bluuebunny/crossref_metadata_2025 huggingface dataset:
Introducing risk inequality metrics in tuberculosis policy development
Authors: Gomes M. Gabriela M. , Oliveira Juliane F. , Bertolde Adelmo , Nguyen Tuan Anh , Maciel Ethel L. , Duarte Raquel , Nguyen Binh Hoa , Shete Priya B. , Lienhardt Christian
Published: August 2018

Global stakeholders including the World Health Organization rely on predictive models for developing strategies and setting targets for tuberculosis care and control programs. Failure to account for variation in individual risk leads to substantial biases that impair data interpretation and policy decisions1,2. Anticipated impediments to estimating heterogeneity for each parameter are discouraging despite considerable technical progress in recent years. Here we identify acquisition of infection as the single process where heterogeneity most fundamentally impacts model outputs, due to cohort selection imposed by dynamic forces of infection. Individuals with higher risk of acquiring infection are predominantly affected by the pathogen, leaving the unaffected pool with those whose intrinsic risk is lower. This causes susceptibility pools to attain average risks which are lower under higher forces of infection. Interventions that modify the force of infection change the strength of selection, and therefore alter average risks in the pools which feed further incidence. Inability to account for these dynamics is what makes homogenous models unsuitable. We introduce concrete metrics to approximate risk inequality in tuberculosis, demonstrate their utility in mathematical models, and pack the information into a risk inequality coefficient which can be calculated and reported by national tuberculosis programs for use in policy development and modeling.
Genome-wide repressive capacity of promoter DNA methylation is revealed through epigenomic manipulation
Authors: Korthauer Keegan , Irizarry Rafael A.
Published: August 2018

The scientific community is increasingly embracing open science. This growing commitment to open science should be applauded and encouraged, especially when it occurs voluntarily and prior to peer review. Thanks to other researchers’ dedication to open science, we have had the privilege of conducting a reanalysis of a landmark experiment published as a preprint with data made available in a public repository. The study in question found that promoter DNA methylation is frequently insufficient to induce transcriptional repression, which appears to contradict a large body of observational studies showing a strong association between DNA methylation and gene expression. This study was the first to evaluate whether forcibly methylating thousands of DNA promoter regions is sufficient to suppress gene expression. The authors’ data analysis did not find a strong relationship between promoter methylation and transcriptional repression. However, their analyses did not make full use of statistical inference and applied a normalization technique that removes global differences that are representative of the actual biological system. Here we reanalyze the data with an approach that includes statistical inference of differentially methylated regions, as well as a normalization technique that accounts for global expression differences. We find that forced DNA methylation of thousands of promoters overwhelmingly represses gene expression. In addition, we show that complementary epigenetic marks of active transcription are reduced as a result of DNA methylation. Finally, by studying whether these associations are sensitive to the CG density of promoters, we find no substantial differences in the association between promoters with and without a CG island. The code needed to reproduce are analysis is included in the public GitHub repository github.com/kdkorthauer/repressivecapacity.
Structure mapping of dengue and Zika viruses reveals new functional long-range interactions
Authors: Huber Roland G. , Lim Xin Ni , Ng Wy Ching , Sim Adelene , Poh Hui Xian , Shen Yang , Lim Su Ying , Sundstrom Anna Karin Beatrice , Sun Xuyang , Aw Jong Ghut , Too Horng Khit , Boey Peng Hee , Wilm Andreas , Chawla Tanu , Choy Ming Ju , Jiang Lu , de Sessions Paola Florez , Loh Xian Jun , Alonso Sylvie , Hibberd Martin , Nagarajan Niranjan , Ooi Eng Eong , Bond Peter J. , Sessions October M. , Wan Yue
Published: August 2018

Dengue and Zika are clinically important members of the Flaviviridae family that utilizes an 11kb positive strand RNA for genome regulation. While structures have been mapped primarily in the UTRs, much remains to be learnt about how the rest of the genome folds to enable function. Here, we performed secondary structure and pair-wise interaction mapping on four dengue serotypes and four Zika strains in their native virus particles and infected cells. Comparative analysis of SHAPE reactivities across serotypes nominated potentially functional regions that are highly structured, show structure conservation, and low synonymous mutation rates, including a structure associated with ribosome pausing. Pair-wise interaction mapping by SPLASH further reveals new pair-wise interactions, in addition to the known circularization sequence. 40% of pair-wise interactions form alternative structures, suggesting extensive structural heterogeneity. Analysis of shared pair-wise interactions between serotypes revealed macro-organization whereby interactions are preserved at their physical locations, beyond their sequence identities. In addition, structure mapping of virus genomes released in solution-as well as inside host cells-showed that other helicases, in addition to the ribosome, play a role in unwinding viral structures inside cells. Mutational experiments that disrupt in cell and in virion pair-wise interactions result in virus attenuation, demonstrating their importance during the virus life-cycle.
Isoform switching as a mechanism of acquired resistance to isocitrate dehydrogenase inhibition
Authors: Harding James J. , Lowery Maeve A. , Shih Alan H. , Schvartzman Juan M. , Hou Shengqi , Famulare Christopher , Patel Minal , Roshal Mikhail , Do Richard K. G. , Zehir Ahmet , You Daoqi , Selcuklu S. Duygu , Viale Agnes , Tallman Martin S. , Hyman David M. , Reznik Ed , Finley Lydia W.S. , Papaemmanuil Elli , Tosolini Alessandra , Frattini Mark G. , MacBeth Kyle J. , Liu Guowen , Fan Bin , Choe Sung , Wu Bin , Janjigian Yelena Y. , Mellinghoff Ingo K. , Diaz Luis A. , Levine Ross L. , Abou-Alfa Ghassan K. , Stein Eytan M. , Intlekofer Andrew M.
Published: August 2018

Somatic mutations in cytosolic or mitochondrial isoforms of isocitrate dehydrogenase (IDH1 or IDH2, respectively) contribute to oncogenesis via production of the metabolite 2-hydroxyglutarate (2HG). Isoform-selective IDH inhibitors suppress 2HG production and induce clinical responses in patients with IDH1- and IDH2-mutant malignancies. Despite the promising activity of IDH inhibitors, the mechanisms that mediate resistance to IDH inhibition are poorly understood. Here, we describe four clinical cases that identify mutant IDH isoform switching, either from mutant IDH1 to mutant IDH2 or vice versa, as a mechanism of acquired clinical resistance to IDH inhibition in solid and liquid tumors.

Significance

IDH-mutant cancers can develop resistance to isoform-selective IDH inhibition by “isoform switching” from mutant IDH1 to mutant IDH2 or vice versa, thereby restoring 2-hydroxyglutarate (2HG) production by the tumor. These findings underscore a role for continued 2HG production in tumor progression and suggest therapeutic strategies to prevent or overcome resistance.
Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race
Authors: McKitterick Amelia C. , LeGault Kristen N. , Angermeyer Angus , Alam Muniral , Seed Kimberley D.
Published: August 2018

CRISPR-Cas systems function as adaptive immune systems by acquiring nucleotide sequences called spacers that mediate sequence-specific defense against competitors. Uniquely, the phage ICP1 encodes a Type I-F CRISPR-Cas system that is deployed to target and overcome PLE, a mobile genetic element with anti-phage activity in Vibrio cholerae. Here, we exploit the arms race between ICP1 and PLE to examine spacer acquisition and interference under laboratory conditions to reconcile findings from wild populations. Natural ICP1 isolates encode multiple spacers directed against PLE, but we find that single spacers do not equally interfere with PLE mobilization. High-throughput sequencing to assay spacer acquisition reveals that ICP1 can also acquire spacers that target the V. cholerae chromosome. We find that targeting the V. cholerae chromosome proximal to PLE is sufficient to block PLE and propose a model in which indirect chromosomal spacers are able to circumvent PLE by Cas2-3-mediated processive degradation of the V. cholerae chromosome before PLE mobilization. Generally, laboratory acquired spacers are much more diverse than the subset of spacers maintained by ICP1 in nature, showing how evolutionary pressures can constrain CRISPR-Cas targeting in ways that are often not appreciated through in vitro analyses.
Skin Lesion Classification Via Combining Deep Learning Features and Clinical Criteria Representations
Authors: Li Xiaoxiao , Wu Junyan , Jiang Hongda , Chen Eric Z. , Dong Xu , Rong Ruichen
Published: August 2018

Skin lesion is a severe disease globally. Early detection of melanoma in dermoscopy images significantly increases the survival rate. However, the accurate recognition of skin lesion is extremely challenging manually visualization. Hence, reliable automatic classification of skin lesions is meaningful to improve pathologists’ accuracy and efficiency. In this paper, we proposed a two-stage method to combine deep learning features and clinical criteria representations to address skin lesion automated diagnosis task. Stage 1 - feature encoding: Modified deep convolutional neural networks (CNNs, in this paper, we used Dense201 and Res50) were fine-tuned to extract rich image global features. To avoid hair noisy, we developed a lesion segmentation U-Net to mask out the decisive regions and used the masked image as CNNs inputs. In addition, color features, texture features and morphological features were exacted based on clinical criteria; Stage 2 - features fusion: LightGBM was used to select the salient features and model parameters, predicting diagnosis confidence for each category. The proposed deep learning frameworks were evaluated on the ISIC 2018 dataset. Experimental results show the promising accuracies of our frameworks were achieved.
Single-cell RNA-seq reveals distinct dynamic behavior of sex chromosomes during early human embryogenesis
Authors: Zhou Qing , Wang Taifu , Leng Lizhi , Zheng Wei , Huang Jinrong , Fang Fang , Yang Ling , Wang Jian , Yang Huanming , Chen Fang , Lin Ge , Wang Wen-Jing , Kristiansen Karsten
Published: August 2018

Background

Several animal and human studies have demonstrated that sex affects kinetics and metabolism during early embryo development. However, the mechanism governing these differences at the molecular level is unknown, warranting a systematic profiling of gene expression in males and females during embryogenesis.

Findings

We performed comprehensive analyses of gene expression comparing male and female embryos using available single-cell RNA-sequencing data of 1607 individual cells from 99 human preimplantation embryos, covering development stages from 4-cell to late blastocyst (E2 to E7). Consistent chromosome-wide transcription of autosomes was observed, while sex chromosomes showed significant differences after embryonic genome activation (EGA). Differentially expressed genes (DE genes) in male and female embryos mainly involved in the cell cycle, protein translation and metabolism. The Y chromosome was initially activated by pioneer genes, RPS4Y1 and DDX3Y, while the two X chromosomes in female were widely activated after EGA. Expression of X-linked genes in female significantly declined at the late blastocyst stage, especially in trophectoderm cells, revealing a rapid process of dosage compensation.

Conclusions

We observed imbalanced expression from sex chromosomes in male and female embryos during EGA, with dosage compensation occurring first in female trophectoderm cells. Studying the effect of sex differences during human embryogenesis, as well as understanding the mechanism of X chromosome inactivation and its correlation with early miscarriage, will provide a basis for advancing assisted reproductive technology (ART) and thereby improve the treatment of infertility and possibly enhance reproductive health.
Demographic inference using a particle filter for continuous Markov Jump processes
Authors: Henderson Donna , Zhu Sha (Joe) , Cole Chris , Lunter Gerton
Published: August 2018

Demographic events shape a population’s genetic diversity, a process described by the coalescent-with-recombination (CwR) model that relates demography and genetics by an unobserved sequence of genealogies. The space of genealogies over genomes is large and complex, making inference under this model challenging.

We approximate the CwR with a continuous-time and -space Markov jump process. We develop a particle filter for such processes, using way-points to reduce the problem to the discrete-time case, and generalising the Auxiliary Particle Filter for discrete-time models. We use Variational Bayes for parameter inference to model the uncertainty in parameter estimates for rare events, avoiding biases seen with Expectation Maximization.

Using real and simulated genomes, we show that past population sizes can be accurately inferred over a larger range of epochs than was previously possible, opening the possibility of jointly analyzing multiple genomes under complex demographic models.

Code is available athttps://github.com/luntergroup/smcsmc

MSC 2010 subject classifications

Primary 60G55, 62M05, 62M20, 62F15; secondary 92D25.
Emergence and features of the multipartite genome structure of the family Burkholderiaceae revealed through comparative and evolutionary genomics
Authors: diCenzo George C , Mengoni Alessio , Perrin Elena
Published: August 2018

The multipartite genome structure is found in a diverse group of important symbiotic and pathogenic bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to study the role and emergence of multipartite genomes. Nearly all essential secondary replicons (chromids) of the β-proteobacteria are found in the family Burkholderiaceae. These replicons arose from just two plasmid acquisition events, and they were likely stabilized early in their evolution by the presence of core genes, at least some of which were likely acquired through an inter-replicon translocation event. On average, Burkholderiaceae genera with multipartite genomes had a larger total genome size, but smaller chromosome, than genera without secondary replicons. Pangenome-level functional enrichment analyses suggested that inter-replicon functional biases are partially driven by the enrichment of secondary replicons in the accessory pangenome fraction. Nevertheless, the small overlap in orthologous groups present in each replicon’s pangenome indicates a clear functional separation of the replicons. Chromids appeared biased to environmental adaptation, as the functional categories enriched on chromids were also over-represented on the chromosomes of the environmental genera (Paraburkholderia, Cupriavidus) compared to the pathogenic genera (Burkholderia, Ralstonia). Using ancestral state reconstruction, it was predicted that the rate of accumulation of modern-day genes by chromids was more rapid than the rate of gene accumulation by the chromosomes. Overall, the data are consistent with a model where the primary advantage of secondary replicons is in facilitating increased rates of gene acquisition through horizontal gene transfer, consequently resulting in a replicon enriched in genes associated with adaptation to novel environments.
Climate Resilience Index as a tool to explore households’ resilience to climate change-induced shocks in Dinki watershed, central highlands of Ethiopia Households’ resilience to climate change impacts
Authors: Asmamaw Mengistu , Ambelu Argaw , Mereta Seid Tiku
Published: August 2018

This study assessed households’ resilience to climate change-induced shocks in Dinki watershed, northcentral highlands of Ethiopia. The data were collected through cross-sectional survey conducted on 288 households, six focus group discussions and 15 key informant interviews. The Climate Resilience Index (CRI) and the Livelihood Resilience Index (LRI) based on the three-resilience capacities (3Ds) frame, using absorptive, adaptive and transformative, were used to measure households’ resilience to climate change-induced shocks on agro-ecological unit of analysis. Findings indicate that the CRI and the resilience capacities based on the indexed scores of major components clearly differentiated the study communities in terms of their agro-ecological zones. Specifically, the LRI score showed that absorptive capacity (0.495) was the leading contributing factor to resilience followed by adaptive (0.449) and transformative (0.387) capacities. Likewise, the midland was relatively more resilient with a mean index value of 0.461. The study showed that access to and use of livelihood resources, such as farmlands and livestock holdings, diversity of income sources, infrastructure and social capital were determinants of households’ resilience. In general, it might be due to their exposure to recurrent shocks coupled with limited adaptive capacities including underdeveloped public services, poor livelihood diversification practices, among others, the study communities showed minimal resilience capacity with a mean score of 0.44. Thus, in addition to short-term buffering strategies, intervention priority focusing on both adaptive and transformative capacities, particularly focusing on most vulnerable localities and constrained livelihood strategies, would contribute to ensure long-term resilience in the study communities.
A standardised framework to identify optimal animal models for efficacy assessment in drug development
Authors: Ferreira Guilherme S. , Veening-Griffioen Désirée , Boon Wouter , Moors Ellen , Wied Christine Gispen-de , Schellekens Huub , van Meer Peter
Published: August 2018

Introduction

Poor translation of efficacy data derived from animal models is a potential contributor to costly and unnecessary attrition in clinical trials.

Objectives

To develop a tool to assess, validate and compare the clinical translatability of animal models used for the preliminary assessment of efficacy.

Design and Results

We conducted an exploratory literature search to identify the key aspects to validate animal models. Eight aspects (Epidemiology, Pathophysiology, Genetic, Biochemistry, Aetiology, Histology, Pharmacology and Endpoints) were identified for which questions were drafted to evaluate the different faces of the human disease simulation. Features of the framework include standardised instructions, a weighting and scoring system to compare models as well as contextualising factors regarding model similarity and evidence uncertainty. We included a quality assessment of the internal validity of drug intervention studies included in the Pharmacological validation section for both effective and ineffective drugs in humans. A web-based survey was conducted with experts from different stakeholders to gather input on the framework. Finally, we present a case study of a preliminary validation and comparison of two animal models for Duchenne Muscular Dystrophy (mdx mouse and GRMD dog) and Diabetes Type 2 (ZDF rat and db/db mouse). We show that there are significant differences between the mdx mouse and the GRMD dog, the latter mimicking the human condition to a greater extent than the mouse despite the considerable lack of published data. In DT2, both the ZDF rat and the db/db mouse are comparable with minor differences in pathophysiology.

Conclusions

FIMD facilitates drug development by serving as the basis to select the most relevant model that can provide meaningful and translatable results to progress drug candidates to the clinic.
Inhibitory muscarinic acetylcholine receptors enhance aversive olfactory conditioning in adult Drosophila
Authors: Bielopolski Noa , Amin Hoger , Apostolopoulou Anthi A. , Rozenfeld Eyal , Lerner Hadas , Huetteroth Wolf , Lin Andrew C. , Parnas Moshe
Published: August 2018

Olfactory associative learning inDrosophilais mediated by synaptic plasticity between the Kenyon cells of the mushroom body and their output neurons. Both Kenyon cells and their inputs are cholinergic, yet little is known about the physiological function of muscarinic acetylcholine receptors in learning in adult flies. Here we show that aversive olfactory learning in adult flies requires type A muscarinic acetylcholine receptors (mAChR-A) specifically in the gamma subtype of Kenyon cells. Surprisingly, mAChR-A inhibits odor responses in both Kenyon cell dendrites and axons. Moreover, mAChR-A knockdown impairs the learning-associated depression of odor responses in a mushroom body output neuron. Our results suggest that mAChR-A is required at Kenyon cell presynaptic terminals to depress the synapses between Kenyon cells and their output neurons, and may suggest a role for the recently discovered axo-axonal synapses between Kenyon cells.
“Quantitative analysis reveals the basic behavioural repertoire of the urochordateCiona intestinalis”
Authors: Rudolf Jerneja , Dondorp Daniel , Canon Louise , Tieo Sonia , Chatzigeorgiou Marios
Published: August 2018

Quantitative analysis of animal behaviour in model organisms is becoming an increasingly essential approach for tackling the great challenge of understanding how activity in the brain gives rise to behaviour. In addition, behavioural analysis can provide insight on the molecular basis of nervous system development and function as demonstrated by genetic screens focused on behavioural phenotyping in some genetically tractable model organisms. The progress in building low-cost automated tracking setups, together with advances in computer vision machine learning have expanded the repertoire of organisms which are amenable to quantitative behavioural analysis. Here we used automated image-based tracking to extract behavioural features from an organism of great importance in understanding the evolution of chordates, the free swimming larval form of the tunicateCiona intestinaliswhich has a compact and fully mapped nervous system composed of only 231 neurons. We analysed hundreds of videos of larvae and we extracted basic geometric and physical descriptors of larval behaviour. Most importantly, we used machine learning methods to create an objective ontology of behaviours forC. intestinalislarvae. We identified eleven behavioural modes using agglomerative clustering. This approach enabled us to produce a quantitative description of the basic larval behavioural repertoire. Furthermore, we tested the robustness of this repertoire by comparing different rearing conditions and ages. Using our pipeline for quantitative behavioural analysis, we successfully reproduced the known photoresponsive behaviour and the first demonstration to our knowledge thatC. intestinalislarvae exhibit sensory arousal and thigmotaxis, both of which can be modulated by the anxiotropic drug modafinil. Remarkably, by comparing the behaviour between animals assayed individually or in small groups, we found that crowd size influences larval behaviour. This study shows thatC. intestinalislarval behaviour can be broken down to a set of stereotyped behaviours that are used to different extents in a context-dependent manner. Furthermore, it raises exciting possibilities such as mapping behaviour to specific neurons of this compact chordate nervous system and it paves the way for comparative quantitative behavioural studies as a means to reconstruct the evolution of behaviour, especially in the chordate lineage.
A Persistence Detector for Metabolic Network Rewiring in an Animal
Authors: Bulcha Jote T. , Giese Gabrielle E. , Ali Md. Zulfikar , Lee Yong-Uk , Walker Melissa D. , Holdorf Amy D. , Yilmaz L. Safak , Brewster Robert C. , Walhout Albertha J.M.
Published: August 2018

Biological systems must possess mechanisms that prevent inappropriate responses to spurious environmental signals. Gene regulatory network circuitries known as coherent type 1 feed-forward loops (FFLs) with AND-logic gates have been proposed to function as a persistence detector because it generates a delay in target activation and prevents target induction unless the input signal is sustained. While such a circuit has been found for the L-arabinose utilization system in E. coli, their existence and relevance multicellular organisms has remained unclear. Here, we identify the first persistence detector in an animal that redirects propionate breakdown to a shunt pathway when flux through the canonical propionate breakdown pathway is perturbed. We propose that this mechanism has evolved to ensure the shunt pathway stays off unless propionate accumulation is persistent because the shunt pathway generates highly toxic acrylate. Our study uniquely connects persistence detector circuitry to a physiological response in an animal.
O-fucosylation of thrombospondin-like repeats is required for processing of MIC2 and for efficient host cell invasion by Toxoplasma gondii tachyzoites
Authors: Bandini Giulia , Leon Deborah R. , Hoppe Carolin M. , Zhang Yue , Agop-Nersesian Carolina , Shears Melanie J. , Mahal Lara K. , Routier Françoise H. , Costello Catherine E. , Samuelson John
Published: August 2018

Toxoplasma gondiiis an intracellular parasite that causes disseminated infections which can lead to neurological damage in fetuses and immunocompromised individuals. Microneme protein 2 (MIC2)2, a member of the thrombospondin-related anonymous protein (TRAP) family, is a secreted protein important for motility, host cell attachment, invasion, and egress. MIC2 contains six thrombospondin type I repeats (TSRs) that are modified by C-mannose and O-fucose inPlasmodiumspp. and mammals.

Here we used mass spectrometry to show that the four TSRs inT. gondiiMIC2 with proteinO-fucosyltransferase 2 (POFUT2) acceptor sites are modified by a dHexHex disaccharide, while Trp residues within three TSRs are also modified withC-mannose. Disruption of genes encoding eitherpofut2or nucleotide sugar transporter 2 (nst2), the putative GDP-fucose transporter, results in loss of MIC2 O-fucosylation, as detected by an antibody against the GlcFuc disaccharide, and markedly reduced cellular levels of MIC2. Furthermore, in 10-15% of theΔpofut2orΔnst2vacuoles, MIC2 accumulates earlier in the secretory pathway rather than localizing to micronemes. Dissemination of tachyzoites in human foreskin fibroblasts is reduced in these knockouts, which both show defects in attachment to and invasion of host cells comparable to the phenotype observed in the Βmic2.

These results, which showO-fucosylation of TSRs is required for efficient processing of MIC2 and for normal parasite invasion, are consistent with the recent demonstration thatP. falciparum Δpofut2has decreased virulence and support a conserved role for this glycosylation pathway in quality control of TSR-containing proteins in eukaryotes.
SSU72 phosphatase is a telomere replication terminator
Authors: Escandell Jose Miguel , Carvalho Edison S. Mascarenhas , Gallo-Fernandez Maria , Reis Clara C. , Matmati Samah , Luís Inês Matias , Abreu Isabel A. , Coulon Stéphane , Ferreira Miguel Godinho
Published: August 2018

Telomeres, the protective ends of eukaryotic chromosomes, are replicated through concerted actions by conventional DNA polymerases and telomerase, though the regulation of this process is not fully understood. Telomere replication requires (C)-Stn1-Ten1, a telomere ssDNA-binding complex that is homologous to RPA. Here, we show that the evolutionarily conserved phosphatase Ssu72 is responsible for terminating the cycle of telomere replication in fission yeast. Ssu72 controls the recruitment of Stn1 to telomeres by regulating Stn1 phosphorylation at S74, a residue that lies within the conserved OB fold domain. Consequently, ssu72Δ mutants are defective in telomere replication and exhibit long 3’ overhangs, which are indicative of defective lagging strand DNA synthesis. We also show that hSSU72 regulates telomerase activation in human cells by controlling the recruitment of hSTN1 to telomeres. Thus, in this study, we demonstrate a previously unknown yet conserved role for the phosphatase SSU72, whereby this enzyme controls telomere homeostasis by activating lagging strand DNA synthesis, thus terminating the cycle of telomere replication.
Ezetimibe inhibits Dengue virus infection in Huh-7 cells by blocking the cholesterol transporter Niemann–Pick C1-like 1 receptor
Authors: Osuna-Ramos Juan Fidel , Reyes-Ruiz José Manuel , Bautista-Carbajal Patricia , Farfán-Morales Noe , Cervantes-Salazar Margot , del Ángel Rosa María
Published: August 2018

Despite the importance of Dengue virus (DENV) infection in human health, there is not a fully effective vaccine or antiviral treatment against the infection. Since lipids such as cholesterol are required during DENV infection, its uptake and synthesis are increased in infected cells. Ezetimibe is an FDA-approved drug that reduces cholesterol uptake in humans by inhibiting the endocytosis through Niemman-Pick C1-Like 1 (NPC1L1) receptor, expressed on the membrane of enterocytes and hepatocytes. Our results indicate that an increase in the amount of NPC1L1 occurs on the surface of Huh-7 cells during DENV infection, which correlates with an increase in cholesterol levels. Blockage of NPC1L1 with ezetimibe in concentrations up to 50 μM does not reduce cell viability but diminished total cellular cholesterol, the percentage of infected cells, viral yield, viral RNA and protein synthesis without affecting DENV binding and/or entry to Huh-7 cells. Moreover, ezetimibe inhibited DENV replicative complex formation and lipid droplets accumulation. All these results indicate that ezetimibe is an excellent drug to inhibit DENV infection and confirm that cholesterol is a key target to inhibit viral infection.
A model-based high throughput method for fecundity estimation in fruit fly studies
Authors: Ng’oma Enoch , King Elizabeth G. , Middleton Kevin M.
Published: August 2018

The ability to quantify fecundity is critically important to a wide range of experimental applications, particularly in widely-used model organisms such as Drosophila melanogaster. However, the standard method of manually counting eggs is time consuming and limits the feasibility of large-scale experiments. We develop a predictive model to automate the counting of eggs from images of eggs removed from the media surface and washed onto dark filter paper. A cross-validation approach demonstrates our method performs well, with a correlation between predicted and manually counted values of 0.88. We show how this method can be applied to a large data set where egg densities vary widely.
Widespread genome instability inSolanum tuberosumplants regenerated from protoplasts
Authors: Fossi Michelle , Comai Luca
Published: August 2018

Non-transgenic genome editing in regenerable protoplasts, cell-wall free plant cells, could revolutionize crop improvement because it reduces regulatory and technical complexity. But, plant tissue culture is known to engender frequent unwanted variation. To evaluate the contribution of genome instability to this phenomenon, we analyzed large scale copy number changes in potatoes regenerated from protoplasts by comparison of Illumina read depth. While a control set of plants that had been propagated by cuttings displayed no changes, the protoplast regenerants were affected by pervasive aneuploidy. In addition, certain chromosomes displayed segmental deletions and duplications ranging from one to many. Resampling the same plant found different dosage profiles in different leaves, indicating frequent persistence of instability.
Item-specific delay activity demonstrates concurrent storage of multiple items in working memory
Authors: Sutterer David W. , Foster Joshua J. , Adam Kirsten C.S. , Vogel Edward K. , Awh Edward
Published: August 2018

A longstanding view holds that information is maintained in working memory (WM) via persistent neural activity that encodes the content of WM. Recent work, however, has challenged the view that all items stored in WM are actively maintained. Instead, “activity-silent” models propose that items can be maintained in WM without the need for persistent neural activity, raising the possibility that only a subset of items – perhaps just a single item – may be actively represented at a given time. While past studies have successfully decoded multiple items stored in WM, these studies cannot rule out an active switching account in which only a single item is actively represented at a time. Here, we directly tested whether multiple representations can be held concurrently in an active state. We tracked spatial representations in WM using alpha-band (8–12 Hz) activity, which encodes spatial positions held in WM. Human observers (male and female) remembered one or two positions over a short delay while we recorded EEG. Using a spatial encoding model, we reconstructed stimulus-specific working memory representations (channel tuning functions, CTFs) from the scalp distribution of alphaband power. Consistent with past work, we found the selectivity of spatial CTFs was lower when two items were stored than when one item was stored. Critically, data-driven simulations revealed that the selectivity of spatial representations in the two-item condition could not be explained by models restricting storage to a single item at a time. Thus, our findings provide robust evidence for the concurrent storage of multiple items in visual working memory.

Author Summary

Working memory (WM) is a mental workspace where we temporarily hold information “online” in pursuit of our current goals. However, recent activity-silent models of WM have challenged the view that all items are held in an “online” state, instead proposing that only a subset of representations in WM – perhaps just one item – are represented by persistent activity at a time. To directly test a single-item model of persistent activity, we used a spatial encoding model to read out the strength of two representations from alpha-band (8–12 Hz) power in the human EEG signal. We provide direct evidence that both locations were maintained concurrently, ruling out the possibility that declines in stimulus-specific activity are due to storing one of two items in an activity-silent state.
Germline SDHA mutations in children and adults with cancer
Authors: Dubard Gault Marianne , Mandelker Diana , DeLair Deborah , Stewart Carolyn R. , Kemel Yelena , Sheehan Margaret R. , Siegel Beth , Kennedy Jennifer , Marcell Vanessa , Arnold Angela , Al-Ahmadie Hikmat , Modak Shakeel , Robson Mark , Shukla Neerav , Roberts Stephen , Vijai Joseph , Topka Sabine , Kentsis Alex , Cadoo Karen , Carlo Maria , Latham Schwark Alicia , Reznik Ed , Dinatale Renzo , Hechtman Jaclyn , Borras Flores Ester , Jairam Sowmaya , Yang Ciyu , Li Yirong , Bayraktar Erol Can , Ceyhan-Birsoy Ozge , Zhang Liying , Kohlman Wendy , Schiffman Joshua , Stadler Zsofia , Birsoy Kivanc , Kung Andrew , Offit Kenneth , Walsh Michael F.
Published: August 2018

Mutations in succinate dehydrogenase complex genes predispose to familial paraganglioma-pheochromocytoma syndrome (FPG) and gastrointestinal stromal tumors (GIST). Here we describe cancer patients undergoing agnostic germline testing at Memorial Sloan Kettering Cancer Center and found to harbor germline SDHA mutations. Using targeted sequencing covering the cancer census genes, we identified 10 patients with SDHA germline mutations. Cancer diagnoses for these patients carrying SDHA germline mutations included neuroblastoma (n = 1), breast (n = 1), colon (n = 1), renal (n = 1), melanoma and uterine (n = 1), prostate (n = 1), endometrial (n = 1), bladder (n = 1), and gastrointestinal stromal tumor (GIST) (n = 2). Immunohistochemical staining and assessment of patient tumors for second hits and loss of heterozygosity in SDHA confirmed GIST as an SDHA-associated tumor and suggests SDHA germline mutations may be a driver in neuroblastoma tumorigenesis.
Robustly Cycling Xenopus laevis Cell-Free Extracts in Teflon Chambers
Authors: Chang Jeremy B. , Ferrell James E.
Published: August 2018

A central advantage of studying Xenopus laevis is the manipulability of its cell-free extracts, which perform the cell cycle in vitro. However, these extracts are known to be experimentally temperamental and will often complete at most one or two cycles. Over the course of developing systems for imaging cell cycle events in extracts in real time, we unexpectedly found that when standard Xenopus extracts are placed in Teflon tubes, they cycle extremely robustly; in one series of experiments, over 90% (n = 13) of extracts cycled an average of seven and as many as 14 times. Extracts incubated in other materials, such as glass and polydimethylsiloxane, do not cycle as robustly. Here we present protocols for preparing Xenopus extracts and imaging them in Teflon tubes. This method extends the usefulness of this powerful model organism.
Analysis of Small RNAs by Northern Hybridization
Authors: Li Chengjian , Zamore Phillip D.
Published: August 2018

This protocol describes how to use northern hybridization to detect 15- to 150-nt small RNAs. Total RNA is fractionated by electrophoresis through a denaturing polyacrylamide gel and then transferred to a nylon membrane by semidry electroblotting. After UV-cross-linking the RNA to the membrane, hybridization is performed in Church buffer using a 32P-radiolabeled oligonucleotide probe followed by PhosphorImager analysis. The use of StarFire probes allows a substantial increase in the specific radioactivity of the hybridization probe. StarFire probes contain two domains. The target-specific domain at the 5′ end hybridizes to the small RNA of interest. The universal template-binding domain at the 3′ end is used to bind a universal template oligonucleotide that carries 10 deoxythymidines at its 5′ end, providing a template for DNA polymerase to incorporate 10 [α-32P]deoxyadenosines at the 3′ end of the StarFire probe.
Microfluidic Encapsulation of Demembranated Sperm Nuclei in Xenopus Egg Extracts
Authors: Oakey John , Gatlin Jesse C.
Published: August 2018

The cell-free nature of Xenopus egg extract makes it a uniquely tractable experimental model system. The extract, effectively unconfined cytoplasm, allows the direct and relatively straight-forward addition of purified proteins and other reagents, a characteristic that renders the system amenable to many biochemical and cell biological manipulations. Accessibility to the system also facilitates the direct physical manipulation and probing of biological structures, in turn enabling mechanical properties of intracellular assemblies and organelles, such as the mitotic spindle and nucleus, to be measured. Recently, multiphase microfluidics have been combined with Xenopus egg extracts to encapsulate discrete cytoplasmic volumes. Described here is a protocol detailing the use of multiphase microfluidic devices to encapsulate sperm nuclei within extract droplets of defined size and shape. This protocol can also be applied more generally to encapsulation of microbeads and other particles.
“Life if elsewhere”
Authors: Wechtler Heidi
Published: August 2018

Purpose

The purpose of this paper is to examine the motives of female childless self-initiated expatriates (SIEs) in deciding to work abroad, so far under-researched.

Design/methodology/approach

The study departs from prior research in using a new methodological approach, i.e. the analysis of online diaries (blogs) to explore the motives of a specific population to relocate.

Findings

The emergent model of motivations is based upon four main dimensions that emerged from the socially constructed experience of these single childless female SIEs: escape as main motivation, confrontation to reality, identity reconstruction and purpose of expatriation.

Originality/value

The findings reveal new elements of motivations to move abroad such as the complete absence of the notion of career from the blog posts, replaced, however, by a feminist and existentialist reflection.
Equality as a threshold conception: challenging future manager’s perceptions
Authors: Dyer Suzette , Hurd Fiona
Published: August 2018

Purpose

The purpose of this paper is to examine the potential to develop a shared understanding of systemic discrimination and the complexity of equality and an appreciation for the range of interventions designed to redress inequality within the context of business school curricula.

Design/methodology/approach

Qualitative material was gathered over a four-year period through written reflections of student interpretations of equality. Participants were enroled in a human resource management (HRM) course critically examining systemic gender discrimination, women’s organisational experiences, gendered employment outcomes and the range of interventions designed to redress gendered employment outcomes. Threshold concepts framed the analysis of participant reflections.

Findings

The paper shows that while the participants developed a shared understanding of systemic gender discrimination, their interpretations of equality and appreciation for the range of interventions available to redress inequality differed. These differences were shaped by the extent to which participants integrated their understanding of systemic discrimination with their interpretations of equality, and the extent to which the interventions to inequality transformed, upheld or challenged participant agendic self-identity and world view.

Research limitations/implications

The study provides support for continued use of equality as a construct in both research and teaching settings. The study highlights that unequal outcomes are an enduring phenomena, and that introducing the notion of equality to the classroom helps develop student’s ability to understand dynamics of discrimination in the workplace. The limitations of the study relate to the sample size, and dependence on a single specialist HRM course, in addition to the specific New Zealand context.

Practical implications

The differences in interpretations have implications for the way educators introduce discussions of equality within the business school classroom.

Originality/value

The paper demonstrates that developing a shared understanding of systemic discrimination does not always lead to developing a shared understanding of the complexity of equality or appreciation for the many forms of interventions available.
Employee resource groups as learning communities
Authors: Green Wendy M.
Published: August 2018

Purpose

The purpose of this paper is to explore the role of employee resource groups (ERGs) in a multi-national, for-profit corporation. The paper focuses on how ERGs facilitate learning.

Design/methodology/approach

A qualitative case study approach was used to examine six social identity based ERGs in one multi-national for-profit organization headquartered in the USA.

Findings

The study found that ERGs facilitate learning and development activities in order to support their membership. ERGs, operating as communities of practice, also engaged in informal learning opportunities that were designed to shift perspectives of non-members and executive-level leaders in the organization.

Originality/value

There is a growing body of literature on ERGs across organizations and higher education that examine how these groups engage in activism, advocacy, recruitment, retention and education. This study examines the processes by which these groups facilitate learning and development activities and the benefits perceived by the membership. The paper provides value to human resources professionals and others who are interested in how ERGs function as learning communities and outcomes the membership perceive as most important.
Performance indicators for facilities operation and maintenance (Part 2)
Authors: Lai Joseph H.K. , Man Chun Sing
Published: August 2018

Purpose

This paper (Part 2 of 2) aims to shortlist performance indicators which are used in evaluating facilities operation and maintenance (O&M) in commercial buildings.

Design/methodology/approach

A three-session focus group meeting, with the use of a customized questionnaire and audio recording, was convened to solicit opinions from O&M experts. Their quantitative responses (ratings on the importance of the indicators) and the qualitative ones (reasons for having the indicators selected or excluded) were taken for analysis, followed by mapping the shortlisted indicators based on the phase-hierarchy (P-H) model for facilities management (FM).

Findings

From a total of 74 performance indicators (71 identified from the literature and three added by the focus group), 17 indicators were shortlisted, and time constraint was the most common reason for having those indicators excluded from the shortlist. Mapping the shortlisted indicators with the P-H model revealed that the performance evaluation focus of the experts was at the tactical level, on the output phase of facilities services delivery.

Research implications

The shortlisted indicators serve as a keystone for establishing a performance evaluation scheme for engineering facilities in commercial buildings. Research on other areas may follow the approach of this study to shortlist key performance indicators (KPIs).

Practical implications

Professionals of the other building types (e.g. residential, industrial and healthcare) or sectors with diverse FM organizations may conduct a similar study to identify indicators for performance evaluation purposes. In particular, the process of shortlisting the O&M KPIs may be used to shortlist KPIs for the other FM services.

Originality/value

The focus group study demonstrates how to rigorously select KPIs for use in managing facilities.
India’s rural healthcare systems: structural modeling
Authors: Kumar Dinesh
Published: August 2018

Purpose

The purpose of this paper is to identify factors related to rural healthcare services and establish a hierarchical model for the effective rural healthcare management in India.

Design/methodology/approach

A questionnaire survey identified and correlated numerous factors related to the Uttarakhand rural healthcare systems. Experts opinion were translated into a reachability matrix and an interpretive structural model. A fuzzy matriced impacts croises-multiplication applique and classment (FMICMAC) analysis arranged the factors as hierarchical stages using their driving power.

Findings

The interpretive structural and FMICMAC hierarchical models suggest four key driving factors: diseases, climatic conditions, population growth and political pressure.

Practical implications

Despite numerous issues, rural healthcare services can be improved by considering key driving factors that could be used as a prediction tool for policy makers.

Originality/value

Results demonstrate that population control, coordinating services with local bodies and rural health center annual maintenance can be game changers toward better healthcare services.