bluuebunny/crossref_metadata_2025 huggingface dataset:
A robust deep neural network for denoising task-based fMRI data: An application to working memory and episodic memory
Authors: Yang Zhengshi , Zhuang Xiaowei , Sreenivasan Karthik , Mishra Virendra , Curran Tim , Cordes Dietmar
Published: August 2019

In this study, a deep neural network (DNN) is proposed to reduce the noise in task-based fMRI data without explicitly modeling noise. TheDNNartificial neural network consists of one temporal convolutional layer, one long short-term memory (LSTM) layer, one time-distributed fully-connected layer, and one unconventionalselectionlayer in sequential order. The LSTM layer takes not only the current time point but also what was perceived in a previous time point as its input to characterize the temporal autocorrelation of fMRI data. The fully-connected layer weights the output of the LSTM layer, and the output denoised fMRI time series is selected by theselectionlayer. Assuming that task-related neural response is limited to gray matter, the model parameters in theDNNnetwork are optimized by maximizing the correlation difference between gray matter voxels and white matter or ventricular cerebrospinal fluid voxels. Instead of targeting a particular noise source, the proposed neural network takes advantage of the task design matrix to better extract task-related signal in fMRI data. TheDNNnetwork, along with other traditional denoising techniques, has been applied on simulated data, working memory task fMRI data acquired from a cohort of healthy subjects and episodic memory task fMRI data acquired from a small set of healthy elderly subjects. Qualitative and quantitative measurements were used to evaluate the performance of different denoising techniques. In the simulation, DNN improves fMRI activation detection and also adapts to varying hemodynamic response functions across different brain regions. DNN efficiently reduces physiological noise and generates more homogeneous task-response correlation maps in real data.
A multiresolution framework to characterize single-cell state landscapes
Authors: Mohammadi Shahin , Davila-Velderrain Jose , Kellis Manolis
Published: August 2019

Dissecting the cellular heterogeneity embedded in single-cell transcriptomic data is challenging. Although a large number of methods and approaches exist, robustly identifying underlying cell states and their associations is still a major challenge; given the nonexclusive and dynamic influence of multiple unknown sources of variability, the existence of state continuum at the time-scale of observation, and the inevitable snapshot nature of experiments. As a way to address some of these challenges, here we introduce ACTIONet, a comprehensive framework that combines archetypal analysis and network theory to provide a ready-to-use analytical approach for multiresolution single-cell state characterization. ACTIONet uses multilevel matrix decomposition and network reconstruction to simultaneously learn cell state patterns, quantify single-cell states, and reconstruct a reproducible structural representation of the transcriptional state space that is geometrically mapped to a color space. A color-enhanced quantitative view of cell states enables novel visualization, prediction, and annotation approaches. Using data from multiple tissues, organisms, and developmental conditions, we illustrate how ACTIONet facilitates the reconstruction and exploration of single-cell state landscapes.
Atrous Convolution with Transfer Learning for Skin Lesions Classification
Authors: Ratul Md. Aminur Rab , Mozaffari Mohammad Hamed , Parimbelli Enea , Lee WonSook
Published: August 2019

Skin cancer is a crucial public health issue and by far the most usual kind of cancer specifically in the region of North America. It is estimated that in 2019, only because of melanoma nearly 7,230 people will die, and 192,310 cases of malignant melanoma will be diagnosed. Nonetheless, nearly all types of skin lesions can be treatable if they can be diagnosed at an earlier stage. The accurate prediction of skin lesions is a critically challenging task even for vastly experienced clinicians and dermatologist due to a little distinction between surrounding skin and lesions, visual resemblance between melanoma and other skin lesions, fuddled lesion border, etc. A well-grounded automated computer-aided skin lesions detection system can help clinicians immensely to prognosis malignant skin lesion in the earliest possible time. From the past few years, the emergence of machine learning and deep learning in the medical imaging has produced several image-based classification systems in the medical field and these systems perform better than traditional image processing classification methods. In this paper, we proposed a popular deep learning technique namely atrous or, dilated convolution for skin lesions classification, which is known to have enhanced accuracy with the same amount of computational cost compared to traditional CNN. To implement atrous convolution we choose the transfer learning technique with several popular deep learning architectures such as VGG16, VGG19, MobileNet, and InceptionV3. To train, validate, and test our proposed models we utilize HAM10000 dataset which contains total 10015 dermoscopic images of seven different skin lesions (melanoma, melanocytic nevi, Basal cell carcinoma, Benign keratosis-like lesions, Dermatofibroma, Vascular lesions, and Actinic keratoses). Four of our proposed dilated convolutional frameworks show promising outcome on overall accuracy and per-class accuracy. For example, overall test accuracy achieved 87.42%, 85.02%, 88.22%, and 89.81% on dilated VGG16, dilated VGG19, dilated MobileNet, and dilated IncaptionV3 respectively. These dilated convolutional models outperformed existing networks in both overall accuracy and individual class accuracy. Among all the architectures dilated InceptionV3 shows superior classification accuracy and dilated MobileNet is also achieving almost impressive classification accuracy like dilated InceptionV3 with the lightest computational complexities than all other proposed model. Compared to previous works done on skin lesions classification we have experimented one of the most complicated open-source datasets with class imbalances and achieved better accuracy (dilated inceptionv3) than any known methods to the best of our knowledge.
Long-Term Potentiation Induces Extrasynaptic Exocytosis of Glun2A-containing NMDA Receptors that is Mainly Controlled by SNAP23
Authors: Yu Xiaojun , Li Wei , Wang Tong
Published: August 2019

NMDA receptors (NMDAR) are key players in the initiation of synaptic plasticity that underlies learning and memory. Long-term potentiation (LTP) of synapses require an increased calcium current via NMDA channels to trigger modifications in postsynaptic density (PSD). It is generally believed that the amount of NMDARs on the postsynaptic surface remains stationary, whereas their subunit composition is dynamically fluctuated during this plasticity process. However, the molecular machinery underlying this subunit-specific regulation remains largely elusive. Here, by detecting the time-lapse changes of surface GluN2A and GluN2B subunit levels using biochemical approaches, surface immunostaining, live-imaging and super-resolution microscopy, we uncovered a transient increase of surface GluN2A-type NMDARs shortly after the induction of chemical long term potentiation (cLTP). These augmented sub-diffraction-limited GluN2A clusters predominantly exist in extrasynaptic domains. We also showed that the spine-enriched SNARE associated protein SNAP-23, and to a minor extent its homologue SNAP-25, control both the basal and regulated surface level of GluN2A receptors. Using a total internal reflection fluorescence microscopy (TIRFM) based live-imaging assay, we resolved and analyzed individual exocytic events of NMDARs in live neurons and found that cLTP raised the frequency of NMDAR exocytosis at extrasynaptic regions, without altering the duration or the package size of these events. Our study thereby provides direct evidence that synaptic plasticity controls the postsynaptic exocytosis machinery, which induces the insertion of more GluN2A receptors into the extrasynaptic area.

Significance Statement

Memory formation involves the long-term modification of synapses, which is called synaptic plasticity. In the postsynaptic density (PSD) of excited neurons, this modification process occurs on a minute timescale, initiated by the opening of NMDARs that trigger downstream cascades to fix the potentiation (LTP) at specific synapses for longer timescales. Here, using a novel live-imaging assay we resolved the dynamic delivery of NMDARs to the cell surface, and found that only the insertion frequency, not the duration of individual insertion or number of GluN2A subunits each of these NMDAR vesicles contains, was altered during the synaptic potentiation process. We also identified SNAP-23 as the key molecule mediating this activity dependent NMDAR surface delivery. This study provides a novel mechanism of how NMDARs are regulated in the short window to initiate the long-lasting synaptic modifications.
Novel Proteomic changes in Yeast Mitochondria provide insights into mitochondrial functioning upon over-expression of human p53
Authors: Redhu Archana Kumari , Bhat Jayadeva Paike
Published: August 2019

Cancer cells display enhanced glycolytic activity and impaired oxidative phosphorylation even in the presence of adequate oxygen (Warburg effect). Mitochondrial physiology is a promising hit target for anti-cancer therapy because of its key role in Warburg effect and activating apoptosis in mammalian as well as yeast cells. Over-expression of human p53 in S.cerevisiae leads to cell cycle arrest and apotosis. In the present work we show that how S.cerevisiae escapes from p53 induced apoptosis in fermentable carbon source, whereas in case of non-fermentable carbon source this phenomenon is not observed. To shed the light on this aspect we performed a quantitative proteomic analysis of yeast mitochondria isolated from the cells grown on sucrose (fermentation) and glycerol (respiration) with and without p53 over-expression. Through this approach, we identified a total dataset of 1120 proteins with 1% FDR, of which 239(133+106) proteins are differentially experssed in both conditions. Interestingly, we observed that after over-expression of p53 in sucrose grown yeast cells, a complete set of pentose phosphate pathway (PPP) enzymes is up-regulated in the mitochondria that leads to enhanced mitochondrial NADPH production and ROS quenching. Increased association of a hexose transporter (HXT6) and a hexokinase (HXK2) with the mitochondria of fermenting yeast cells upon over-expression of p53, may direct glucose towards PPP inside the mitochondria. In conclusion, our results provide the evidence that up-regulated PPP inside the mitochondria is a key to evade apoptosis by S.cerevisiae upon p53 over-expression.
Functional Anabolic Network Analysis of Human-associatedLactobacillusStrains
Authors: Moutinho Thomas J. , Neubert Benjamin C. , Jenior Matthew L. , Carey Maureen A. , Medlock Gregory L. , Kolling Glynis L. , Papin Jason A.
Published: August 2019

Members of theLactobacillusgenus are frequently utilized in the probiotic industry with many species conferring demonstrated health benefits; however, these effects are largely strain-dependent. We designed a method called PROTEAN (Probabilistic Reconstruction Of constituent Anabolic Networks) to computationally analyze the genomic annotations and predicted metabolic production capabilities of 144 strains across 16 species ofLactobacillusisolated from human intestinal, oral, and vaginal body sites. Using PROTEAN we conducted a genome-scale metabolic network comparison between strains, revealing that metabolic capabilities differ by isolation site. Notably, PROTEAN does not require a well-curated genome-scale metabolic network reconstruction to provide biological insights. We found that predicted metabolic capabilities of lactobacilli isolated from the vaginal microbiota cluster separately from intestinal and oral isolates, and we also uncovered an overlap in the predicted metabolic production capabilities of intestinal and oral isolates. Using machine learning, we determined the most informative metabolic products driving the difference between predicted metabolic capabilities of intestinal, oral, and vaginal isolates. Notably, intestinal and oral isolates were predicted to have a higher likelihood of producing D-alanine, D/L-serine, and L-proline, while the vaginal isolates were distinguished by a higher predicted likelihood of producing L-arginine, citrulline, and D/L-lactate. We found the distinguishing products to be consistent with published experimental literature. This study showcases a systematic technique, PROTEAN, for comparing the predicted functional metabolic output of microbes using genome-scale metabolic network analysis and computational modeling and provides unique insight into human-associatedLactobacillusbiology.

Importance

TheLactobacillusgenus has been shown to be important for human health. Lactobacilli have been isolated from human intestinal, oral, and vaginal sites. Members of the genus contribute significantly to the maintenance of vaginal health by providing colonization resistance to invading pathogens. A wide variety of clinical studies have indicated thatLactobacillus-based probiotics confer health benefits for several gut- and immune-associated diseases. Microbes interact with the human body in several ways, including the production of metabolites that influence physiology or other surrounding microbes. We have conducted a strain-level genome-scale metabolic network reconstruction analysis of human-associatedLactobacillusstrains, revealing that predicted metabolic capabilities differ when comparing intestinal/oral isolate to vaginal isolates. The technique we present here allows for direct interpretation of discriminating features between the experimental groups.
High-throughput multi-parallel enteropathogen quantification via nano-liter qPCR
Authors: Grembi Jessica A. , Mayer-Blackwell Koshlan , Luby Stephen P. , Spormann Alfred M.
Published: August 2019

Quantitative molecular diagnostic methods, such as qPCR, can effectively detect pathogen-specific nucleic acid sequences. However, costs associated with multi-pathogen quantitative molecular diagnostics hinder their widespread use. Nano-liter qPCR (nL-qPCR) is a miniaturized tool for quantification of multiple targets in large numbers of samples based on assay parallelization on a single chip, with potentially significant cost-savings due to rapid throughput and reduced reagent volumes. We evaluated a suite of novel and published assays to detect 17 enteric pathogens using a commercially available nL-qPCR technology. Assay efficiencies ranged from 88-98% (mean 91%) and were reproducible across four operators at two separate facilities. When applied to complex fecal material, assays were sensitive and selective (99.8% of DNA amplified were genes from the target organism). Detection limits were 1-2 orders of magnitude higher for nL-qPCR than an existing enteric TaqMan Array Card (TAC), due to nanofluidic volumes. Compared to the TAC, nL-qPCR displayed 97% (95% CI 0.96, 0.98) negative percent agreement and 63% (95% CI 0.60, 0.66) overall positive percent agreement. Positive percent agreement was 90% for target concentrations above the nL-qPCR detection limits. nL-qPCR assays showed an underestimation bias of 0.34 log10copies/gram of stool [IQR -0.41, -0.28] compared with the enteric TAC. Higher detection limits, inherent to nL-qPCR, do not hinder detection of clinically relevant pathogen concentrations. With 12 times higher throughput for a sixth of the per-sample cost of the enteric TAC, the nL-qPCR chip described here is a viable alternative for enteropathogen quantification for studies where other technologies are cost-prohibitive.
Single-cell analysis of intestinal immune cells during helminth infection
Authors: Ferrer-Font Laura , Mehta Palak , Harmos Phoebe , Schmidt Alfonso , Price Kylie M , Hermans Ian F , Ronchese Franca , Le Gros Graham , Mayer Johannes U
Published: August 2019

Single cell isolation from helminth infected intestines has been notoriously difficult, due to the strong anti-parasite type 2 immune responses that drive mucus production, tissue remodeling and immune cell infiltration. Through the systematic optimization of a standard intestinal digestion protocol, we were able to isolate millions of immune cells from heavily infected tissues. Using this protocol, we validated many hallmarks of anti-parasite immunity and analyzed immune cells from the lamina propria and granulomas during helminth development, as well as acute and chronic worm infection.
Wild songbirds exhibit consistent individual differences in inter-specific social behaviour
Authors: Hillemann F. , Cole E. F. , Farine D. R. , Sheldon B. C.
Published: August 2019

ABSTRACT

Natural populations and communities consist of individuals that differ in their phenotypes. There is increasing evidence in community ecology that consistent intraspecific variation in behaviour changes the outcome of ecological interactions.

Differences in intra- and inter-specific interactions are expected to play a major role in determining patterns of species coexistence and community structure. However, the question of whether individuals vary in their propensity to associate with heterospecifics has been neglected.

We used social network analysis to characterise pattern of heterospecific associations in wild mixed-species flocks of songbirds, and assessed whether individuals adopt consistent social strategies in their broader, heterospecific, social environment. We quantified heterospecific foraging associations using data from a large automatically monitored PIT-tagged population of birds, involving more than 300 000 observations of flock membership, collected over three winters, for two tit species (Paridae), blue tits, Cyanistes caeruleus, and great tits, Parus major.

We assessed individual consistency in interspecific social preferences over both short-term (week-to-week) and longer-term (year-to-year) timescales for a total of 4610 individuals, and found that blue tits and great tits exhibited marked and consistent intraspecific differences in heterospecific social phenotypes in terms of both absolute and relative number of associates. Further, we found that these consistent differences were significantly greater than expected from spatial and temporal differences in population densities.

Heterospecific associations represent a major component of the social environment for many species, and our results show that individuals vary consistently in their social decisions with respect to heterospecifics. These findings provide support for the notion that intraspecific trait variation contributes to patterns at community and ecosystem levels.
Interleukin-4 signaling plays a major role in urogenital schistosomiasis-associated bladder pathogenesis
Authors: Mbanefo Evaristus C. , Fu Chi-Ling , Ho Christina P. , Le Loc , Ishida Kenji , H. Hsieh Michael
Published: August 2019

IL-4 is crucial in many helminth infections, but its role in urogenital schistosomiasis, infection withSchistosoma haematobiumworms, remains poorly understood due to a historical lack of animal models. The bladder pathology of urogenital schistosomiasis is caused by immune responses to eggs deposited in the bladder wall. A range of pathology occurs, including urothelial hyperplasia and cancer, but associated mechanisms and links to IL-4 are largely unknown. We modeled urogenital schistosomiasis by injecting the bladder walls of IL-4 receptor-alpha knockout(Il4ra−/−) and wild type mice withS. haematobiumeggs. Readouts included bladder histology andex vivoassessments of urothelial proliferation, cell cycle and ploidy status. We also quantified the effects of exogenous IL-4 on urothelial cell proliferationin vitro, including cell cycle status and phosphorylation patterns of major downstream regulators in the IL-4 signaling pathway. There was a significant decrease in the intensity of granulomatous responses to bladder-wall injectedS. haematobiumeggs inIl4ra−/−versus wild type mice.S. haematobiumegg injection triggered significant urothelial proliferation, including evidence of urothelial hyperdiploidy and cell cycle skewing in wild type but notIl4ra−/−mice. Urothelial exposure to IL-4in vitroled to cell cycle polarization and increased phosphorylation of AKT. Our results show IL-4 signaling is required for key pathogenic features of urogenital schistosomiasis, and that particular aspects of this signaling pathway may exert these effects directly on the urothelium. These findings point to potential mechanisms by which urogenital schistosomiasis promotes bladder carcinogenesis.
Protein-surfactant-polysaccharide nanoparticles increase the catalytic activity of an engineered β-lactamase maltose-activated switch enzyme
Authors: Fuenzalida J.P. , Xiong T. , Moerschbacher B. M. , Ostermeier Marc , Goycoolea F.M.
Published: August 2019

We present polysaccharide-based nanoparticles able to associate and increase the catalytic activity of the maltose-binding MBP317-347 switch enzyme. Fluorescence quenching and molecular docking studies along with the partial resistance to increasing pH and ionic strength indicate that the increase in enzymatic activity is due to a specific interaction between the maltose binding pocket on MBP317-347 and alginate exposed on the surface of the nanoparticles. Finally, we show that the hybrid self co-assembled particles increase the half-life of MBP317-347 over six-fold at 37°C, thus reflecting their potential use as a macromolecular drug delivery system.
Inhibition of Microbial Beta-Glucuronidase Does Not Prevent Breast Carcinogenesis in the Polyoma Middle T Mouse
Authors: Beck Amanda P. , Li Hao , Ervin Samantha M. , Redinbo Matthew R. , Mani Sridhar
Published: August 2019

Purpose

To demonstrate whether inhibition of intestinal microbial beta (β)-glucuronidase (BGUS) abrogates tumor formation in a MMTV-PyMT mouse breast cancer model.

Methods

Female MMTV-PyMT heterozygote mice (4 weeks old) were randomized to oral gavage with vehicle or UNC10201652 (20 μg/day), a microbial BGUS inhibitor, for 9 weeks. The entire animal carcass was assessed for tumor deposits by histology and immunohistochemical staining for tumor (Ki67, PCNA) and breast specific (ER, PR, Cyclin D1, aSMA, Integrin β1) markers.

Results

The MMTV-PyMT breast pathology in our study simulates prior published reports of tumor incidence and aggressiveness. There was no significant difference in the tumor histology, number of tumors (lesions), and patterns of spread of tumors in the UNC10201652 versus the vehicle treated mice. Similarly, there were no significant differences in the semi-quantitative scores for expression of ER, PR, Ki67, PCNA, or Integrin β1. There were also no major differences seen in qualitative screening of Cyclin D1 and aSMA.

Conclusions

MMTV-PyMT mice administered UNC10201652, when compared to vehicle treated mice, show a similar abundance of breast tumor (and tumor initiating) lesions ranging from hyperplasia to frank carcinoma. There is a trend, however small, that the incidence of hyperplastic and adenomas may be decreased in UNC10201652 treated mice. Further refined dosing strategies in MMTV-PyMT are planned to clarify its biological significance. To our knowledge this is the first report of use of any BGUS inhibitor in chemoprevention of breast tumors using a genetic model simulating human breast cancer.
Natural variation in the Arabidopsis AGO2 gene is associated with susceptibility to potato virus X
Authors: Brosseau Chantal , Adurogbangba Ayooluwa , Roussin-Léveillée Charles , Zhao Zhenxing , Biga Sébastien , Moffett Peter
Published: August 2019

RNA silencing functions as an anti-viral defence in plants through the action of DICER-like (DCL) and ARGONAUTE (AGO) proteins. However, there are few known examples of functional variation in RNA silencing components. The AGO2 protein is important for antiviral defense against multiple viruses and has been shown to be a major limiting factor to infection by potato virus X (PVX) of Arabidopsis thaliana but not Nicotiana benthamiana. We show that the AGO2 proteins from these two plants have differential activity against PVX, suggesting that variation in AGO2 is important in plant-virus interactions. Consistent with this, we find that the Arabidopsis thaliana AGO2 gene shows a high incidence of polymorphisms between accessions, with evidence of selective pressure. AGO2 protein variants can be assigned to two groups, in near equal frequency, based on an amino acid change and small deletions in the protein N-terminus. Inoculation of a large number of Arabidopsis accessions shows strong correlation between these alleles and resistance or susceptibility to PVX. These observations were validated using genetic and transgenic complementation analysis, which showed that one type of AGO2 variant is specifically affected in its antiviral activity, without interfering with other AGO2-associated functions such as anti-bacterial resistance or DNA methylation. Our results demonstrate a novel type of genetically-encoded virus resistance and suggest that plant-virus interactions have influenced natural variation in RNA silencing components.
An easy-to-assemble, robust, and lightweight drive implant for chronic tetrode recordings in freely moving animals
Authors: Voigts Jakob , Newman Jonathan P. , Wilson Matthew A. , Harnett Mark T.
Published: August 2019

Tetrode arrays are the gold-standard method for neuronal recordings in many studies with behaving animals, especially for deep structures and chronic recordings. Here we outline an improved drive design for use in freely behaving animals. Our design makes use of recently developed technologies to reduce the complexity and build time of the drive while maintaining a low weight. The design also presents an improvement over many existing designs in terms of robustness and ease of use. We describe two variants: a 16 tetrode implant weighing ∼2 g for mice, bats, tree shrews and similar animals, and a 64 tetrode implant weighing ∼16 g for rats, and similar animals.These designs were co-developed and optimized alongside a new class of drive-mounted feature-rich amplifier boards with ultra-thin RF tethers, as described in an upcoming paper (Newman, Zhang et al., in prep). This design significantly improves the data yield of chronic electrophysiology experiments.
Proteinase-Activated Receptor 4 (PAR4) Activation Triggers Cell Membrane Blebbing through RhoA and β-arrestin
Authors: Vanderboor Christina MG , Thibeault Pierre E , Nixon Kevin CJ , Gros Robert , Kramer Jamie , Ramachandran Rithwik
Published: August 2019

Proteinase-Activated Receptors (PARs) are a four-member family of G-protein coupled receptors that are activated via proteolysis. PAR4 is a member of this family that is cleaved and activated by serine proteinases such as thrombin, trypsin and cathepsin-G. PAR4 is expressed in a variety of tissues and cell types including platelets, vascular smooth muscle cells and neuronal cells. In studying PAR4 signalling and trafficking, we observed dynamic changes in the cell membrane with spherical membrane protrusions that resemble plasma membrane blebbing. Since non-apoptotic membrane blebbing is now recognized as an important regulator of cell migration, cancer cell invasion, and vesicular content release we sought to elucidate the signalling pathway downstream of PAR4 activation that leads to such events. Using a combination of pharmacological inhibition and CRISPR/Cas9-mediated gene-editing approaches we establish that PAR4-dependent membrane blebbing occurs independently of the Gαq/11and Gαisignalling pathways and is dependent on signalling via the β-arrestin-1/-2 and RhoA signalling pathways. In order to gain a more comprehensive understanding of β-arrestin-mediated signalling downstream of PAR4 and to guide future studies, we undertook RNA-seq analysis of PAR4 activated genes in control cells and in cells lacking β-arrestin-1/-2. A list of differentially expressed genes was generated followed by Gene Ontology (GO) and enrichment analysis, revealing PAR4 regulation of genes involved in processes including blood coagulation and circulation, cell-cell adhesion, sensory perception and neuron-neuron synaptic transmission-terms that relate back to known functions of PAR4 and are consistent with our finding of membrane blebbing triggered by PAR4 activation. Together these studies provide further mechanistic insight into PAR4 regulation of cellular function.

Significance Statement

We find that the thrombin receptor PAR4 triggers cell membrane blebbing in a RhoA- and β-arrestin-dependent manner. In addition to identifying novel cellular responses mediated by PAR4, these data provide further evidence for biased signaling in PAR4 since membrane blebbing was dependent on some, but not all, signaling pathways activated by PAR4. Finally through CRISPR/Cas9-mediated targeting and RNA-seq analysis we catalogue here PAR4-dependent transcription that is dependent on β-arrestin.
Engineering “self-homing” circulating tumour cells as novel cancer theranostics
Authors: Parkins Katie M , Dubois Veronica P , Kelly John J , Chen Yuanxin , Foster Paula J , Ronald John A
Published: August 2019

Purpose: New ways to target and treat metastatic disease are urgently needed. Tumor “self-homing” describes the recruitment of circulating tumor cells (CTCs) back to a previously excised primary tumor location, contributing to tumor recurrence, as well as their migration to established metastatic lesions. Recently, self-homing CTCs have been exploited as delivery vehicles for anti-cancer therapeutics in preclinical primary tumor models. However, the ability of CTCs to self-home and treat metastatic disease is largely unknown. Methods: Here, we employ molecular imaging to explore whether systemically-administered CTCs home to metastatic lesions and if CTCs armed with both a reporter gene and a cytotoxic prodrug gene therapy can be used to visualize and treat metastatic disease. Results: Bioluminescence imaging (BLI) performed over time revealed a remarkable ability of CTCs to home to primary and metastatic tumors throughout the body. Mice that received therapeutic CTCs had less BLI signal as well as less primary tumour burden than control mice. Preliminary data also showed self-homing therapeutic CTCs may be effective at treating disseminated breast cancer metastases. Conclusion: Using dual-luciferase BLI, this study demonstrates the noteworthy ability of experimental CTCs to home to disseminated breast cancer lesions. Moreover, by incorporating a prodrug gene therapy system into our self-homing CTCs, we show exciting progress towards effective and targeted delivery of gene-based therapeutics to treat both primary and metastatic lesions.
Fatty acid-induced lipotoxicity inhibits choline metabolism independent of ER stress in mouse primary hepatocytes
Authors: O’Dwyer Conor , Yaworski Rebecca , LeBlond Nicholas D. , Ghorbani Peyman , Nunes Julia R.C. , Margison Kaitlyn D. , Smith Tyler T.K. , Odai Kaelan Gobeil , Han Shauna , Fullerton Morgan D.
Published: August 2019

Choline is an essential nutrient that is critical component of the membrane phospholipid phosphatidylcholine (PC), the neurotransmitter acetylcholine and the methylation pathway. In the liver specifically, PC is the major membrane constituent and can be synthesized by the CDP-choline or the phosphatidylethanolamine (PE) N-methyltransferase (PEMT) pathway. With the continuing global rise in the rates of obesity and non-alcoholic fatty liver disease, we sought to explore how excess fatty acids (FA), typical of an obesity and hepatic steatosis, affect choline uptake and metabolism in primary hepatocytes. Our results demonstrate that hepatocytes chronically treated with palmitate, but not oleate or a mixture, had decreased choline uptake, which was associated with lower choline incorporation into PC and lower expression of choline transport proteins. Interestingly, a reduction in the rate of degradation spared PC levels in response to palmitate when compared to control. PE synthesis was slightly diminished; however, no compensatory changes in the PEMT pathway were observed. We next hypothesized that ER stress may be a potential mechanism by which palmitate treatment diminished choline. However, when we exposed primary hepatocytes to the common ER stress inducing compound tunicamycin, choline uptake, contrary to our expectation was augmented, concomitant with the transcript expression of choline transporters. Moreover, tunicamycin-induced ER stress divorced the observed increase in choline uptake from CDP-choline pathway flux since ER stress significantly diminished the incorporation and total PC content, similar to PE.Conclusion: Therefore, our results suggest that the altered FA milieu seen in obesity and fatty liver disease progression may adversely affect choline metabolism, but that compensatory mechanisms work to maintain phospholipid homeostasis.

Abstract Figure
Characterization of LXR-activating nanoparticle formulations in primary mouse macrophages
Authors: Smith Tyler KT , Kahiel Zaina , LeBlond Nicholas D , Ghorbani Peyman , Farah Eliya , Cote Marceline , Gadde Suresh , Fullerton Morgan D
Published: August 2019

Activation of the transcription factor liver X receptor (LXR), has shown to be efficient at curbing aberrant lipid metabolism and inflammation. While small molecule delivery via nanomedicine has promising applications for a number of chronic diseases, there remain questions as to how nanoparticle formulation might be tailored to suit different tissue microenvironments and aid in drug delivery. In the current study, we compared the drug delivery capability of three nanoparticle (NP) formulations encapsulating the LXR activator, GW-3956. We observed little difference in the base characteristics of standard PLGA-PEG NP when compared to two redox-active polymeric NP formulations (DD and DB). Moreover, we also observed similar uptake of these NP into primary mouse macrophages. After an initial acute uptake period and using the transcript and protein expression of the cholesterol efflux protein ATP binding cassette A1 (ABCA1) as a readout, we determined that while the induction of transcript expression was similar between NPs, treatment with the redox-sensitive DB formulation resulted in a higher level of ABCA1 protein 24 h after the removal of the drug-containing NPs. Our results suggest that NP formulations responsive to cellular cues may be an effective tool for targeted and disease-specific drug release.
Interpretation of Phase Boundary Fluctuation Spectra in Biological Membranes with Nanoscale Organization
Authors: Iyer S. S. , Negi A. , Srivastava A.
Published: August 2019

In this work, we use Support Vector Machine algorithm to detect simple and complex interfaces in atomistic and coarse-grained molecular simulation trajectories of phase separating lipid bilayer systems. We show that the power spectral density of the interfacial height fluctuations and in turn the line tension of the lipid bilayer systems depend on the order parameter used to identify the intrinsic interface. To highlight the effect of artificial smoothing of the interface on the fluctuation spectra and the ensuing line tension calculations, we perform a convolution of the boundaries identified at molecular resolution with a 2D Gaussian function of variance ε2 equal to the resolution limit, (1/2πε2)exp(−|r|2/2ε2). The convolution function is given by h⊗g, where h is the instantaneous height fluctuation and g is the Gaussian function. This is similar to the effect of point spread functions in experiments. We find that the region of fluctuation spectra that scales according to capillary wave theory formalism depends on the complexity of the interfacial geometry, which may not always be detected at experimental resolutions. We propose that the different q-regimes in the fluctuation spectra can be used to characterize mode dependent inter-facial tensions to understand the interfaces beyond the linear line tension calculations. This could also be useful in interpretation of fluctuating boundaries in out-of-equilibrium in-vivo membrane systems that carry information about the nature of non-thermal (active) fluctuations in these systems.
Mitochondrial RNA granules are fluid condensates, positioned by membrane dynamics
Authors: Rey Timo , Zaganelli Sofia , Cuillery Emilie , Martinou Jean-Claude , Manley Suliana
Published: August 2019

Mitochondria contain the genetic information and expression machinery to produce proteins essential for cellular respiration. Within the mitochondrial matrix, newly synthesized RNA, RNA processing proteins, and mitoribosome assembly factors are known to form punctate subcompartments referred to as mitochondrial RNA granules (MRGs) 1–3. Despite their proposed role in regulating gene expression, little is known about the structural and dynamic properties of MRGs. We investigated the organization of MRGs using fluorescence super-resolution localization microscopy and correlative electron microscopy techniques, obtaining ultrastructural details of their internal architecture. We find that MRGs are organized into nanoscale RNA cores surrounded by a protein shell. Using live-cell super-resolution structured illumination microscopy and photobleaching perturbations, we reveal that MRGs undergo fusion and rapidly exchange components, consistent with liquid-liquid phase separation (LLPS). Furthermore, MRGs associate with the inner mitochondrial membrane and their fusion coincides with membrane remodeling. Inhibition of mitochondrial fission leads to an aberrant distribution of MRGs into concentrated pockets, where they remain as distinct individual units despite their close apposition. Together, our results reveal a role for LLPS in concentrating RNA and its processing proteins into MRGs, which are positioned along mitochondria by membrane dynamics.
Optimization of high pressure processing to reduce the safety risk of low-salt ready-to-eat sliced turkey breast supplemented with carvacrol
Authors: Oliveira Thales Leandro Coutinho de , Haddad Gabriela de Barros Silva , Ramos Alcinéia de Lemos Souza , Ramos Eduardo Mendes , Piccoli Roberta Hilsdorf , Cristianini Marcelo
Published: August 2019

Purpose

The purpose of this paper is to evaluate the optimization of high hydrostatic pressure (HHP) processing for the microbial inactivation on low-sodium sliced vacuum-packaged turkey breast supplemented with a natural antimicrobial compound (carvacrol).

Design/methodology/approach

A response surface methodology was used to model and describe the effects of different pressures (200–650 MPa) and holding times (30–300 s) during HHP processing of low-salt ready-to-eat turkey breast supplemented with 200 mg/kg of carvacrol on survival of the target pathogen (Listeria sp.) and spoilage microflora and on the quality attributes, including pH, syneresis, CIE color and lipid oxidation.

Findings

The HHP parameters influenced (p<0.05) the lethality rates and syneresis but did not affect the pH values and lipid oxidation of the products evaluated. According to the required performance criteria for Listeria post-lethality treatment, a treatment at 600 MPa/180 s (at 25°C) appears to be suitable for the studied low-sodium product. The HHP bacterial inactivation effects can notably be potentiated via the presence of carvacrol, and is useful at sensory acceptable sub-inhibitory levels.

Originality/value

This study shows that combined HHP plus additives may produce similar safety and shelf-life extension effects with mild HHP treatments, creating a global increase in the quality of HHP-processed food in addition to reducing costs on equipment maintenance and increasing industry productivity.
When do job insecure employees adapt to change?
Authors: Lavigne Kristi N. , Whitaker Victoria L. , Jundt Dustin K. , Shoss Mindy K.
Published: August 2019

Purpose

The purpose of this paper is to examine the relationship between job insecurity and adaptive performance (AP), contingent on changes to core work tasks, which we position as a situational cue to employees regarding important work behaviors.

Design/methodology/approach

Employees and their supervisors were invited to participate in the study. Supervisors were asked to provide ratings of employees’ AP and changes to core tasks; employees reported on job insecurity.

Findings

As predicted, changes to core tasks moderated the relationship between job insecurity and AP. Job insecurity was negatively related to AP for those experiencing low levels of change, but was not related to AP for those experiencing high levels of change. Counter to expectations, no main effect of job insecurity was found.

Research limitations/implications

This study employed a fairly small sample of workers from two organizations, which could limit generalizability.

Practical implications

The study identifies changes to core tasks as a boundary condition for the job insecurity–AP relationship. Findings suggest that organizations may not observe deleterious consequences of job insecurity on AP when changes to core tasks are high.

Originality/value

Few researchers have examined boundary conditions of the impact of job insecurity on AP. Furthermore, inconsistent findings regarding the link between job insecurity and AP have emerged. This study fills the gap and expands upon previous research by examining changes to core tasks as a condition under which job insecurity does not pose an issue for AP.
Translating sustainability into competitive advantage: the case of Mexico’s hospitality industry
Authors: Gutiérrez-Martínez Isis , Duhamel Francois
Published: August 2019

Purpose

The purpose of this paper is to explore how business organizations design and implement sustainability practices to foster competitive advantage.

Design/methodology/approach

This qualitative study is based on an exploratory multiple case study involving 11 Mexican hotels recognized as “champions” in sustainability. Data gathering took place via in-depth interviews with hotel managers.

Findings

The key internal resources and capabilities must be supported by integrated microfoundations. The interaction between attributes of key resources and microfoundations reveals four transversal dimensions, namely, leadership orientation, organizational culture, team-based organizational structures and human resources and control management systems to build a sustainability-based competitive advantage in the hospitality industry.

Practical implications

The implementation of sustainability processes in the hospitality industry depends on the ability of leaders to craft systems, build commitment and align interests and goals consistent with sustainability. Business managers may find some guidance for implementing sustainability-related initiatives from the results of this paper.

Originality/value

This work presents both theoretical and practical contributions, integrating and operationalizing a set of key resources (using the VRIO framework) and microfoundations approach to create and maintain a sustainability-based competitive advantage, in contrast to existing studies where those resources and conditions are examined in a piecemeal fashion.
Development of femoral component design geometry by using DMROVAS (design method requiring optimum volume and safety)
Authors: Öztürk Burak , Erzincanli Fehmi
Published: August 2019

Purpose

This study aims to design a femoral component with minimum volume and maximum safety coefficient. Total knee prosthesis is a well-established therapy in arthroplasty applications. And in particular, with respect to damaged or weakened cartilage, new prostheses are being manufactured from bio-materials which are compatible with the human body to replace these damages. A new universal method (design method requiring optimum volume and safety [DMROVAS]) was propounded to find the optimum design parameters of tibial component.

Design/methodology/approach

The design montage was analyzed via the finite element method (FEM). To ensure the stability of the prosthesis, the maximum stress angle and magnitude of the force on the knee were taken into consideration. In the analysis process, results revealed two different maximum stress areas which were supported by case reports in the literature. Variations of maximum stress, safety factor and weight were revealed by FEM analysis, and ANOVA was used to determine the F force percentage for each of the design parameters.

Findings

Optimal design parameter levels were chosen for the individual’s minimum weight. Stress maps were constructed to optimize design choices that enabled further enhancement of the design models. The safety factor variation (SFV) of 5.73 was obtained for the volume of 39,219 mL for a region which had maximum stress. At the same time, for a maximum SFV and at the same time an average weight, values of 37,308 mL and 5.8 for volume and SFV were attained, respectively, using statistical methods.

Originality/value

This proposed optimal design development method is new and one that can be used for many biomechanical products and universal industrial designs.
On Minkowski difference-based contact detection in discrete/discontinuous modelling of convex polygons/polyhedra
Authors: Feng Y.T. , Tan Yuanqiang
Published: August 2019

Purpose

Contact detection for convex polygons/polyhedra has been a critical issue in discrete/discontinuous modelling, such as the discrete element method (DEM) and the discontinuous deformation analysis (DDA). The recently developed 3D contact theory for polyhedra in DDA depends on the so-called entrance block of two polyhedra and reduces the contact to evaluate the distance between the reference point to the corresponding entrance block, but effective implementation is still lacking.

Design/methodology/approach

In this paper, the equivalence of the entrance block and the Minkowski difference of two polyhedra is emphasised and two well-known Minkowski difference-based contact detection and overlap computation algorithms, GJK and expanding polytope algorithm (EPA), are chosen as the possible numerical approaches to the 3D contact theory for DDA, and also as alternatives for computing polyhedral contact features in DEM. The key algorithmic issues are outlined and their important features are highlighted.

Findings

Numerical examples indicate that the average number of updates required in GJK for polyhedral contact is around 6, and only 1 or 2 iterations are needed in EPA to find the overlap and all the relevant contact features when the overlap between polyhedra is small.

Originality/value

The equivalence of the entrance block in DDA and the Minkowski difference of two polyhedra is emphasised; GJK- and EPA-based contact algorithms are applied to convex polyhedra in DEM; energy conservation is guaranteed for the contact theory used; and numerical results demonstrate the effectiveness of the proposed methodologies.