bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient Functional Status at Transplant and Its Impact on Posttransplant Survival of Adult Deceased-donor Kidney Recipients
Authors: Bui Kevin , Kilambi Vikram , Rodrigue James R. , Mehrotra Sanjay
Published: August 2018

Background.

Recorded at the time of transplant and reported to the Organ Procurement and Transplantation Network, patient’s functional status is measured using the Karnofsky performance score (KPS), ranging 0 to 100. Functional status analysis may provide insights on candidate listing and posttransplant survival outcomes for deceased-donor kidney transplants.

Methods.

The cohort consisted of adult deceased-donor kidney transplant recipients transplanted beginning January 2007. One-year and 3-year Cox models for posttransplant survival were fitted with current Scientific Registry of Transplant Recipients (SRTR) variables and KPS. Comparative analyses were performed between the SRTR model without KPS and augmented model with it. Using the augmented model, we examined the impact of Kidney Donor Profile Index on posttransplant survivals for 5 different KPS strata: 10 to 30, 40 to 50, 60 to 70, 80 to 90, and 100.

Results.

Comparative analyses showed that KPS was a statistically significant predictor for posttransplant survival: it improved model calibration, discrimination, and predictive accuracy. From the augmented model, the survival curves illustrated that recipients with KPS 40 to 50 and kidneys with Kidney Donor Profile Index as high as 99 have expected survival probabilities of above 90% in 1 year and above 80% in 3 years. The expected survival probabilities improve as KPS increases. Recipients with KPS 10 to 30 have the worst survival probability, even if they received high-quality kidneys.

Conclusions.

Insights from the survival analyses recommend possible inclusion of functional status into SRTR’s risk-adjusted models. Moreover, they invite further examination of its use to improve current listing and transplantation strategies at transplant centers and potentially reduce deceased-donor kidney discard rate.
Effect of Donor Age on Outcome of Lung Transplantation Stratified by Recipient Diagnosis: A Nordic Multicenter Study
Authors: Auråen Henrik , Durheim Michael Thomas , Dellgren Göran , Hämmäinen Pekka , Larsson Hillevi , Geiran Odd , Schultz Hans Henrik Lawaetz , Leuckfeld Inga , Iversen Martin , Fiane Arnt , Holm Are Martin
Published: August 2018

Background.

Organs from older donors are increasingly used in lung transplantation, and studies have demonstrated that this could be safe in selected recipients. However, which recipient groups that have the largest benefit of older organs are unclear. This multicenter study reviews all bilateral lung transplantations (BLTx) from donors 55 years or older stratified by recipient diagnosis and compares outcomes with transplantations from younger donors.

Methods.

All BLTx recipients (excluding retransplantation) at 5 Scandiatransplant centers between 2000 and 2013 were included (n = 913). Recipients were stratified to diagnosis groups including cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD), interstitial lung disease (ILD), and “other.” Intensive care unit (ICU) length of stay (LOS) and survival were assessed.

Results.

Overall, there was no difference in survival among patients transplanted from donors 55 years or older compared with younger donors. However, in CF recipients, donor age 55 years or older was associated with inferior survival (P = 0.014), and this remained significant in a multivariate model (hazard ratio, 5.0; 95% confidence interval, 1.8–14.1; P = 0.002). There was no significant effect of donor age on survival in recipients with COPD, ILD, or in the “other” group in multivariate models. Utilization of older donors was associated with increased ICU LOS for recipients with CF and ILD, but not in the COPD or “other” group.

Conclusions.

The BLTx recipients with CF had inferior survival and longer ICU LOS when receiving organs from donors 55 years or older. Recipients with COPD, ILD, or in the “other” group did not have inferior survival in multivariate models.
Polyhexanide Versus Metronidazole for Odor Management in Malignant (Fungating) Wounds
Authors: Villela-Castro Diana Lima , Santos Vera Lucia Conceição de Gouveia , Woo Kevin
Published: August 2018

PURPOSE:

The aim of this study was to compare the effects of 0.2% polyhexamethylene biguanide (PHMB) to 0.8% metronidazole on malignant wound (MW) odor, health-related quality of life (HRQOL), and pain upon application.

DESIGN:

A double-blinded, randomized, clinical trial.

SUBJECTS AND SETTING:

Twenty-four patients with malodorous MWs hospitalized in a referral cancer center in Sao Paulo, Brazil, participated in the trial.

METHODS:

Participants were randomly allocated to treatment with 0.8% metronidazole solution (control group) or 0.2% PHMB (experimental group). Study outcomes were measured at baseline (day 0), 4 days, and 8 days. The primary end point was the odor that was measured in terms of its intensity, quality, and impact on participants during the study period. Health-related quality of life was measured with the Ferrans and Powers Quality of Life Index–Wounds Version (FPQLI-WV) on day 0 and on the day when odor was completely eliminated as per evaluation by the investigators. Pain intensity related to application of the control and experimental solutions was measured as a secondary outcome using a scale of 0 to 10.

RESULTS:

Twenty patients (83.3%) were classified as having “no wound odor” at 4 days, and 100% achieved no wound odor by day 8 (P< .001). Odor control in patients with MW significantly influenced their general HRQOL (P= .002). We found no difference in odor elimination, or HRQOL, when patients managed with PHMB were compared to those managed with metronidazole. There were no statistically significant differences over time in pain measurement between the 2 groups.

CONCLUSIONS:

Both PHMB and metronidazole significantly reduced odor in malodorous MWs within 4 days. Neither solution was found to be more effective than the other in the magnitude of odor reduction or its effect on condition-specific HRQOL.
One species, two genomes: A critical assessment of inter-isolate variation and identification of assembly incongruence inHaemonchus contortus
Authors: Wintersinger Jeff A. , Mariene Grace M. , Wasmuth James D.
Published: August 2018

Background

Numerous quality issues may compromise genomic data’s representation of its underlying organism. In this study, we compared two genomes published by different research groups for the parasitic nematodeHaemonchus contortus, corresponding to divergent isolates. We analyzed differences between the genomes, attempting to ascertain which were attributable to legitimate biological differences, and which to technical error in one or both genomes.

Results

We found discrepancies between theH. contortusgenomes in both assembly and annotation. The genomes differed in representation of genes that are highly conserved across eukaryotes, with clear evidence of misassembly underlying conserved genes missing from one genome or the other. Only 45% of genes in one genome were orthologous to genes in the other genome, with one genome exhibiting almost as much orthology toC. elegansas its counterpartH. contortusstrain. The two genomes differed substantially in probable causes underlying this unexpectedly low orthology. One genome included many more inparalogues than the other, and more frequently assembled inparalogues together on the same portions of contiguous sequence. It also exhibited cases of better-conserved gene position relative toC. elegans.

Conclusion

The discrepancies between the two genomes far exceeded those expected as a consequence of biological differences between the twoH. contortusisolates. This implies substantial quality issues in one or both genomes, suggesting that researchers must exercise caution when using genomic data for newly sequenced species.
Two-step concentration of complex water samples for the detection of viruses
Authors: Farkas Kata , McDonald James E. , Malham Shelagh K. , Jones Davey L.
Published: August 2018

The accurate detection and quantification of pathogenic viruses in water is essential to understand and reduce the risk of human infection. This paper describes a two-step method suitable for the concentration of viruses in water and wastewater samples. The method involves a tangential flow ultrafiltration step that reduces the sample volume of 1-10 l to approx. 50 ml, followed by secondary precipitation using polyethylene glycol 6000 that reduces the volume to 1-4 ml. For method validation, water samples were spiked with different concentrations of enteric viruses and viral recoveries in the concentrates exceeded 10% in all experiments. The method is suitable for water samples with high and low salinity and turbidity, allowing the accurate comparison of viral titers in a diverse range of water types. Furthermore, the method has the potential to concentrate other pathogens, e.g. bacteria or protozoa. Hence, the use of this method can improve the holistic assessment of risks associated with wastewater-contaminated environments.
Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis
Authors: Lees John A. , Ferwerda Bart , Kremer Philip H. C. , Wheeler Nicole E. , Valls Serón Mercedes , Croucher Nicholas J. , Gladstone Rebecca A. , Bootsma Hester J. , Rots Nynke , Wijmega-Monsuur Alienke J. , Sanders Elisabeth A. M. , Trzciński Krzysztof , Wyllie Anne L. , Zwinderman Aeilko H. , den Berg Leonard H. van , Rheenen Wouter van , H. Veldink Jan , Harboe Zitta B. , Lundbo Lene F. , Groot Lisette C. P. G. M. de , Schoor Natasja M. van , Velde Nathalie van der , Ängquist Lars H. , Sørensen Thorkild I.A. , Nohr Ellen A. , Mentzer Alexander J. , C. Mills Tara , Knight Julian C. , du Plessis Mignon , Nzenze Susan , N. Weiser Jeffrey , Parkhill Julian , Madhi Shabir , Benfield Thomas , von Gottberg Anne , Ende Arie van der , Brouwer Matthijs C. , Barrett Jeffrey C. , Bentley Stephen D. , de Beek Diederik van
Published: August 2018

Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, and identified variants in CCDC33 associated with susceptibility. Pneumococcal variation explained a large amount of invasive potential, but serotype explained only half of this variation. Newly developed methods identified pneumococcal genes involved in invasiveness including pspC and zmpD, and allowed a human-bacteria interaction analysis, finding associations between pneumococcal lineage and STK32C.
Establishing Synthesis Pathway-Host Compatibility via Enzyme Solubility
Authors: Amin Sara A. , Gopinarayanan Venkatesh Endalur , Nair Nikhil U. , Hassoun Soha
Published: August 2018

Current pathway synthesis tools identify possible pathways that can be added to a host to produce a desired target molecule through the exploration of abstract metabolic and reaction network space. However, not many of these tools do explore gene-level information required to physically realize the identified synthesis pathways, and none explore enzyme-host compatibility. Developing tools that address this disconnect between abstract reactions/metabolic design space and physical genetic sequence design space will enable expedited experimental efforts that avoid exploring unprofitable synthesis pathways. This work describes a workflow, termed Probabilistic Pathway Assembly with Solubility Scores (ProPASS), which links synthesis pathway construction with the exploration of the physical design space as imposed by the availability of enzymes with characterized activities within the host. Predicted protein solubility propensity scores are used as a confidence level to quantify the compatibility of each pathway enzyme with the host (E. coli). This work also presents a database, termed Protein Solubility Database (ProSol DB), which provides solubility confidence scores inE. colifor 240,016 characterized enzymes obtained fromUniProtKB/Swiss-Prot. The utility ofProPASSis demonstrated by generating genetic implementations of heterologous synthesis pathways inE. colithat target several commercially useful biomolecules.

Availability

ProSol DBdata and code forProPASSare available for download fromhttps://github.com/HassounLab/
An Evolutionarily Conserved piRNA-producing Locus Required for Male Mouse Fertility
Authors: Wu Pei-Hsuan , Fu Yu , Cecchini Katharine , Özata Deniz M. , Arif Amena , Yu Tianxiong , Colpan Cansu , Gainetdinov Ildar , Weng Zhiping , Zamore Phillip D.
Published: August 2018

Pachytene piRNAs, which comprise >80% of small RNAs in the adult mouse testis, have been proposed to bind and regulate target RNAs like miRNAs, cleave targets like siRNAs, or lack biological function altogether. Although piRNA pathway protein mutants are male sterile, no biological function has been identified for any mammalian piRNA-producing locus. Here, we report that males lacking piRNAs from a conserved mouse pachytene piRNA locus on chromosome 6 (pi6) produce sperm with defects in capacitation and egg fertilization. Moreover, heterozygous embryos sired bypi6−/−fathers show reduced viability in utero. Molecular analyses suggest thatpi6piRNAs repress gene expression by cleaving mRNAs encoding proteins required for sperm function.pi6also participates in a network of piRNA-piRNA precursor interactions that initiate piRNA production from a second piRNA locus on chromosome 10 as well aspi6itself. Our data establish a direct role for pachytene piRNAs in spermiogenesis and embryo viability.

Highlights

Normal male mouse fertility and spermiogenesis require piRNAs from thepi6locus

Sperm capacitation and binding to the zona pellucida of the egg requirepi6piRNAs

Heterozygous embryos sired bypi6−/−fathers show reduced viability in utero

Defects inpi6mutant sperm reflect changes in the abundance of specific mRNAs.
iProteinDB: an integrative database of Drosophila post-translational modifications
Authors: Hu Yanhui , Sopko Richelle , Chung Verena , Studer Romain A. , Landry Sean D. , Liu Daniel , Rabinow Leonard , Gnad Florian , Beltrao Pedro , Perrimon Norbert
Published: August 2018

Post-translational modification (PTM) serves as a regulatory mechanism for protein function, influencing stability, protein interactions, activity and localization, and is critical in many signaling pathways. The best characterized PTM is phosphorylation, whereby a phosphate is added to an acceptor residue, commonly serine, threonine and tyrosine. As proteins are often phosphorylated at multiple sites, identifying those sites that are important for function is a challenging problem. Considering that many phosphorylation sites may be non-functional, prioritizing evolutionarily conserved phosphosites provides a general strategy to identify the putative functional sites with regards to regulation and function. To facilitate the identification of conserved phosphosites, we generated a large-scale phosphoproteomics dataset from Drosophila embryos collected from six closely-related species. We built iProteinDB (https://www.flyrnai.org/tools/iproteindb/), a resource integrating these data with other high-throughput PTM datasets, including vertebrates, and manually curated information for Drosophila. At iProteinDB, scientists can view the PTM landscape for any Drosophila protein and identify predicted functional phosphosites based on a comparative analysis of data from closely-related Drosophila species. Further, iProteinDB enables comparison of PTM data from Drosophila to that of orthologous proteins from other model organisms, including human, mouse, rat, Xenopus laevis, Danio rerio, and Caenorhabditis elegans.
Lateral gene transfer shapes the distribution of RuBisCO among Candidate Phyla Radiation bacteria and DPANN archaea
Authors: Jaffe Alexander L. , Castelle Cindy J. , Dupont Christopher L. , Banfield Jillian F.
Published: August 2018

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the most abundant enzyme on Earth. Despite this, its full diversity and distribution across the domains of life remain to be determined. Here, we leverage a large set of bacterial, archaeal, and viral genomes recovered from the environment to expand our understanding of existing RuBisCO diversity and the evolutionary processes responsible for its distribution. Specifically, we report a new type of RuBisCO present in Candidate Phyla Radiation (CPR) bacteria that is related to the archaeal Form III enzyme and contains the amino acid residues necessary for catalytic activity. Genome-level metabolic analyses supported the inference that these RuBisCO function in a nucleotide-based, CO2-incorporating pathway. Importantly, some Gottesmanbacteria (CPR) also encode a phosphoribulokinase that may augment carbon metabolism through a partial Calvin-Benson-Bassham Cycle. Based on the scattered distribution of RuBisCO and its discordant evolutionary history, we conclude that this enzyme has been extensively laterally transferred across the CPR bacteria and DPANN archaea. We also report RuBisCO-like proteins in phage genomes from diverse environments. These sequences cluster with proteins in the Beckwithbacteria (CPR), implicating phage as a possible mechanism of RuBisCO transfer. Finally, we synthesize our metabolic and evolutionary analyses to suggest that lateral gene transfer of RuBisCO may have facilitated major shifts in carbon metabolism in several important bacterial and archaeal lineages.
Locomotion-dependent remapping of distributed cortical networks
Authors: Clancy Kelly B. , Orsolic Ivana , Mrsic-Flogel Thomas D.
Published: August 2018

The interactions between areas of the neocortex are fluid and state-dependent, but how individual neurons couple to cortex-wide network dynamics remains poorly understood. We correlated the spiking of individual neurons in primary visual (V1) and retrosplenial (RSP) cortex to activity across dorsal cortex, recorded simultaneously by calcium imaging. Individual neurons were correlated with distinct and reproducible patterns of activity across the cortical surface; while some fired predominantly with their local area, others coupled to activity in subsets of distal areas. The extent of distal coupling was predicted by how strongly neurons correlated with the local network. Changes in brain state triggered by locomotion re-structured how neurons couple to cortical activity patterns: running strengthened affiliations of V1 neurons with visual areas, while strengthening distal affiliations of RSP neurons with sensory cortices. Thus, individual neurons within a cortical area can independently engage in different cortical networks depending on the animal's behavioral state.
Can patients with cerebellar disease switch learning mechanisms to reduce their adaptation deficits?
Authors: Wong Aaron L. , Marvel Cherie L. , Taylor Jordan A. , Krakauer John W.
Published: August 2018

Systematic perturbations in motor adaptation tasks are primarily countered by learning from sensory-prediction errors, with secondary contributions from other learning processes. Despite the availability of these additional processes, particularly the use of explicit re-aiming to counteract observed target errors, patients with cerebellar degeneration are surprisingly unable to compensate for their sensory-prediction-error deficits by spontaneously switching to another learning mechanism. We hypothesized that if the nature of the task was changed – by allowing vision of the hand, which eliminates sensory-prediction errors – patients could be induced to preferentially adopt aiming strategies to solve visuomotor rotations. To test this, we first developed a novel visuomotor rotation paradigm that provides participants with vision of their hand in addition to the cursor, effectively setting the sensory-prediction-error signal to zero. We demonstrated in younger healthy controls that this promotes a switch to strategic re-aiming based on target errors. We then showed that with vision of the hand, patients with spinocerebellar ataxia could also switch to an aiming strategy in response to visuomotor rotations, performing similarly to age-matched participants (older controls). Moreover, patients could retrieve their learned aiming solution after vision of the hand was removed, and retain it for at least one year. Both patients and older controls, however, exhibited impaired overall adaptation performance compared to younger healthy controls (age, 18-33), likely due to age-related reductions in spatial and working memory. Moreover, patients failed to generalize, i.e., they were unable to adopt analogous aiming strategies in response to novel rotations, nor could they further improve their performance without vision of the hand. Hence, there appears to be an inescapable obligatory dependence on sensory-prediction-error-based learning – even when this system is impaired in patients with cerebellar degeneration. The persistence of sensory-prediction-error-based learning effectively suppresses a switch to target-error-based learning, which perhaps explains the unexpectedly poor performance by patients with spinocerebellar ataxia in visuomotor adaptation tasks.
Transcriptional regulation of voltage-gated sodium channels contributes to GM-CSF induced pain
Authors: Zhang Fan , Wang Yiying , Zhang Dandan , Fan Xizhenzi , Han Hao , Du Xiaona , Gamper Nikita , Zhang Hailin
Published: August 2018

Granolocyte-macrophage colony stimulating factor (GM-CSF) induces production of granulocyte and macrophage populations from the hematopoietic progenitor cells; it is one of the most common growth factors in the blood. GM-CSF is also involved in bone cancer pain development by regulating tumor-nerve interactions, remodeling of peripheral nerves and sensitization of damage-sensing (nociceptive) nerves. However, the precise mechanism for GM-CSF-dependent pain is unclear. In this study, we found that GM-CSF is highly expressed in human malignant osteosarcoma. Rats implanted with bone cancer cells develop mechanical and thermal hyperalgesia but antagonizing GM-CSF in these animals significantly reduced such hypersensitivity. Nociceptor-specific voltage gated Na+channels Nav1.7, Nav1.8 and Nav1.9 were found to be selectively up-regulated in rat DRG neurons treated with GM-CSF, which resulted in enhanced excitability. GM-CSF activated the Jak2 and Stat3 signaling pathway which promoted the transcription of Nav1.7-1.9 in DRG neurons. Accordingly targeted knocking down either Nav1.7-1.9 or Jak2/Stat3 in DRG neurons alleviated the hyperalgesia in rats. Our findings describe a new bone cancer pain mechanism and provide a new insight into the physiological and pathological functions of GM-CSF.
Familiarity increases aggressiveness among clonal fish
Authors: Doran Carolina , Bierbach David , Laskowski Kate L.
Published: August 2018

Understanding how animal groups form and function is a major goal in behavioural ecology. Both genetic relatedness and familiarity among group mates have been shown to be key mediators of group composition. However, disentangling the two in most species is challenging as the most familiar individuals are often the most related, and vice versa. In order to gain a complete understanding of how individual interactions shape group behaviour it is crucial to understand the role each of this social relationship factors plays individually. To this end, we manipulated the level of familiarity among groups of the naturally clonal, and genetically identical fish, the Amazon molly (Poecilia formosa) and monitored group behaviour in an open-field and when given the opportunity to forage. Contrary to our predictions, fish that were the most familiar with each other showed the highest levels of aggression. Additionally, fish that were less familiar with each other exhibited the highest group cohesion and took the longest to begin feeding, compared to the more familiar fish. These results suggest that familiarity may socially buffer individuals from the perception of risk in novel environments, such as is common in most behavioural tests designed to test group behaviour. Increases in aggression that are associated with increasing familiarity as shown here might be a mechanism by which fish maintain a fission-fusion society with important consequences for the patterns of associations in group living animals.
Camphor white oil induces tumor regression through cytotoxic T cell-dependent mechanisms
Authors: Moayedi Yalda , Greenberg Sophie A , Jenkins Blair A , Marshall Kara L , Dimitrov Lina V , Nelson Aislyn M , Owens David M , Lumpkin Ellen A
Published: August 2018

Bioactive derivatives from the camphor laurel tree,Cinnamomum camphora, are posited to exhibit chemopreventive properties but the efficacy and mechanism of these natural products have not been established. We tested an essential-oil derivative, camphor white oil (CWO), for anti-tumor activity in a mouse model of keratinocyte-derived skin cancer. Daily topical treatment with CWO induced dramatic regression of pre-malignant skin tumors and a two-fold reduction in cutaneous squamous cell carcinomas. We next investigated underlying cellular and molecular mechanisms. In cultured keratinocytes, CWO stimulated calcium signaling, resulting in calcineurin-dependent activation of nuclear factor of activated T cells (NFAT).In vivo, CWO induced transcriptional changes in immune-related genes, resulting in cytotoxic T cell-dependent tumor regression. Finally, we identified chemical constituents of CWO that recapitulated effects of the admixture. Together, these studies identify T cell-mediated tumor regression as the mechanism through which a plant-derived essential oil diminishes established tumor burden.

SUMMARY BLURB

Essential oil derived from the camphor tree acts by stimulating immune cell-dependent regression of skin tumors in a mouse model of cutaneous squamous cell carcinoma.
Shared genetic aetiology between cognitive performance and brain activations in language and math tasks
Authors: Guen Yann Le , Amalric Marie , Pinel Philippe , Pallier Christophe , Frouin Vincent
Published: August 2018

Cognitive performance is highly heritable. However, little is known about common genetic influences on cognitive ability and brain activation when engaged in a cognitive task. The Human Connectome Project (HCP) offers a unique opportunity to study this shared genetic etiology with an extended pedigree of 785 individuals. To investigate this common genetic origin, we took advantage of the HCP dataset, which includes both language and mathematics activation tasks. Using the HCP multimodal parcellation, we identified areals in which inter-individual functional MRI (fMRI) activation variance was significantly explained by genetics. Then, we performed bivariate genetic analyses between the neural activations and behavioral scores, corresponding to the fMRI task accuracies, fluid intelligence, working memory and language performance. We observed that several parts of the language network along the superior temporal sulcus, as well as the angular gyrus belonging to the math processing network, are significantly genetically correlated with these indicators of cognitive performance. This shared genetic etiology provides insights into the brain areas where the human-specific genetic repertoire is expressed. Studying the association of polygenic risk scores, using variants associated with human cognitive ability and brain activation, would provide an opportunity to better understand where these variants are influential.
Directed exploration in the Iowa Gambling Task: model-free and model-based analyses in a large dataset of young and old healthy participants
Authors: Ligneul Romain
Published: August 2018

The Iowa Gambling Task (IGT) is one of the most common paradigms used to assess decision-making and executive functioning in neurological and psychiatric disorders. Several reinforcement-learning (RL) models were recently proposed to refine the qualitative and quantitative inferences that can be made about these processes based on IGT data. Yet, these models do not account for the complex exploratory patterns which characterize participants’ behavior in the task. Using a dataset of more than 500 subjects, we demonstrate the existence of such patterns and we describe a new computational architecture (Explore-Exploit) disentangling exploitation, random exploration and directed exploration in this large population of participants. The EE architecture provided a better fit to the choice data on multiple metrics. Parameter recovery and simulation analyses confirmed the superiority of the EE scheme over alternative schemes. Furthermore, using the EE model, we were able to replicate the reduction in directed exploration across lifespan, as previously reported in other paradigms. Finally, we provide a user-friendly toolbox enabling researchers to easily fit computational models on the IGT data, hence promoting reanalysis of the numerous datasets acquired in various populations of patients.
Blocking the Necroptosis Pathway Decreases RPE and Photoreceptor Damage Induced by NaIO3
Authors: Lin Haijiang , Roh Miin , Matsumoto Hidetaka , Atik Alp , Bouzika Peggy , Alhatem Albert , Miller Joan W. , Vavvas Demetrios G.
Published: August 2018

Purpose

Sodium iodate (NaIO3) has been extensively used as a retinotoxin to induce RPE cell damage and degeneration of photoreceptorsin vitroandin vivo. RIP-Kinase dependent programmed necrosis is an important redundant cell death pathway involved in photoreceptor cell death. We wanted to determine whether these pathways are actively involved in RPE and photoreceptor cell death after NaIO3 insult.

Methods

ARPE-19 cells were exposed to different concentrations of NaIO3 in the presence or absence of various concentrations of a RIPK inhibitor (Nec-1) or a pan-caspase inhibitor (Z-VAD), individually or combined. Cell death was determined at different time points by MTT (Sigma-Aldrich), LDH (Promega) and TUNEL (Millipore) assay. C57BL/6 and RIP3−/-mice were treated with a peritoneal injection of NaIO3 and eyes were enucleated at day 3 or 7. TUNEL staining was used to evaluate photoreceptor cell death. Photoreceptor cell loss was evaluated by measuring the thickness of outer nuclear layer (ONL). Microglia in the ONL were quantified in a retinal whole mount with Iba-1 antibody. RPE degeneration was also assessed in a RPE whole mount, with ZO-1 antibody.

Results

NaIO3 resulted in significant cell death of ARPE-19 cells. Treatment with Nec-1 resulted in better protection than treatment with Z-VAD (P<0.01). A synergistic protective effect was observed when co-treating the cells with Nec-1 and Z-VAD. Nec-1 treatment also decreased the ARPE-19 mitochondrial damage caused by NaIO3.In vivoadministration of NaIO3 resulted in significant RPE and photoreceptor destruction with substantial inflammatory cell infiltration. RIP3 knockout animals displayed considerably less RPE and photoreceptor cell loss, as well as drastically less inflammation.

Conclusions

Programmed necrosis is an important cell death pathway mediating NaIO3 RPE and photoreceptor cell toxicity. Blocking the necroptosis pathway may serve as a novel therapeutic strategy for various RPE degenerative diseases.
Non-linear causality between exchange rates, inflation, interest rate differential and terms of trade in Tunisia
Authors: Charef Fahima , Ayachi Fethi
Published: August 2018

Purpose

The purpose of this paper is to investigate the dynamic relationship between inflation, interest rate differential, the exchange trade and exchange rate parities, i.e. (USD/TND, EUR/TND and JPY/TND).

Design/methodology/approach

Given the existing non-linear form between the different time series in this study, the empirical analysis is based on the using of non-parametric method such as the artificial neural networks. In order to detect the causality relationship between the variables, the authors use an NARX model.

Findings

Mixed results were found; there is a bidirectional relationship between inflation and exchange rate among others. Results also show that there is a strong correlation between the terms of trade and inflation, which says that trade openness increases the demand for imported goods and, therefore, causes more inflation for Tunisia.

Originality/value

After these results, it is important for policymakers to know which factors influence exchange rate stability, especially in developing countries like Tunisia.
Quality changes of nugget prepared from fresh and smoked rainbow trout during chilled storage
Authors: Duman Muhsine , Karaton Kuzgun Nermin
Published: August 2018

Purpose

The purpose of this paper is to produce fish nugget from fresh or smoked fish and to investigate the quality characteristics of fish nuggets during refrigerated storage.

Design/methodology/approach

The study was designed to evaluate the effect of fresh and smoked fish on the storage quality parameters of fish nuggets. The products were developed by incorporating optimum level of fresh and smoked separately and were vacuum packaged in low-density polyethylene pouches and assessed for various storage quality parameters under refrigerated (2±1°C) conditions for 27 days of storage. The products were evaluated for various chemical, microbiological and sensory parameters at regular interval of three day.

Findings

Nuggets from smoked fish had lower (p<0.05) moisture, higher fat and crude protein compared to fresh fish nuggets. Total volatile basic nitrogen for fresh nugget samples exceeded the limit value of 30 mg N/100 g fish muscle on the 24 days of storage. At the end of storage period, TBA values were 2.8 mg malonaldehyde/kg for fresh nugget samples and 2.1 mg malonaldehyde/kg for smoked nugget samples. Microbial counts were found to be significantly (p<0.05) higher in fresh nugget than in smoked nugget samples. Sensory quality scores of smoked nuggets were significantly higher, than fresh nugget. The shelf life of fish nugget was found to be 24 days for fresh nuggets and 27 days for smoked nugget samples according to sensory assessment results.

Originality/value

The paper has demonstrated that the smoked fish meat prouduce nuggets of better quality, as indicated by lower microbial counts and higher sensory attributes compared to fresh fish meat.
Motivation-based segmentation of local food in urban cities
Authors: Arsil Poppy , Li Elton , Bruwer Johan , Lyons Graham
Published: August 2018

Purpose

The purpose of this paper is twofold: first, to investigate the motives of urban consumers when purchasing local food products using means-end chain (MEC) analysis and second, to introduce an alternative approach to segment the market based on consumers’ motivation using decision segmentation analysis (DSA).

Design/methodology/approach

DSA was used as advanced segmentation procedure of hierarchy value maps (HVMs) produced by MEC analysis.

Findings

The findings suggest that there are two main segments of local food consumers in urban Indonesia: value-for-money and health benefits. The value-for-money segment is dominant when making local food purchasing.

Research limitations/implications

This study sample is not representative of local food consumers in urban Indonesia as only three urban cities were interviewed.

Practical implications

An understanding of the motivation-based segmentation of local food in urban cities is a useful tool in order to reinforce and attract local food consumers to consume more locally grown food.

Originality/value

This study reveals the motivation-based segmentation of local food in urban cities in Indonesia.
Exploring the visual appeal of food guide graphics
Authors: Truman Emily
Published: August 2018

Purpose

Food guides are graphic representations of food-based dietary guidelines that support national health policies and programming. They are visual aids simplifying complex nutritional messaging for the public. While pyramid and circle formats are the most common shapes in use worldwide, the dinner plate format is increasing in use due to its perceived effectiveness. However, research examining visual attributes of food guide graphics, and the dinner plate model specifically, is limited. The purpose of this paper is to systematically compare and analyse key visual attributes of plate food guide graphics (across multiple examples) to assess their potential for effective visual communication of nutrition messaging.

Design/methodology/approach

This study engages in a qualitative analysis of compositional elements of food guide graphics. Data collection and analysis are grounded in the methods of compositional interpretation, which includes a qualitative, descriptive approach to establishing a thematic survey of the data.

Findings

Unique visual attributes of the plate food guide (including image content, spatial organisation and expressive content) present challenges in the communication of key nutritional messaging regarding proportionality, moderation and overall usability.

Practical implications

A better understanding of the visual attributes of the plate food guide model will contribute to improved design and development of this key public health tool by researchers, educators and health practitioners. Additionally, the examination of visual attributes has implications for the study of food guide understanding and use.

Originality/value

This study highlights the need for critical visual skills in qualitative health research, and to address gaps in health education more broadly.
Studies on the potential application of various blends of essential oils as antioxidant and antimicrobial preservatives in emulsion based chicken sausages
Authors: Sharma Heena , Mendiratta Sanjod K. , Agrawal Ravi Kant , Talukder Suman , Kumar Sudheer
Published: August 2018

Purpose

Oxidative rancidity is a major problem in chicken meat because of its higher content of polyunsaturated fatty acids. Besides this, microbial contamination is also one of the major problems of chicken meat which leads to deterioration in quality during storage. Therefore, the purpose of this paper is to investigate anti-microbial and anti-oxidant effects of various blends of essential oils (EOs) on the quality of emulsion-based (ready-to-eat) chicken sausages.

Design/methodology/approach

Sausages were incorporated with optimum level of four different blends of EOs containing six different EOs (Clove oil, Holybasil oil, Thyme oil, Cassia oil, Ajowan oil and Beetel oil), namely, Blend-1 (0.25 per cent), Blend-2 (0.25 per cent), Blend-3 (0.25 per cent) and Blend-4 (0.125 per cent); vacuum packaged and stored at −18±1°C for 60 days. Duplicate samples were taken for each parameter, and three trials were conducted for each experiment, total being six observations (n=6) for consistency of the results.

Findings

Significant decrease (p<0.05) in pH of control products was observed at each interval of storage period; however, in case of treatment products, significant decrease (p<0.05) was noticed from day 30 onwards. Blend-2 was observed with significantly lower (p<0.05) thio-barbituric acid reacting substances followed by Blend-1. Significantly lower (p<0.05) total phenolics content was observed in Blend-4 products as compared to other treatments. Regarding DPPH activity, control products showed significant decrease (p<0.05); however, in case of treatment products, DPPH activity showed significant (p<0.05) decrease after day 15 of storage. Microbial count increased with progressive storage period; however, the counts were well below the permissible limit of frozen meat products. All the blend incorporated products received very good sensory scores in consistent manner.

Practical implications

The work under this study would be very useful for the meat processing industries dealing with the perishable meat products. Use of natural anti-oxidants will also restore faith towards the consumers who are becoming more health conscious day by day.

Originality/value

The research work is original.
Halal logistics service quality: conceptual model and empirical evidence
Authors: Zailani Suhaiza , Jafarzadeh Shima , Iranmanesh Mohammad , Nikbin Davoud , Selim Nur Izatul Irani
Published: August 2018

Purpose

The purpose of this paper is to devise and test a model of halal logistic service quality.

Design/methodology/approach

To develop the halal logistics service quality model, the relevant literature was reviewed and a qualitative study was carried out on halal logistics service providers and their customers. A survey of 253 halal food and beverage firms in Malaysia was conducted, and based on the results, a model was developed and tested empirically.

Findings

Based on the literature review, interviews, pretest and empirical study, a valid and reliable measurement instrument for halal logistics service quality was developed.

Practical implications

The findings can help managers of halal logistics service providers to understand the criteria that halal food and beverage firms are considered to judge the quality of halal logistics services.

Originality/value

This study makes a valuable contribution by proposing a halal logistics service quality model.
Influence of sensory attributes on consumers’ emotions and hedonic liking of chocolate
Authors: Schouteten Joachim J. , De Pelsmaeker Sara , Juvinal Joel , Lagast Sofie , Dewettinck Koen , Gellynck Xavier
Published: August 2018

Purpose

The purpose of this paper is to examine the influence of sensory attributes of milk chocolate on consumers’ emotions and their hedonic ratings using three commercial brands of milk chocolate.

Design/methodology/approach

Quantitative descriptive analysis by a trained panel (n=8) was performed to obtain the sensory evaluation of the samples. A group of 127 consumers evaluated the samples to indicate their hedonic ratings (nine-point hedonic scale) and emotions (EsSense Profile®).

Findings

The sensory profiles for the three chocolate types showed clear differences. EsSense Profile® methodology revealed that each type of chocolate had a distinct emotional profile. The premium brand was associated with the highest number of positive emotions, whereas the traditional brand was associated with most of the negative emotions (“bored”, “disgusted” and “worried”). The drivers of liking were mainly positive and unclassified emotions. Also, gender differences in emotional profiling were found.

Practical implications

This study illustrates that sensory and emotional measurements can contribute to a better understanding of consumers’ hedonic liking. Moreover, gender differences found in emotional profiling should raise awareness that gender may lead to different emotional profiling. These gender differences are of interest to food companies, for instance, for food product development or marketing purposes.

Originality/value

This study further contributes to the growing literature on emotions. By combining sensory evaluation by a trained panel and emotional profiling by consumers, this paper explores how combining these measurements can contribute to a better understanding of the drivers of liking for milk chocolate.
Classification of pork quality by hierarchical cluster analysis
Authors: Torres Filho Robledo de Almeida , Silva Vanelle Maria da , Rodrigues Lorena Mendes , Fontes Paulo Rogério , Ramos Alcinéia de Lemos Souza , Ramos Eduardo Mendes
Published: August 2018

Purpose

The purpose of this paper is to evaluate the classification ability of pork quality by cluster analysis in relation to reference criteria proposed in the literature. Verify if clusters were theoretically significant with major pork quality categories. Verify if classificatory parameter values of quality attributes determined “a posteriori” may be used for following categorization.

Design/methodology/approach

In total, 60 pork loins were classified into pale, soft and exudative, reddish-pink, soft and exudative, RFN and dark, firm and dry by reference criteria and hierarchical cluster analyses were performed to identify groups of samples with different attributes, based on only pH45min and on pHu, L* and drip loss.

Findings

Cluster analysis divided total samples into different (p<0.05) smaller groups. Two groups were formed based on only pH45min and five groups were formed based on pHu, L* and drip loss. By these five groups, L* of 44 and 52 distinguished between dark, reddish-pink and pale meat colors and drip loss of 2 and 6 percent distinguished between dry, non-exudative and exudative meats. Cluster analyses identify pork groups with different attributes and the proposed parameters can be used to distinguish between groups theoretically similar to major pork quality categories.

Originality/value

To decide the best destination to pork carcass and to reduce economic losses, the correctly classify of the pork quality is decisive. This study proves that cluster analysis is able to classify pork into groups with significantly different quality attributes, which are significant with major pork quality categories, without unclassified samples.
Combining means-end chain analysis and goal-priming to analyze Tanzanian farmers’ motivations to invest in quality seed of new potato varieties
Authors: Okello Julius J. , Lagerkvist C.J. , Kakuhenzire Rogers , Parker Monica , Schulte-Geldermann Elmar
Published: August 2018

Purpose

Potato is a major food staple in Africa, but its production is constrained by poor quality of seed. A recent private–public partnership in Tanzania resulted in introduction of new higher yielding varieties. The purpose of this paper is to examine smallholder farmers’ motivations to invest in the purchase of quality seed of new potato varieties, and if the motivational structure differs by gender.

Design/methodology/approach

The paper used means-end chain (MEC) theory combined with goal priming, and laddering interviews on randomly sampled participants (n=45) of an experimental auction conducted among smallholder farmers in Tanzania. The auction was designed to goal-prime respondents on benefits of quality seed. The mental constructs obtained were grouped into attributes, consequences and values, and MECAnalyst software used to generate hierarchical value maps.

Findings

Farmers invest in quality seed of a new variety to increase yields, hence income, and also to pursue personal life goals (values) or meet psychosocial needs. The structure of mental constructs associated with the decision to invest in quality seed of a new variety differ by gender.

Research limitations/implications

The study focused on only two new varieties, hence not robust to all new potato varieties. Results need to be tested under different socioeconomic contexts. Furthermore, the MEC approach does not allow for control of other variables that likely influence farmer adoption decision-making process. Future studies should be designed to tackle these limitations.

Practical implications

Investment in quality seed of new variety is driven by monetary goals and psychosocial factors, and some of these factors differ between male and female farmers.

Originality/value

This is the first study to explore drivers of farmers’ decision to use quality seed of a new variety using MEC analysis, and role psychosocial factors play.