levels of air pollution indicators were presented based on the qualitative and quantitative analysis of cloud models, which realized the uncertainty conversion between qualitative concepts and their corresponding quantitative values, as well as taking the fuzziness and randomness into account. Air quality assessment results including SO
2
, NO
2
, CO, O
3
, PM
10
and PM
2.5
were analysed. Third, the cloud model adopted in the assessment process of air quality was validated by grey relational analysis, and the results confirmed the validity of cloud model assessment. Fourth, the air pollution level of the air quality index (AQI) was determined, and the fuzziness and randomness of the assessment results were thoroughly analysed by taking entropy and hyper entropy into consideration. Fifth, seasonal variations in different air pollution indicators were analysed to proffer a series of recommendations for government policy decision-makers and travellers. The cloud model provided a new method for air quality assessment.
Hypergravity-assisted chemical liquid deposition of nano-granular film on the inner surface of a quartz tube
Authors: Shen Y. K. , He X. Q. , Gu X. , Liu Z. , He Z. H.
Published: September 2018

Transparent tubes with functions of heating and temperature measurement are badly required in the visualization investigation of two-phase flows and flow-boiling heat transfer. In order to prepare such a tube, we introduced a cost-effective and energy-efficient procedure of hypergravity-assisted chemical liquid deposition (HACLD) to produce transparent and conductive silver (Ag) films on the inner surfaces of quartz tubes, typically 50 mm in length and 8 mm in inner diameter with a set-up that was designed and built for this purpose. Precursors of organometallic Ag precursor solutions were prepared by dissolving silver citrate and 1,2-diaminopropane in 2-methoxyethanol with required concentration for the chemical liquid deposition process. Semitransparent and conductive Ag films formed inside the required quartz tubes under specific heating process in hypergravity. One of the films was about 47 nm in thickness, 23 Ω per square sheet resistance, and 30% optical transmittance. This attempt may pave a way for the understanding of the film forming mechanism in hypergravity, and the development of a film preparation technology of HACLD.
Planar morphometrics using Teichmüller maps
Authors: Choi Gary P. T. , Mahadevan L.
Published: September 2018

Inspired by the question of quantifying wing shape, we propose a computational approach for analysing planar shapes. We first establish a correspondence between the boundaries of two planar shapes with boundary landmarks using geometric functional data analysis and then compute a landmark-matching curvature-guided Teichmüller mapping with uniform quasi-conformal distortion in the bulk. This allows us to analyse the pair-wise difference between the planar shapes and construct a similarity matrix on which we deploy methods from network analysis to cluster shapes. We deploy our method to study a variety ofDrosophilawings across species to highlight the phenotypic variation between them, and Lepidoptera wings over time to study the developmental progression of wings. Our approach of combining complex analysis, computation and statistics to quantify, compare and classify planar shapes may be usefully deployed in other biological and physical systems.
Points of constancy of the periodic linearized Korteweg–deVries equation
Authors: Olver Peter J. , Tsatis Efstratios
Published: September 2018

We investigate the points of constancy in the piecewise constant solution profiles of the periodic linearized Korteweg–deVries equation with step function initial data at rational times. The solution formulae are given by certain Weyl sums, and we employ number theoretic techniques, including Kummer sums, in our analysis. These results constitute an initial attempt to understand the complementary phenomenon of ‘fractalization’ at irrational times.
Pain relief provided by an outgroup member enhances analgesia
Authors: Hein Grit , Engelmann Jan B. , Tobler Philippe N.
Published: September 2018

Pain feels different in different social contexts, yet the mechanisms behind social pain modulation remain poorly understood. To elucidate the impact of social context on pain processing, we investigated how group membership, one of the most important social context factors, shapes pain relief behaviourally and neurally in humans undergoing functional neuroimaging. Participants repeatedly received pain relief from a member of their own group (ingroup treatment) or a member of a disliked outgroup (outgroup treatment). We observed a decrease in pain ratings and anterior insula (AI) pain responses after outgroup treatment, but not after ingroup treatment. Moreover, path analyses revealed that the outgroup treatment induced a stronger relief learning in the AI, which in turn altered pain processing, in particular if the participant entered the treatment with a negative impression toward the outgroup individual. The finding of enhanced analgesia after outgroup treatment is relevant for intergroup clinical settings. More generally, we found that group membership affects pain responses through neural learning and we thus elucidate one possible mechanism through which social context impacts pain processing.
A nematode retrotransposon in the common shrew: horizontal transfer between parasite and host
Authors: Dunemann Sonja M. , Wasmuth James D.
Published: September 2018

Reports of horizontal transposon and gene transfers involving metazoan species has increased with the sequencing of their genomes. Horizontal transfer could be facilitated by the intimate relationship between a parasite and its hosts. To date, two studies have identified horizontal transfer of RTEs, a class of retrotransposable elements, involving parasites: ticks might act as vector for BovB between ruminants and squamates, and AviRTE was transferred between birds and parasitic nematodes. We wanted to know if parasitic nematodes are involved in other cases of horizontal transfer of RTEs. We searched 33 mSammalian RTEs in 81 nematode assemblies, and 10 nematode RTEs in 98 mammalian assemblies. We identified RTE1õ Sar from Sorex araneus, the common shrew, in parasitic nematodes and show that it originates from nematodes. To exclude contamination of the S. araneus assembly, we developed an approach that uses long reads and paired-end reads. With phylogenetic analysis and copy age estimation, we show that RTE1_Sar was horizontally transferred from nematodes to S. araneus. We confirm horizontal transfer of RTEs in host-parasite interactions, and we present a new method to distinguish between contamination and horizontal transfer.
Mycobacterium tuberculosisinhibits autocrine type I interferon signaling to increase intracellular survival
Authors: Banks Dallas A. , Ahlbrand Sarah E. , Keith Hughitt V. , Shah Swati , Vogel Stefanie N. , El-Sayed Najib M. , Briken Volker
Published: September 2018

The type I interferons (IFN-αand -β) are important for host defense against viral infections. In contrast, their role in defense against non-viral pathogens is more ambiguous. Here we report that IFN-β-signaling in macrophages has protective capacity againstMycobacterium tuberculosis(Mtb) via the increased production of nitric oxide. Furthermore, Mtb is able to inhibit IFN-α/β-receptor-mediated cell signaling and the transcription of 309 IFN-βstimulated genes which includes genes associated with innate host cell defense. The molecular mechanism of inhibition by Mtb involves reduced phosphorylation of the IFNAR-associated protein kinases JAK1 and TYK2 leading to reduced phosphorylation of the downstream targets STAT1 and STAT2. Overall, our study supports the novel concept that Mtb evolved to inhibit autocrine type I IFN signaling in order to evade host defense mechanisms.
Cancer as a tissue anomaly: classifying tumor transcriptomes based only on healthy data
Authors: Quinn Thomas P. , Nguyen Thin , Lee Samuel C. , Venkatesh Svetha
Published: September 2018

Since the turn of the century, researchers have sought to diagnose cancer based on gene expression signatures measured from the blood or biopsy as biomarkers. This task, known as classification, is typically solved using a suite of algorithms that learn a mathematical rule capable of discriminating one group (e.g., cases) from another (e.g., controls). However, discriminatory methods can only identify cancerous samples that resemble those that the algorithm already saw during training. As such, we argue that discriminatory methods are fundamentally ill-suited for the classification of cancer: because the possibility space of cancer is definitively large, the existence of a one-of-a-kind gene expression signature becomes very likely. Instead, we propose using an established surveillance method that detects anomalous samples based on their deviation from a learned normal steady-state structure. By transferring this method to transcriptomic data, we can create an anomaly detector for tissue transcriptomes, a “tissue detector”, that is capable of identifying cancer without ever seeing a single cancer example. Using models trained on normal GTEx samples, we show that our “tissue detector” can accurately classify TCGA samples as normal or cancerous and that its performance is further improved by including more normal samples in the training set. We conclude this report by emphasizing the conceptual advantages of anomaly detection and by highlighting future directions for this field of study.
Homeolog expression quantification methods for allopolyploids
Authors: Kuo Tony , Hatakeyama Masaomi , Tameshige Toshiaki , Shimizu Kentaro K. , Sese Jun
Published: September 2018

Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi, and plants, and is especially common in crop plants. There is increasing interest in the study of allopolyploids due to advances in polyploid genome assembly, however the high level of sequence similarity in duplicated gene copies (homeologs) pose many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately. We examined mapping error using our previous and new RNA-seq data in which a subgenome is experimentally added (synthetic allotetraploid Arabidopsis kamchatica) or reduced (allohexaploid wheat Triticum aestivum versus extracted allotetraploid) as ground truth. The error rates in the two species were very similar. The standard approaches showed higher error rates (> 10% using pseudo-alignment with Kallisto) while subgenome-classification approaches showed much lower error rates (< 1% using EAGLE-RC, < 2% using HomeoRoq). Although downstream analysis may partly mitigate mapping errors, the difference in methods was substantial in hexaploid wheat, where Kallisto appeared to have systematic differences relative to other methods. Only approximately half of the differentially expressed homeologs detected using Kallisto overlapped with those by any other method. In general, disagreement in low expression genes was responsible for most of the discordance between methods, which is consistent with known biases in Kallisto. We also observed that there exist uncertainties in genome sequences and annotation which can affect each method differently. Overall, subgenome-classification approaches tend to perform better than standard approaches with EAGLE-RC having the highest precision.
Assessment of biological role and insight into druggability of the Plasmodium falciparum protease plasmepsin V
Authors: Polino Alexander J. , Nasamu Armiyaw S. , Niles Jacquin C. , Goldberg Daniel E.
Published: September 2018

Upon infection of a red blood cell (RBC), the malaria parasite Plasmodium falciparum drastically remodels its host by exporting hundreds of proteins into the RBC cytosol. This program of protein export is essential for parasite survival, hence there is interest in export-related proteins as potential drug targets. One proposed target is plasmepsin V (PMV), an aspartic protease that cleaves export-destined proteins in the parasite ER at a motif called the Plasmodium export element (PEXEL). This cleavage is essential for effector export across the vacuolar membrane. Despite long-standing interest in PMV, functional studies have been hindered by the failure of current technologies to produce a regulatable lethal depletion of PMV. To overcome this technical barrier, we designed a facile system for stringent post-transcriptional regulation, allowing a tightly controlled, tunable knockdown of PMV. Under maximal knockdown conditions, parasite growth was arrested, validating PMV as essential for parasite survival in RBCs. We found that PMV levels had to be dramatically depleted to affect parasite growth, suggesting that the parasite maintains this enzyme in substantial excess. This has important implications for antimalarial development. Additionally, we found that PMV-depleted parasites arrest immediately after invasion of the host cell, suggesting that PMV has an unappreciated role in early development that is distinct from its previously reported role in protein export in later-stage parasites.

Importance

Malaria is endemic to large swaths of the developing world, causing nearly 500,000 deaths each year. While infection can be treated with antimalarial drugs, resistance continues to emerge to frontline antimalarials, spurring calls for new drugs and targets to feed the drug development pipeline. One proposed target is the aspartic protease plasmepsin V (PMV) that processes exported proteins, enabling the export program that remodels the host cell. This work uses facile genetic tools to produce lethal depletion of PMV, validating it as a drug target and showing that PMV is made in substantial excess in blood-stage parasites. Unexpectedly, PMV depletion leads to parasite death immediately after invasion of RBCs, distinct from other disruptions of the export pathway. This suggests that PMV inhibitors could lead to relatively rapid parasite death, and that PMV has additional unexplored role(s) during RBC infection.
The ecological drivers of variation in global language diversity
Authors: Hua Xia , Greenhill Simon J. , Cardillo Marcel , Schneemann Hilde , Bromham Lindell
Published: September 2018

Language diversity is distributed unevenly over the globe. Why do some areas have so many different languages and other areas so few? Intriguingly, patterns of language diversity resemble biodiversity patterns, leading to suggestions that similar mechanisms may underlie both linguistic and biological diversification. Here we present the first global analysis of language diversity that identifies the relative importance of two key ecological mechanisms suggested to promote language diversification - isolation and ecological risk - after correcting for spatial autocorrelation and phylogenetic non-independence. We find significant effects of climate on language diversity consistent with the ecological risk hypothesis that areas of high year-round productivity lead to more languages by supporting human cultural groups with smaller distributions. Climate has a much stronger effect on language diversity than landscape features that might contribute to isolation of cultural groups, such as altitudinal variation, river density, or landscape roughness. The association between biodiversity and language diversity appears to be an incidental effect of their covariation with climate, rather than a causal link between the two. While climate and landscape provide strong explanatory signal for variation in language diversity, we identify a number of areas of high unexplained language diversity, with more languages than would be predicted from environmental features alone; notably New Guinea, the Himalayan foothills, West Africa, and Mesoamerica. Additional processes may be at play in generating higher than expected language diversity in these regions.
Mapping DNA replication with nanopore sequencing
Authors: Hennion Magali , Arbona Jean-Michel , Cruaud Corinne , Proux Florence , Tallec Benoît Le , Novikova Elizaveta , Engelen Stefan , Lemainque Arnaud , Audit Benjamin , Hyrien Olivier
Published: September 2018

We have harnessed nanopore sequencing to study DNA replication genome-wide at the single-molecule level. Using in vitro prepared DNA substrates, we characterized the effect of bromodeoxyuridine (BrdU) substitution for thymidine on the MinION nanopore electrical signal. Using a neural-network basecaller trained on yeast DNA containing either BrdU or thymidine, we identified BrdU-labelled tracts in yeast cells synchronously entering S phase in the presence of hydroxyurea and BrdU. As expected, the BrdU-labelled tracts coincided with previously identified early-firing, but not late-firing, replication origins. These results open the way to high-throughput, high-resolution, single-molecule analysis of DNA replication in many experimental systems.
The Structure of Oxalate Decarboxylase at its Active pH
Authors: Burg M. J. , Goodsell J. L. , Twahir U. T. , Bruner S. D. , Angerhofer A.
Published: September 2018

Oxalate decarboxylase catalyzes the redox-neutral unimolecular disproportionation reaction of oxalic acid. The pH maximum for catalysis is ~4.0 and activity is negligible above pH7. Here we report on the first crystal structure of the enzyme in its active pH range at pH4.6, and at a resolution of 1.45 Å, the highest to date. The fundamental tertiary and quaternary structure of the enzyme does not change with pH. However, the low pH crystals are heterogeneous containing both a closed and open conformation of a flexible loop region which gates access to the N-terminal active site cavity. Residue E162 in the closed conformation points away from the active-site Mn ion owing to the coordination of a buffer molecule, acetate. Since the quaternary structure of the enzyme appears unaffected by pH many conclusions drawn from the structures taken at high pH remain valid. Density functional theory calculations of the possible binding modes of oxalate to the N-terminal Mn ion demonstrate that both mono- and bi-dentate coordination modes are possible in the closed conformation with an energetic preference for the bidentate binding mode. The simulations suggest that R92 plays an important role as a guide for positioning the substrate in its catalytically competent orientation. A strong hydrogen bond is seen between the bi-dentate bound substrate and E101, one of the coordinating ligands for the N-terminal Mn ion. This suggests a more direct role of E101 as a transient base during the first step of catalysis.
Sequence effects on size, shape, and structural heterogeneity in Intrinsically Disordered Proteins
Authors: Baul Upayan , Chakraborty Debayan , Mugnai Mauro L. , Straub John E. , Thirumalai D.
Published: September 2018

Intrinsically disordered proteins (IDPs) lack well-defined three-dimensional structures, thus challenging the archetypal notion of structure-function relationships. Determining the ensemble of conformations that IDPs explore under physiological conditions is the first step towards understanding their diverse cellular functions. Here, we quantitatively characterize the structural features of IDPs as a function of sequence and length using coarse-grained simulations. For diverse IDP sequences, with the number of residues (NT) ranging from 24 to 441, our simulations not only reproduce the radii of gyration (Rg) obtained from experiments, but also predict the full scattering intensity profiles in very good agreement with Small Angle X-ray Scattering experiments. TheRgvalues are well-described by the standard Flory scaling law,, withv≈ 0.588, making it tempting to assert that IDPs behave as polymers in a good solvent. However, clustering analysis reveals that the menagerie of structures explored by IDPs is diverse, with the extent of heterogeneity being highly sequence-dependent, even though ensemble-averaged properties, such as the dependence ofRgon chain length, may suggest synthetic polymer-like behavior in a good solvent. For example, we show that for the highly charged Prothymosin-α, a substantial fraction of conformations is highly compact. Even if the sequence compositions are similar, as is the case forα-Synuclein and a truncated construct from the Tau protein, there are substantial differences in the conformational heterogeneity. Taken together, these observations imply that metrics based on net charge or related quantities alone, cannot be used to anticipate the phases of IDPs, either in isolation or in complex with partner IDPs or RNA. Our work sets the stage for probing the interactions of IDPs with each other, with folded protein domains, or with partner RNAs, which are critical for describing the structures of stress granules and biomolecular condensates with important cellular functions.

Graphical TOC Entry
Structural brain alterations in youth with psychosis and bipolar spectrum symptoms
Authors: Jalbrzikowski Maria , Freedman David , Hegarty Catherine E. , Mennigen Eva , Karlsgodt Katherine H. , Loohuis Loes M. Olde , Ophoff Roel A. , Gur Raquel E. , Bearden Carrie E.
Published: September 2018

Objective

Adults with established diagnoses of serious mental illness (bipolar disorder and schizophrenia) exhibit structural brain abnormalities, yet less is known about how such abnormalities manifest earlier in development.

Methods

We analyzed the data publicly available from the Philadelphia Neurodevelopmental Cohort (PNC). Structural magnetic resonance neuroimaging data (sMRI) were collected on a subset of the PNC (N=989, ages 9-22 years old). We calculated measures of cortical thickness (CT) and surface area (SA), along with subcortical volumes. Study participants were assessed for psychiatric symptomatology via structured interview and the following groups were created: typically developing (TD, N=376), psychosis spectrum (PS, N=113), bipolar spectrum (BP, N=117), and BP + PS (N=109). We examined group and developmental differences in sMRI measures. We also examined to what extent any structural aberration was related to neurocognition, global functioning, and clinical symptomatology.

Results

In comparison to all other groups, PS youth exhibited significantly reduced SA in orbitofrontal, cingulate, precentral, and postcentral regions. PS youth also exhibited reduced thalamic volume in comparison to all other groups. Strongest effects for precentral and posterior cingulate SA reductions were seen during early adolescence (ages 13-15) in PS youth. Strongest effects for reductions in thalamic volume and orbitofrontal and postcentral SA were observed in mid-adolescence (16-18 years) in PS youth. Across groups, better overall functioning was associated with increased lateral orbitofrontal SA. Increased postcentral SA was associated with better executive cognition and less severe negative symptoms in the entire sample.

Conclusion

In a community-based sample, we found that reduced cortical SA and thalamic volume are present early in adolescent development in youth with psychosis spectrum symptoms, but not in youth with bipolar spectrum symptoms, or with both bipolar and psychosis spectrum symptoms. These findings point to potential biological distinctions between psychosis and bipolar spectrum conditions, which may suggest additional biomarkers relevant to early identification.
Exploiting selection at linked sites to infer the rate and strength of adaptation
Authors: Uricchio Lawrence H. , Petrov Dmitri A. , Enard David
Published: September 2018

Genomic data encodes past evolutionary events and has the potential to reveal the strength, rate, and biological drivers of adaptation. However, robust estimation of adaptation rate (α) and adaptation strength remains a challenging problem because evolutionary processes such as demography, linkage, and non-neutral polymorphism can confound inference. Here, we exploit the influence of background selection to reduce the fixation rate of weakly-beneficial alleles to jointly infer the strength and rate of adaptation. We develop a novel MK-based method (ABC-MK) to infer adaptation rate and strength, and estimateα= 0.135 in human protein-coding sequences, 72% of which is contributed by weakly adaptive variants. We show that in this adaptation regimeαis reduced ≈ 25% by linkage genome-wide. Moreover, we show that virus-interacting proteins (VIPs) undergo adaptation that is both stronger and nearly twice as frequent as the genome average (α= 0.224, 56% due to strongly-beneficial alleles). Our results suggest that while most adaptation in human proteins is weakly-beneficial, adaptation to viruses is often strongly-beneficial. Our method provides a robust framework for estimating adaptation rate and strength across species.
The augmentation of retinogeniculate communication during thalamic burst mode
Authors: Alitto Henry , Rathbun Daniel L. , Vandeleest Jessica J. , Alexander Prescott C. , Usrey W. Martin
Published: September 2018

Retinal signals are transmitted to cortex via neurons in the lateral geniculate nucleus (LGN), where they are processed in burst or tonic response mode. Burst mode occurs when LGN neurons are sufficiently hyperpolarized for T-Type Ca2+ channels to de-inactivate, allowing them to open in response to a depolarization which can trigger a high-frequency sequence of Na+-based spikes (i.e. burst). In contrast, T-type channels are inactivated during tonic mode and do not contribute to spiking. Although burst mode is commonly associated with sleep and the disruption of retinogeniculate communication, bursts can also be triggered by visual stimulation, thereby transforming the retinal signals relayed to the cortex.

To determine how burst mode affects retinogeniculate communication, we made recordings from monosynaptically connected retinal ganglion cells and LGN neurons in the cat during visual stimulation. Our results reveal a robust augmentation of retinal signals within the LGN during burst mode. Specifically, retinal spikes were more effective and often triggered multiple LGN spikes during periods likely to have increased T-Type Ca2+ activity. Consistent with the biophysical properties of T-Type Ca2+ channels, analysis revealed that effect magnitude was correlated with the duration of the preceding thalamic interspike interval and occurred even in the absence of classically defined bursts. Importantly, the augmentation of geniculate responses to retinal input was not associated with a degradation of visual signals. Together, these results indicate a graded nature of response mode and suggest that, under certain conditions, bursts facilitate the transmission of visual information to the cortex by amplifying retinal signals.

Significance

The thalamus is the gateway for retinal information traveling to the cortex. The lateral geniculate nucleus (LGN), like all thalamic nuclei, has two classically defined categories of spikes—tonic and burst—that differ in their underlying cellular mechanisms. Here we compare retinogeniculate communication during burst and tonic response modes. Our results show that retinogeniculate communication is enhanced during burst mode and visually evoked thalamic bursts, thereby augmenting retinal signals transmitted to cortex. Further, our results demonstrate that the influence of burst mode on retinogeniculate communication is graded and can be measured even in the absence of classically defined thalamic bursts.
Microbial communities of the Mediterranean rocky coast: ecology and biotechnological potential
Authors: Tanner Kristie , Molina-Menor Esther , Vidal-Verdú Àngela , Peretó Juli , Porcar Manuel
Published: September 2018

Microbial communities from harsh environments hold great promise as sources of biotechnologically-relevant strains. In the present work, we have deeply characterized the microorganisms from three different rocky locations of the Mediterranean coast, an environment characterised by being subjected to harsh conditions such as high levels of irradiation and large temperature and salinity fluctuations. Through culture-dependent and culture-independent techniques, we have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. A culture-independent approach through high-throughput 16S rRNA amplicon sequencing revealed that all three locations display very similar microbial communities, suggesting that there is a stable community associated to the sampled region, withStanieria cyanosphaera, Rubrobactersp. and the families Flammeovirgaceae, Phyllobacteriaceae, Rhodobacteraceae and Trueperaceae being the most abundant taxa. Furthermore, shotgun metagenomic sequencing results were in concordance with the high-thoughput 16S rRNA, and allowed a description of the eukaryotic and archaeal members of the community, which were abundant in Ascomycota and halotolerant archaea, respectively. The culture-dependent approach yielded a collection of 100 isolates (mainly pigmented), out of which 12 displayed high antioxidant activities, as proved with twoin vitro(hydrogen peroxide and DPPH) and anin vivo(model organismC. elegans) assays.
Endoplasmic Reticulum Network Formation withXenopusEgg Extracts
Authors: Wang Songyu , Romano Fabian B. , Rapoport Tom A.
Published: September 2018

The endoplasmic reticulum (ER) consists of morphologically distinct domains, including a polygonal network of tubules that is connected by three-way junctions. This network is found in all eukaryotic cells. Extracts fromXenopus laeviseggs contain stockpiles of components that allow the assembly of an ER network in vitro. Here we provide protocols for assembly of ER networks in extracts that are arrested at different stages of the cell cycle. UnfertilizedXenopus laeviseggs contain a cytostatic factor (CSF) that keeps them in the metaphase stage of the cell cycle. Disruption of the eggs by low-speed centrifugation releases calcium and the eggs cycle into interphase. This state can then be maintained by the addition of cycloheximide, which prevents the synthesis of cyclin B. CSF extracts can be also prepared in the presence of a calcium chelator, thus keeping the extract in metaphase. In this protocol, we outline procedures for the assembly of an ER network using either interphase- or metaphase-arrestedXenopusegg extracts. The network assembled is strikingly similar to the network observed in tissue culture cells. The extract allows easy biochemical manipulation, permitting the effects of purified proteins or small molecules, or the depletion of cytosolic components to be tested.
Mass Spectrometry-Based Absolute Quantification of SingleXenopusEmbryo Proteomes
Authors: Lindeboom Rik G.H. , Smits Arne H. , Perino Matteo , Veenstra Gert Jan C. , Vermeulen Michiel
Published: September 2018

EarlyXenopusdevelopment is characterized by a poor correlation between global mRNA and protein abundances due to maternal mRNA and protein loading. Therefore, proteome profiling is necessary to study gene expression dynamics during earlyXenopusdevelopment. In contrast to mammals, singleXenopuseggs and embryos contain enough protein to allow identification and quantification of thousands of proteins using mass spectrometry-based proteomics. In addition to investigating developmental processes, single egg or blastomere proteomes can be used to study cell-to-cell variability at an unprecedented depth. In this protocol, we describe a mass spectrometry-based proteomics approach for the identification and absolute quantification ofXenopus laevisegg or embryo proteomes, including sample preparation, peptide fractionation and separation, and data analysis.
Cell Transplantation as a Method to Investigate Spinal Cord Regeneration in Regenerative and Nonregenerative Xenopus Stages
Authors: Méndez-Olivos Emilio E. , Larraín Juan
Published: September 2018

Mammals are not capable of regenerating their central nervous system (CNS); anamniotes, however, can regenerate in response to injury. The mechanisms that explain the different regenerative capabilities include: (i) extrinsic mechanisms that consider the cellular environment and extracellular matrix composition, (ii) intrinsic factors implicating the presence or absence of genetic programs that promote axon regeneration, and (iii) the presence or absence of neural stem and progenitors cells (NSPCs) that allow neurogenesis. Xenopus laevis is able to regenerate its CNS during larval stages (i.e., the regenerative stage [R-stage]). However, concomitant with metamorphosis this capacity decreases and is lost completely in juvenile froglets (i.e., nonregenerative stages [NR-stages]). The loss of the regenerative ability correlates with a reduction in the percentage of Sox2+ cells, which are putative NSPCs. This protocol shows the effect of transplantation of spinal cord cells from R-stage Xenopus larvae into NR-stage froglets. Using this procedure, it is possible to study axon regeneration and stem cell biology in vivo.
Tracing Central Nervous System Axon Regeneration in Xenopus
Authors: Gibbs Kurt M. , Szaro Ben G.
Published: September 2018

Axonal tracing allows visualizing connectivity between neurons, providing useful information about structure, neuronal location, and function of the nervous system. Identifying regenerating axons and their neuron cell bodies present the particular challenges of labeling the projections of interest while unambiguously demonstrating regrowth of those axons that have been damaged. In the developing brain, an additional labeling challenge arises, as new connections are being made throughout the duration of an experiment. Various strategies have been used to label regenerating axons, including transgenic animals expressing neuron-specific fluorescent proteins, and application of a single labeling molecule after axotomy and regeneration. However, the single label approach is limited in its application to the developing brain, primarily because it leads to the conclusion that every axon that is labeled has regenerated. Double-labeling overcomes these obstacles by identifying regenerating cells as those that are labeled with two different tracing molecules. Moreover, the use of dextran amines, which are only taken up by injured axons and transported retrogradely, provides further confidence of labeling regenerating axons and neuron cell bodies. The procedure described herein provides a straightforward method for using fluorescently labeled dextran amines to identify regenerating supraspinal neurons in Xenopus, but can be applied to other areas of the central and peripheral nervous system as well.
The Swiss mental healthcare system for people with intellectual disabilities
Authors: Georgescu Dan , Styp von Rekowski Anne
Published: September 2018

Purpose

The purpose of this paper is to describe the mental healthcare system for people with intellectual disabilities (ID) in Switzerland. It covers the current provision of mental healthcare services as well as educational and research aspects, and summarises both the historical development and the current data on demography, health economics, legislation and national policy.

Design/methodology/approach

The authors performed an extensive literature research and evaluated the (very sparse) literature, conducted some interviews with recognised experts and carried out extensive internet-based research on the topic.

Findings

There are numerous, well-funded, well-staffed and well-equipped facilities for people with ID. These facilities have highly trained special education teachers and social education workers. Legislation, the insurance system as well as the policies and strategies on a national level are basically in line with people’s with ID needs. On the other hand, there are too few specialist physicians and psychologists, not enough training centres and too few specialist psychiatric services, both inpatient and outpatient. Medical and psychological research in this field is also insufficient.

Practical implications

In Switzerland, the development of treatment facilities typically does not start with a decision by a central authority to implement a policy in a top-down process. Usually, these organisations develop on the basis of some local initiatives and spread throughout the country. The process is likely to be similar in the case of services for people with mental health and intellectual disabilities (MHID), and the situation can be expected to be much better throughout the country within a few years. Furthermore, specific training programmes are expected to be created for physicians and psychologists of various disciplines, to promote an interdisciplinary approach.

Originality/value

This review fills a gap in that there are very few published reviews on the provision of MHID services in Switzerland.
Permanent magnet shaping for cogging torque and torque ripple reduction of PMSM
Authors: Ladghem Chikouche Brahim , Boughrara Kamel , Ibtiouen Rachid
Published: September 2018

Purpose

This paper aims to the improvement of permanent magnet shape in the popular permanent magnet synchronous machine (PMSM) is proposed in this paper in view to mitigate cogging torque magnitude and torque ripple.

Design/methodology/approach

A two-dimensional exact analytical approach of magnetic field distribution is established for the PMSM considering magnet shape and slot opening. The optimal magnet shape is constituted of small number of layers stacked radially. The thickness of each magnet layer is considered equal to about one mm or more; however, a parametric study was performed to determine pole pitch ratio value. The finite element method is used to validate the analytical results.

Findings

Cogging torque peaks and torque ripples can be mitigated significantly more than 90 per cent compared to results issued from machine having classical magnet shape. Raising the number of magnet layers can give better results. The results of this paper are compared also with those issued from the machine having sinusoidal magnet shape and give a good solution.

Originality/value

A new technique for cogging torque and torque ripple mitigation is proposed in this paper by changing permanent magnet shape. The proposed final magnet shape is constituted of a set of stacked and well-dimensioned layers relative to the opening angle.
Social eating patterns, identity and the subjective well-being of Chinese teenagers
Authors: Veeck Ann , Yu Hongyan , Zhang Hongli , Zhu Hong , Yu Fang (Grace)
Published: September 2018

Purpose

The purpose of this study is to explore the association between eating patterns, social identity and the well-being of adolescents via a mixed methods study of Chinese teenagers. The specific research questions presented in this study are as follows: What is the relationship between social eating and well-being? How is the relationship between social eating and well-being mediated by social identity?

Design/methodology/approach

This study is based on a sequential mixed methods study, including interviews with 16 teenage–parent dyads, and a large-scale survey of over 1,000 teenagers on their eating patterns, conducted with the support of public schools. A model that tests relationships among social eating, social identity and subjective well-being is developed and tested.

Findings

The results show that dining with family members leads to improved subjective well-being for teenagers, through a partial mediator of stronger family identity. However, dining with peers is not found to influence subjective well-being.

Research limitations/implications

The privileged position of family meals demonstrated through this study may be an artifact of the location of this study in one Chinese city. Further research is needed related to the connections among social identity, objective well-being and the social patterns of teenagers’ food consumption behavior.

Practical implications

To improve the subjective well-being of teenagers, families, public policy-makers and food marketers should support food consumption patterns that promote family meals.

Originality/value

While many food-related consumer studies focus on the individual, social and environmental influences of food choices of adolescents, few studies address how eating patterns affect overall well-being. These results reinforce the importance of understanding the effect of the social context of teenagers’ eating patterns on health and well-being.
The electric energy stored in PEDOT:PSS capacitors integrated on textile substrate
Authors: Odhiambo Sheilla Atieno , Fiszer Piotr , De Mey Gilbert , Hertleer Carla , Nuramdhani Ida , Van Langenhove Lieva , Napieralski Andrzej
Published: September 2018

Purpose

The purpose of this paper is to develop a capacitor fully integrated into a wearable textile fabric for the application on smart clothing.

Design/methodology/approach

A small capacitor with stainless steel yarns as the electrodes and poly-(3,4–ethylenedioxythiophene): polystryrene sulphonate (PEDOT:PSS) as the dielectric material has been made, integrated into a textile fabric. The electric performance of the capacitor was analyzed and compared with other kinds of electric capacitors.

Findings

The fabricated small, PEDOT:PSS capacitor could finally power a calculator for 37 s with the energy stored in it.

Originality/value

This finding is of an important significance for a further development on the capacitor with a better performance.
Learners’ perceptions on online library resources at Namibian College of Open Learning
Authors: Matheus Elizabeth , Abankwah Ruth
Published: September 2018

Purpose

The purpose of this paper is to determine the learners’ perceptions on the use of online resources at the Namibian College of Open Learning (NAMCOL) Yetu Yama Resource Center.

Design/methodology/approach

This study used a mixed methods research approach which was also used by other researchers such as Hamutumwa (2014). It enabled the researchers to delve into the topic under study by conducting a survey using self-administered questionnaires to collect data from learners, and a semi-structured interview guide, to collect data from the Librarian, the Director and tutors. The target population for the study was Grade 12 distance learners registered with NAMCOL for the academic year 2016, librarians and tutors. Convenient sampling was used to select 200 Grade 12 distance NAMCOL learners: one Director, one Librarian and five tutors were purposeful selected as they manage the Yetu Yama Resource Centre. The Statistical Package for the Social Sciences (SPSS) was used to generate descriptive data, while qualitative data were manually analysed using content analysis. This approach enabled the researcher to identify key themes which emerged from the interviews.

Findings

Almost all the learners (159) opted for printed materials. The challenges experienced by learners included slow internet, as indicated by 78 (39 per cent); limited facilities, 60 (30 per cent); and inability to find relevant information, 46 (23 per cent), coupled with lack of proper guidance on the use of e-resources as indicated by 16 (8 per cent) learners.

Research limitations/implications

This study was limited to Yetu Yama Resource Center. The results cannot be generalised to all distance learners in Namibia.

Practical implications

The results of this study could guide librarians in Namibia when planning and/or upgrading e-resources.

Social implications

Once the learners are equipped with the required skills, they will make optimum use of the e-resources which are provided by NAMCOL.

Originality/value

This is the first study to be conducted at NAMCOL, and it is hoped that the results will be applied to other tertiary institutions which offer distance education in Namibia.
Demand prediction in health sector using fuzzy grey forecasting
Authors: Zor Ceyda , Çebi Ferhan
Published: September 2018

Purpose

The purpose of this paper is to apply GM (1, 1) and TFGM (1, 1) models on the healthcare sector, which is a new area, and to show TFGM (1, 1) forecasting accuracy on this sector.

Design/methodology/approach

GM (1, 1) and TFGM (1, 1) models are presented. A hospital’s nine months (monthly) demand data is used for forecasting. Models are applied to the data, and the results are evaluated with MAPE, MSE and MAD metrics. The results for GM (1, 1) and TFGM (1, 1) are compared to show the accuracy of forecasting models. The grey models are also compared with Holt–Winters method, which is a traditional forecasting approach and performs well.

Findings

The results of this study indicate that TFGM (1, 1) has better forecasting performance than GM (1, 1) and Holt–Winters. GM (1, 1) has 8.01 per cent and TFGM (1, 1) 7.64 per cent MAPE, which means excellent forecasting power. So, TFGM (1, 1) is also an applicable forecasting method for the healthcare sector.

Research limitations/implications

Future studies may focus on developed grey models for health sector demand. To perform better results, parameter optimisation may be integrated to GM (1, 1) and TFGM (1, 1). The demand may be predicted not only for the total demand on hospital, but also for the demand of hospital departments.

Originality/value

This study contributes to relevant literature by proposing fuzzy grey forecasting, which is used to predict the health demand. Therefore, the new application area as the health sector is handled with the grey model.
Analysing mall attributes in defining the desire of consumers to stay
Authors: Santoso Djoen San , Joewono Tri Basuki , Sunanto Sandra
Published: September 2018

Purpose

The purpose of this paper is to examine how attributes of a mall contribute to the amount of time spent in the shopping centre.

Design/methodology/approach

The study used data collected from the questionnaire survey distributed to visitors of four major shopping centres in Bandung City, Indonesia. Ordinal logit was applied to analyse the mall built environment attributes in relation to the duration of stay. Factors related to the visit and socio-demographic background of the shoppers are also considered in this analysis.

Findings

The results show that each shopping centre has its own unique attribute(s) that keep consumers in the mall. However, attributes that boost or strengthen the image of a shopping centre do not necessarily contribute much to explaining the desire of consumers to stay. Factors pertaining to the visit and socio-demographic background of consumers have been found to play a more important role in defining the duration of visit.

Originality/value

The study provides an analysis of how the mall attributes worked in defining the visit duration in comparison to the factors related to the visit and socio-demographic factors at four shopping centres, while most studies typically only focussed on one shopping centre.