bluuebunny/crossref_metadata_2025 huggingface dataset:
Community disassembly and disease: realistic—but not randomized—biodiversity losses enhance parasite transmission
Authors: Johnson Pieter T. J. , Calhoun Dana M. , Riepe Tawni , McDevitt-Galles Travis , Koprivnikar Janet
Published: May 2019

Debates over the relationship between biodiversity and disease dynamics underscore the need for a more mechanistic understanding of how changes in host community composition influence parasite transmission. Focusing on interactions between larval amphibians and trematode parasites, we experimentally contrasted the effects of host richness and species composition to identify the individual and joint contributions of both parameters on the infection levels of three trematode species. By combining experimental approaches with field surveys from 147 ponds, we further evaluated how richness effects differed between randomized and realistic patterns of species loss (i.e. community disassembly). Our results indicated that community-level changes in infection levels were owing to host species composition, rather than richness. However, when composition patterns mirrored empirical observations along a natural assembly gradient, each added host species reduced infection success by 12–55%. No such effects occurred when assemblages were randomized. Mechanistically, these patterns were due to non-random host species assembly/disassembly: while highly competent species predominated in low diversity systems, less susceptible hosts became progressively more common as richness increased. These findings highlight the potential for combining information on host traits and assembly patterns to forecast diversity-mediated changes in multi-host disease systems.
Patterns of mammalian jaw ecomorphological disparity during the Mesozoic/Cenozoic transition
Authors: Benevento Gemma Louise , Benson Roger B. J. , Friedman Matt
Published: May 2019

The radiation of mammals after the Cretaceous/Palaeogene (K/Pg) boundary was a major event in the evolution of terrestrial ecosystems. Multiple studies point to increases in maximum body size and body size disparity, but patterns of disparity for other traits are less clear owing to a focus on different indices and subclades. We conducted an inclusive comparison of jaw functional disparity from the Early Jurassic–latest Eocene, using six mechanically relevant mandibular ratios for 256 species representing all major groups. Jaw functional disparity across all mammals was low throughout much of the Mesozoic and remained low across the K/Pg boundary. Nevertheless, the K/Pg boundary was characterized by a pronounced pattern of turnover and replacement, entailing a substantial reduction of non-therian and stem-therian disparity, alongside a marked increase in that of therians. Total mammal disparity exceeded its Mesozoic maximum for the first time during the Eocene, when therian mammals began exploring previously unoccupied regions of function space. This delay in the rise of jaw functional disparity until the Eocene probably reflects the duration of evolutionary recovery after the K/Pg mass extinction event. This contrasts with the more rapid expansion of maximum body size, which occurred in the Palaeocene.
Dietary macronutrient content, age-specific mortality and lifespan
Authors: Senior Alistair M. , Solon-Biet Samantha M. , Cogger Victoria C. , Le Couteur David G. , Nakagawa Shinichi , Raubenheimer David , Simpson Stephen J.
Published: May 2019

Protein and calorie restrictions extend median lifespan in many organisms. However, studies suggest that among-individual variation in the age at death is also affected. Ultimately, both of these outcomes must be caused by effects of nutrition on underlying patterns of age-specific mortality (ASM). Usingmodel life tables, we tested for effects of dietary macronutrients on ASM in mice (Mus musculus). High concentrations of protein and fat relative to carbohydrates were associated with low life expectancy and high variation in the age at death, a result caused predominantly by high mortality prior to middle age. A lifelong diet comprising the ratio of macronutrients self-selected by mouse (in early adulthood) was associated with low mortality up until middle age, but higher late-life mortality. This pattern results in reasonably high life expectancy, but very low variation in the age at death. Our analyses also indicate that it may be possible to minimize ASM across life by altering the ratio of dietary protein to carbohydrate in the approach to old age. Mortality in early and middle life was minimized at around one-part protein to two-parts carbohydrate, whereas in later life slightly greater than equal parts protein to carbohydrate reduced mortality.
A methodology for morphological feature extraction and unsupervised cell classification
Authors: Bhaskar Dhananjay , Lee Darrick , Knútsdóttir Hildur , Tan Cindy , Zhang MoHan , Dean Pamela , Roskelley Calvin , Edelstein-Keshet Leah
Published: May 2019

Cell morphology is an important indicator of cell state, function, stage of development, and fate in both normal and pathological conditions. Cell shape is among key indicators used by pathologists to identify abnormalities or malignancies. With rapid advancements in the speed and amount of biological data acquisition, including images and movies of cells, computer-assisted identification and analysis of images becomes essential. Here, we report on techniques for recognition of cells in microscopic images and automated cell shape classification. We illustrate how our unsupervised machine-learning-based approach can be used to classify distinct cell shapes from a large number of microscopic images.

Technical Abstract

We develop a methodology to segment cells from microscopy images and compute quantitative descriptors that characterize their morphology. Using unsupervised techniques for dimensionality reduction and density-based clustering, we perform label-free cell shape classification. Cells are identified with minimal user input using mathematical morphology and region-growing segmentation methods. Physical quantities describing cell shape and size (including area, perimeter, Feret diameters, etc.) are computed along with other features including shape factors and Hu’s image moments.

Correlated features are combined to obtain a low-dimensional (2-D or 3-D) embedding of data points corresponding to individual segmented cell shapes. Finally, a hierarchical density-based clustering algorithm (HDBSCAN) is used to classify cells. We compare cell classification results obtained from different combinations of features to identify a feature set that delivers optimum classification performance for our test data consisting of phase-contrast microscopy images of a pancreatic-cancer cell line, MIA PaCa-2.
Regulation of Cyclin E by transcription factors of the naïve pluripotency network in mouse embryonic stem cells
Authors: Gonnot Fabrice , Langer Diana , Bourillot Pierre-Yves , Doerflinger Nathalie , Savatier Pierre
Published: May 2019

Continuous, non-cell cycle-dependent expression of cyclin E is a characteristic feature of mouse embryonic stem cells (ESCs). We studied the 5’ regulatory region of Cyclin E, also known as Ccne1, and identified binding sites for transcription factors of the naïve pluripotency network, including Esrrb, Klf4, and Tfcp2l1 within 1 kilobase upstream of the transcription start site. Luciferase assay and chromatin immunoprecipitation-quantitative polymerase chain reaction (ChiP–qPCR) study highlighted one binding site for Esrrb that is essential to transcriptional activity of the promoter region, and three binding sites for Klf4 and Tfcp2l1. Knockdown of Esrrb, Klf4, and Tfcp2l1 reduced Cyclin E expression whereas overexpression of Esrrb and Klf4 increased it, indicating a strong correlation between the expression level of these factors and that of cyclin E. We observed that cyclin E overexpression delays differentiation induced by Esrrb depletion, suggesting that cyclin E is an important target of Esrrb for differentiation blockade. We observed that mESCs express a low level of miR-15a and that transfection of a miR-15a mimic decreases Cyclin E mRNA level. These results lead to the conclusion that the high expression level of Cyclin E in mESCs can be attributed to transcriptional activation by Esrrb as well as to the absence of its negative regulator, miR-15a.
Alternate subunit assembly diversifies the function of a bacterial toxin
Authors: Fowler Casey , Stack Gabrielle , Jiao Xuyao , Lara-Tejero Maria , Galán Jorge E.
Published: May 2019

Bacterial toxins with an AB5architecture are central to bacterial pathogenesis. Functionally diverse and evolutionarily distant AB5toxins adopt synonymous structures in which a discrete domain of the toxin’s active (A) subunit is inserted into a ring-like platform comprised of five delivery (B) subunits.SalmonellaTyphi, the cause of typhoid fever, produces an unusual A2B5toxin known as typhoid toxin, a major virulence factor. Here, we report that upon infection of human cells,S. Typhi produces two forms of typhoid toxin that have distinct delivery components but share common active subunits. We demonstrate that the two typhoid toxins exhibit substantially different trafficking properties, elicit markedly different effects when administered to laboratory animals, and are expressed in response to different regulatory mechanisms and distinct metabolic cues. Collectively, these results indicate that the evolution of two typhoid toxin variants has conferred functional versatility to this virulence factor. More broadly, this study reveals a new paradigm in toxin biology and suggests that the evolutionary expansion of AB5toxins was likely fueled by the remarkable plasticity inherent to their structural design coupled to the functional versatility afforded by the combination of homologous toxin components.
The Role of Sevenless in Drosophila R7 Photoreceptor Specification
Authors: Tomlinson Andrew , Mavromatakis Yannis Emmanuel , Arias Ronald
Published: May 2019

Sevenless (Sev) is a Receptor Tyrosine Kinase (RTK) that is required for the specification of theDrosophilaR7 photoreceptor. OtherDrosophilaphotoreceptors are specified by the action of another RTK; the Drosophila EGF Receptor (DER). Why Sev is required specifically in the R7 precursor, and the exact role it plays in the cell’s fate assignment have long remained unclear. Notch (N) signaling plays many roles in R7 specification, one of which is to prevent DER activity from establishing the photoreceptor fate. Our current model of Sev function is that it hyperactivates the RTK pathway in the R7 precursor to overcome in the N-imposed block on photoreceptor specification. From this perspective DER and Sev are viewed as engaging the same transduction machinery, the only difference between them being the level of pathway activation that they induce. To test this model, we generated a Sev/DER chimera in which the intracellular domain of Sev is replaced with that of DER. This chimerical receptor acts indistinguishably from Sev itself; a result that is entirely consistent with the two RTKs sharing identical transduction abilities. A long-standing question in regard to Sev is the function of a hydrophobic domain some 60 amino acids from the initiating Methionine. If this represents a transmembrane domain, it would endow Sev with N-terminal intracellular sequences through which it could engage internal transduction pathways. However, we find that this domain acts as an internal signal peptide, and that there is no Sev N-terminal intracellular domain.phyllopod(phyl) is the target gene of the RTK pathway, and we show that R7 precursors are selectively lost whenphylgene function is mildly compromised, and that other photoreceptors are removed when the gene function is further reduced. This result adds a key piece of evidence for the hyperactivation of the RTK pathway in the R7 precursor. To facilitate the hyperactivation of the RTK pathway, Sev is expressed at high levels. However, when we express DER at the levels at which Sev is expressed, strong gain-of-function effects result, consistent with ligand-independent activation of the receptor. This highlights another key feature of Sev; that it is expressed at high levels yet remains strictly ligand dependent. Finally, we find that activated Sev can rescue R3/4 photoreceptors when their DER function is abrogated. These results are collectively consistent with Sev and DER activating the same transduction machinery, with Sev generating a pathway hyperactivation to overcome the N-imposed block to photoreceptor specification in R7 precursors.
Context-Dependent Probability Estimation and its Neurocomputational Substrates
Authors: Lin Wei-Hsiang , Gardner Justin L. , Wu Shih-Wei
Published: May 2019

Many decisions rely on how we evaluate potential outcomes associated with the options under consideration and estimate their corresponding probabilities of occurrence. Outcome valuation is subjective as it requires consulting internal preferences and is sensitive to context. In contrast, probability estimation requires extracting statistics from the environment and therefore imposes unique challenges to the decision maker. Here we show that probability estimation, like outcome valuation, is subject to context effects that bias probability estimates away from other stimuli present in the same context. However, unlike valuation, these context effects appeared to be scaled by estimated uncertainty, which is largest at intermediate probabilities. BOLD imaging showed that patterns of multivoxel activity in dorsal anterior cingulate cortex (dACC) and ventromedial prefrontal cortex (VMPFC) predicted individual differences in context effects on probability estimate. These results establish VMPFC as the neurocomputational substrate shared between valuation and probability estimation and highlight the additional involvement of dACC that can be uniquely attributed to probability estimation. As probability estimation is a required component of computational accounts from sensory inference to higher cognition, the context effects found here may affect a wide array of cognitive computations.

Highlights

Context impacts subjective estimates on reward probability – Stimuli carrying greater variance are more strongly affected by other stimuli present in the same context

This phenomenon can be explained by reference-dependent computations that are gated by reward variance

Multivoxel patterns of dACC and VMPFC activity predicts individual differences in context effect on probability estimate
A New Suite of Allelic Exchange Vectors for the Scarless Modification of Proteobacterial Genomes
Authors: Lazarus Jacob E. , Warr Alyson R. , Kuehl Carole J. , Giorgio Rachel T. , Davis Brigid M. , Waldor Matthew K.
Published: May 2019

Despite the advent of new techniques for genetic engineering of bacteria, allelic exchange through homologous recombination remains an important tool for genetic analysis. Currently,sacB-based vector systems are often used for allelic exchange, but counter-selection escape, which prevents isolation of cells with the desired mutation, limits its utility. To circumvent this limitation, we engineered a series of “pTOX” allelic exchange vectors. Each plasmid encodes one of a set of inducible toxins, chosen for their potential utility in a wide range of medically important Proteobacteria. A codon-optimizedrhaStranscriptional activator with a strong synthetic ribosome binding site enables tight toxin induction even in organisms lacking an endogenous rhamnose regulon. Expression of the blueamilCPor magentatsPurplenon-fluorescent chromoproteins facilitates monitoring of successful single- and double-crossover events using these vectors. The versatility of these vectors was demonstrated by deleting genes inSerratia marcescens,Escherichia coliO157:H7,Enterobacter cloacae, andShigella flexneri. Finally, pTOX was used to characterize the impact of disruption of all combinations of the 3 orthologousS. marcescenspeptidoglycan amidohydrolases on chromosomalampCbeta-lactamase activity and corresponding beta-lactam antibiotic resistance. Mutation of multiple amidohydrolases was necessary for high levelampCderepression and beta-lactam resistance. These data suggest why beta-lactam resistance may emerge during treatment less frequently inS. marcescensthan in other AmpC-producing pathogens likeE. cloacae.Collectively, our findings suggest that the pTOX vectors should be broadly useful for genetic engineering of Gram-negative bacteria.

Importance

Targeted modification of bacterial genomes is critical for genetic analyses of microorganisms. Allelic exchange is a technique that relies on homologous recombination to substitute native loci for engineered sequences. However, current allelic exchange vectors often enable only weak selection for successful homologous recombination. We developed a suite of new allelic exchange vectors, pTOX, which were validated in several medically important Proteobacteria. They encode visible non-fluorescent chromoproteins that enable easy identification of colonies bearing integrated vector, and permit stringent selection for the second step of homologous recombination, yielding modified loci. We demonstrate the utility of these vectors by using them to investigate the effect of inactivation ofSerratia marcescenspeptidoglycan amidohydrolases on beta-lactam antibiotic resistance.
Feral pig exclusion fencing provides limited fish conservation value on tropical floodplains
Authors: Waltham N. J. , Schaffer J.
Published: May 2019

Efforts to protect and restore tropical wetlands impacted by feral pigs (Sus scrofa) in northern Australia have more recently included exclusion fences, an abatement response proposing fences improve wetland condition by protecting habitat for fish production and water quality. Here we tested: 1) whether the fish assemblage are similar in wetlands with and without fences; and 2) whether specific environmental processes influence fish composition differently between fenced and unfenced wetlands. Twenty-one floodplain and riverine wetlands in the Archer River catchment (Queensland) were surveyed during post-wet (June-August) and late-dry season (November-December) in 2016, 2017 and 2018, using a fyke soaked overnight (~14-15hrs). A total of 6,353 fish representing twenty-six species from 15 families were captured. There were no multivariate differences in fish assemblages between seasons, years and for fenced and unfenced wetlands (PERMANOVA, Pseduo-F <0.58, P<0.68). Late-dry season fish were considerably smaller compared to post-wet season: a strategy presumably to maximise rapid disposal following rain. At each wetland a calibrated Hydrolab was deployed (between 2-4 days, with 20min logging) in the epilimnion (0.2m), and revealed distinct diel water quality cycling of temperature, dissolved oxygen and pH (conductivity represented freshwater wetlands) which was more obvious in the late-dry season survey, because of extreme summer conditions. Water quality varied among wetlands, in terms of the daily amplitude, and extent of daily photosynthesis recovery, which highlights the need to consider local site conditions rather than applying general assumptions around water quality conditions for these types of wetlands examined here. Though many fish access (fenced and unfenced) wetlands during wet season connection, the seasonal effect of reduced water level conditions seems to be more over-improvised compared to whether fences are installed or not, as all wetlands supported few, juvenile, or no fish species because they had dried completed regardless of whether fences were present or not.
Palmitoylation is critically required for cancer intrinsic PD-1 expression and functions
Authors: Yao Han , Li Chushu , Brosseau Jean-Philippe , Wang Huanbin , Lu Haojie , Fang Caiyun , Shi Hubing , Lan Jiang , Xu Jie
Published: May 2019

Programmed cell death protein 1 (PD-1) is a crucial anticancer target, but the relatively low response rate and acquired resistance to existing antibody drugs highlight an urgent need to develop alternative targeting strategies. Here we report the palmitoylation of PD-1, discovered the main DHHC enzyme for this modification, revealed the mechanism for its effect on PD-1 expression, and rationally developed a peptide for targeting PD-1 expression. Palmitoylation promoted the trafficking of PD-1 to recycling endosome, thus preventing its lysosome-dependent degradation. Palmitoylation was required for the activation of PD-1 downstream signaling, and targeting palmitoylation by pharmacological inhibitor or depleting the modification enzyme caused significant anti-tumor effects. A peptide was designed to competitively inhibit PD-1 palmitoylation and expression, opening a new route for developing PD-1 inhibitors as a strategy for cancer immunotherapy.

Significance

We show for the first time that PD-1 is palmitoylated, identify DHHC9 as the predominant enzyme for its palmitoylation, and reveal the molecular mechanisms underlying its effects on PD-1 stability and functions. Importantly, we also designed a competitive inhibitor targeting PD-1 palmitoylation, and this first-in-class molecule may inspire the development of new checkpoint inhibitors.
The SONATA Data Format for Efficient Description of Large-Scale Network Models
Authors: Dai Kael , Hernando Juan , Billeh Yazan N. , Gratiy Sergey L. , Planas Judit , Davison Andrew P. , Dura-Bernal Salvador , Gleeson Padraig , Devresse Adrien , Dichter Benjamin K. , Gevaert Michael , King James G. , Van Geit Werner A. H. , Povolotsky Arseny V. , Muller Eilif , Courcol Jean-Denis , Arkhipov Anton
Published: May 2019

Increasing availability of comprehensive experimental datasets and of high-performance computing resources are driving rapid growth in scale, complexity, and biological realism of computational models in neuroscience. To support construction and simulation, as well as sharing of such large-scale models, a broadly applicable, flexible, and high-performance data format is necessary. To address this need, we have developed the Scalable Open Network Architecture TemplAte (SONATA) data format. It is designed for memory and computational efficiency and works across multiple platforms. The format represents neuronal circuits and simulation inputs and outputs via standardized files and provides much flexibility for adding new conventions or extensions. SONATA is used in multiple modeling and visualization tools, and we also provide reference Application Programming Interfaces and model examples to catalyze further adoption. SONATA format is free and open for the community to use and build upon with the goal of enabling efficient model building, sharing, and reproducibility.
Humans exploit robust locomotion by improving the stability of control signals
Authors: Santuz Alessandro , Brüll Leon , Ekizos Antonis , Schroll Arno , Eckardt Nils , Kibele Armin , Schwenk Michael , Arampatzis Adamantios
Published: May 2019

Is the control of movement less stable when we walk or run in challenging settings? One might intuitively answer affirmatively, given that adding constraints to locomotion (e.g. rough terrain, age-related impairments, etc.) imply less stable movements. We investigated how young and old humans synergistically activate muscles during locomotion, when different perturbation levels are introduced. Of these control signals, called muscle synergies, we then analyzed the stability over time. Surprisingly, we found that perturbations and older age force the central nervous system to produce more stable signals. These outcomes show that robust locomotion in challenging settings is achieved by increasing the stability of control signals, whereas easier tasks allow for more unstable control.
cohorts: A Python package for clinical ‘omics data management
Authors: Giangreco Nicholas P. , Fine Barry , Tatonetti Nicholas P.
Published: May 2019

Precision medicine uses patient clinical and molecular characteristics to personalize diagnosis and treatment. This emerging discipline integrates multi-modal data into large-scale studies of human disease to make accurate individual-level predictions. The success of these studies will depend on the generalizability of the results, the ability of other researchers and clinicians to replicate studies, and the understandability of the methods used. Tools for data management and standardization are needed to promote flexible, transparent, and reproducible analyses. Here we present cohorts, a python package facilitating clinical and biomarker data management to enhance standardization and reproducibility of clinical findings.

Availability

The python package cohorts is available at http://www.github.com/ngiangre/cohorts.

CONTACT

NPT2105@CUMC.COLUMBIA.EDU
Experimental evidence of invasion facilitation in the zebra mussel-killer shrimp system
Authors: Rolla Matteo , Consuegra Sofia , Carrington Ellie , Hall David , Garcia de Leaniz Carlos
Published: May 2019

Invasion facilitation, whereby one species has a positive effect on the establishment of another species, could help explain the rapid colonisation shown by some freshwater invasive species, but the underlying mechanisms remain unclear. We employed two-choice test arenas to test whether the presence of zebra mussel (Dreissena polymorpha) could facilitate the establishment of the killer shrimp (Dikerogammarus villosus). Killer shrimp preferred to settle on mats of zebra mussel, but this was unrelated to mat size, and was not different from attraction shown to artificial grass, suggesting that zebra mussel primarily provides substrate and refuge to the killer shrimp. Killer shrimp were strongly attracted to water scented by zebra mussel, but not to water scented by fish. Chemical attraction to the zebra mussel’s scent did not differ between sympatric and allopatric populations of killer shrimp, suggesting that chemical facilitation is not an acquired or learned trait. Our results have implications for managing the spread of killer shrimp, and perhaps other freshwater invasive species, because invasion facilitation could significantly increase establishment success. Failure to consider invasion facilitation may underestimate the risk of establishment and likely impact of some aquatic invaders.
Intersection of motor volumes predicts the outcome of ambush predation of larval zebrafish
Authors: Bhattacharyya Kiran , McLean David L. , MacIver Malcolm A.
Published: May 2019

The escape maneuvers of animals are key determinants of their survival. Consequently these maneuvers are under intense selection pressure. Current work indicates that a number of escape maneuver parameters contribute to survival including response latency, escape speed, and direction. This work has found that the relative importance of these parameters is context dependent, suggesting that interactions between escape maneuver parameters and the predatory context together determine the likelihood of escape success. However, it is unclear how escape maneuver parameters interact to contribute to escape success across different predatory contexts. To clarify these issues, we investigated the determinants of successful escape maneuvers by analyzing the responses of larval zebrafish to the attacks of dragonfly nymphs. We found that the strongest predictor of the outcome was the time needed for the nymph to reach the fish’s initial position at the onset of the attack, measured from the time that the fish initiates its escape response. We show how this result is related to the intersection of the swept volume of the nymph’s grasping organs with the volume containing all possible escape trajectories of the fish. By analyzing the intersection of these volumes, we compute the survival benefit of recruiting the Mauthner cell, a neuron in anamniotes devoted to producing escapes. We discuss how escape maneuver parameters interact in determining escape response. The intersection of motor volume approach provides a framework that unifies the influence of many escape maneuver parameters on the likelihood of survival.
3D super-resolution microscopy performance and quantitative analysis assessment using DNA-PAINT and DNA origami test samples
Authors: Lin Ruisheng , Clowsley Alexander H. , Lutz Tobias , Baddeley David , Soeller Christian
Published: May 2019

Assessment of the imaging quality in localisation-based super-resolution techniques relies on an accurate characterisation of the imaging setup and analysis procedures. Test samples can provide regular feedback on system performance and facilitate the implementation of new methods. While multiple test samples for regular, 2D imaging are available, they are not common for more specialised imaging modes. Here, we analyse robust test samples for 3D and quantitative super-resolution imaging, which are straightforward to use, are time-and cost-effective and do not require experience beyond basic laboratory and imaging skills. We present two options for assessment of 3D imaging quality, the use of microspheres functionalised for DNA-PAINT and a commercial DNA origami sample. A method to establish and assess a qPAINT workflow for quantitative imaging is demonstrated with a second, commercially available DNA origami sample.
Vascular endothelial growth factor (VEGF) expression and neuroinflammation is increased in the frontopolar cortex of individuals with autism spectrum disorder
Authors: Gnanasekaran Aswini , Kelchen Megan N. , Brogden Nicole K. , Smith Ryan M.
Published: May 2019

Autism spectrum disorder (ASD) etiology is a complex mixture of genetic and environmental factors, the relative contributions of which varies across patients. Despite complex etiology, researchers observe consistent neurodevelopmental features in ASD patients, notably atypical forebrain cortical development. Growth factors, cytokines, and chemokines are important mediators of forebrain cortical development, but have not been thoroughly examined in brain tissues from individuals with autism. Here, we performed an integrative analysis of RNA and protein expression using frontopolar cortex tissues dissected from individuals with ASD and controls, hypothesizing that ASD patients will exhibit aberrant expression of growth factors, cytokines, and chemokines critical for neurodevelopment. We performed group-wise comparisons of RNA expression via RNA-Seq and growth factor, cytokine, and chemokine expression via multiplex enzyme-linked immunosorbent assay (ELISA). We also analyzed single cell sequencing data from the frontopolar cortex of typically developed individuals to identify cell types that express the growth factors we found differentially expressed in ASD. Our RNA-Seq analysis revealed 11 differentially expressed genes in ASD versus control brains, the most significant of which encodes for vascular endothelial growth factor (VEGF-A). Both RNA and protein levels of VEGF-A were upregulated in ASD brains. Our single cell analysis revealed that VEGF is expressed primarily by non-neuronal cells. We also found that the differentially expressed genes from our RNA-Seq analysis are enriched in microglia. The increased VEGF-A expression we observed in ASD, coupled with the enrichment of differentially expressed genes in microglia, begs the question of the role VEGF-A is playing in ASD. Microglia activation, as indicated by our RNA-Seq results, and the VEGF-A isoform expression we see in the ASD cortex, leads us to conclude that VEGF-A is playing a pro-inflammatory role, perhaps with unwanted long-term consequences for neurodevelopment.
Surprise response as a probe for compressed memory states
Authors: Levi-Aharoni Hadar , Shriki Oren , Tishby Naftali
Published: May 2019

The limited capacity of recent memory inevitably leads to partial memory of past stimuli. There is also evidence that behavioral and neural responses to novel or rare stimuli are dependent on one’s memory of past stimuli. Thus, these responses may serve as a probe of different individuals’ remembering and forgetting characteristics. Here, we utilize two lossy compression models of stimulus sequences that inherently involve forgetting, which in addition to being a necessity under many conditions, also has theoretical and behavioral advantages. One model is based on a simple stimulus counter and the other on the Information Bottleneck (IB) framework. These models are applied to analyze a novelty-detection event-related potential commonly known as the P300. The trial-by-trial variations of the P300 response, recorded in an auditory oddball paradigm, were subjected to each model to extract two stimulus-compression parameters for each subject: memory length and representation accuracy. These parameters were then utilized to estimate the subjects’ recent memory capacity limit under the task conditions. The results, along with recently published findings on single neurons on the IB model, underscore how a lossy compression framework can be utilized to account for trial-by-trial variability of neural responses at different spatial scales and in different individuals, while at the same time providing estimates of individual memory characteristics at different levels of representation using a theoretically-based parsimonious model.

Author summary

Surprise responses reflect expectations based on preceding stimuli representations, and hence can be used to infer the characteristics of memory utilized for a task. We suggest a quantitative method for extracting an individual estimate of effective memory capacity dedicated for a task based on the correspondence between a theoretical surprise model and electrophysiological single-trial surprise responses. We demonstrate this method on EEG responses recorded while participants were performing a simple auditory task; we show the correspondence between the theoretical and physiological surprise, and calculate an estimate of the utilized memory. The generality of this framework allows it to be applied to different EEG features that reflect different modes and levels of the processing hierarchy, as well as other physiological measures of surprise responses. Future studies may use this framework to construct a handy diagnostic tool for a quantitative, individualized characterization of memory-related disorders.
Amplification of cDNA Generated by Reverse Transcription of mRNA: Two-Step Reverse Transcription-Polymerase Chain Reaction (RT-PCR)
Authors: Green Michael R. , Sambrook Joseph
Published: May 2019

Reverse transcription-polymerase chain reaction (RT-PCR) is a powerful method to detect and synthesize cDNA copies of low-copy-number mRNAs. Two enzymes are used: reverse transcriptase to produce single-stranded cDNA copies, which are then used as templates in an amplification reaction catalyzed by a thermostable DNA polymerase. For this reason, the method is known as “two-step RT-PCR.” This protocol describes the traditional method of RT-PCR in which the two synthetic reactions are performed separately and sequentially.
Governance and transparency of the Chinese charity foundations
Authors: Xue Qingmei , Niu Yuning
Published: May 2019

Purpose

The purpose of this paper is to investigate the relation between various governance mechanisms and the transparency level by using a sample of the top 200 Chinese charity foundations on net assets.

Design/methodology/approach

Three types of governance forces are examined, including the board, the management and the capital providers. The Foundation Transparency Index (FTI), published by Chinese Foundation Center, is used as a proxy for the transparency level.

Findings

The evidences show that for the public foundations that can elicit fund from the public, providing compensation to the foundation managers could encourage them to increase the transparency level. Furthermore, the sophisticated donors also represent a useful governance force. For the non-public foundations that can only seek donors through private contacts, getting more members in their supervisory board and having more government grants are helpful in improving their transparency. The results are robust even after controlling for lagged FTI and other characteristics of foundations. And the transparency level is positively associated with the international connections for both types of foundations.

Research limitations/implications

This research is based on a limited sample. The results can hardly generalize to the other smaller foundations. However, the results are still meaningful for to the legislators, regulators and managers of Chinese charity foundations. Because the result implies that the overseas donors are effective monitors that could improve the foundation transparency, the newly published law may weaken this governance force.

Originality/value

This is the first paper that studies the governance of Chinese charity foundations. By using a third-party index to proxy for the transparency, the results complement existing literature.
Coerced CSR: lessons from consumer values and purchasing behavior
Authors: Ijabadeniyi Abosede , Govender Jeevarathnam Parthasarathy
Published: May 2019

Purpose

The purpose of this paper is to investigate the underlying corporate social responsibility (CSR) factors which trigger consumers’ scrutiny of corporate behavior in the purchasing experience. There is more focus on how the direct effects of CSR can predict consumer behavior than the expression of value-based purchasing habits, especially in relation to how the multidimensionality of consumers’ expectations of CSR indirectly informs such behavior.

Design/methodology/approach

Mall-intercept survey interviews were conducted with 411 shoppers across five shopping malls in South Africa. Data were based on the emotional, social and functional values consumers derive from the purchasing experiencevis-à-viseconomic, legal, ethical and philanthropic expectations of CSR and analyzed using the path analysis technique of structural equation modeling.

Findings

It was found that the relationship between consumers’ sense of value and purchasing behavior is mediated by perceived fulfillment of legal expectations of CSR (a primary redressing tool). Conversely, the fulfillment of ethical and economic CSR expectations (secondary redressing tools) serves as moderators of the relationship.

Research limitations/implications

The benefit of approaching corporate communication from a value-based perspective is a proactive risk mitigation strategy. Consumers’ sense of value in the purchasing experience is triggered by companies’ adherence to institutionalized law on corporate behavior and reinforced by compliance to code of ethics and financial viability.

Practical implications

This study offers insights for understanding how consumers redress corporate misconduct during crisis through the buying experience and explains how such understanding can be used to better predict and manage crisis communication.

Social implications

The findings of this study suggest that CSR and corporate communication practices should be informed by the taken-for-granted assumptions which underpin espoused consumer values, where negligence of unspoken patterns of CSR-based consumer behavior could signal a crisis risk.

Originality/value

This study offers a model which demonstrates for the first time that consumers implicitly utilize CSR to redress corporate misconduct in the purchasing experience.
Inclusiveness and effectiveness of agricultural cooperatives: recent evidence from Ethiopia
Authors: Wassie Solomon Bizuayehu , Kusakari Hitoshi , Masahiro Sumimoto
Published: May 2019

Purpose

Using a recent rural farm household survey, the purpose of this paper is to investigate inclusiveness and effectiveness of agricultural cooperatives in Ethiopia.

Design/methodology/approach

The study employs a logit model to examine inclusiveness and an endogenous switching regression (ESR) model to evaluate the effectiveness of agricultural cooperatives.

Findings

The results show that agricultural cooperatives are less inclusive of land-poor and illiterate households. On the other hand, the estimated results indicate that cooperatives effectively improved agricultural performance and welfare of its member households – i.e. membership in cooperatives increases yield and income by 1.37 quintal/hectare and 1,804 birr, respectively. Moreover, the result shows that marketing cooperatives effectively increased marketed surplus of their members by 34 percent.

Research limitations/implications

The study has important implications regarding the ways to improve the effectiveness and/or inclusiveness of agricultural cooperatives.

Originality/value

While accounting for the collective behavior of cooperatives, this study uses multiple outcome variables in examining the effectiveness of cooperatives in Ethiopia. Furthermore, this paper employs the ESR model and accounts for potential problems in estimating impact using non-experimental data.
Employee social sustainability: prioritizing dimensions in the UAE’s airlines industry
Authors: Al Marzouqi Abdulla Hasan , Khan Mehmood , Hussain Matloub
Published: May 2019

Purpose

This paper aims to identify and prioritize the dimensions that impact employee social sustainability in the airline industry in the United Arab Emirates (UAE).

Design/methodology/approach

The five main criteria (employee well-being, communication, management support, reward and control system and training) and 18 sub-criteria were identified from the literature. The sample comprised four experts covering the HR, finance and training functions from a major UAE airline organization. Applying the analytical-hierarchy-process (AHP) methodology resulted in obtaining priority weights for the factors assigned to employee-social-sustainability implementation.

Findings

Management support was found to have the highest priority among the study dimensions impacting employee social sustainability. Surprisingly, reward system was found to be the least important dimension.

Research limitations/implications

The study was carried out on a single airline organization, limiting the generalizability of the findings. Future studies should be extended to cater to different organizational contexts and varying operational conditions.

Practical implications

The findings should be of value to human resource management and policymakers in developing countries, such as the UAE, where employee social sustainability should be sought as a means to develop an efficient and sustainable workforce in different industrial sectors.

Originality/value

This study is among the few pioneering studies that focus on employee social sustainability. The use of AHP to prioritize employee-social-sustainability dimensions is also considered pioneering within the field and is anticipated to support future studies, and a deeper understanding, of employee social sustainability.
Green cost calculus for corporate environmental responsibility
Authors: Ghosh Ray Kamal
Published: May 2019

Purpose

The purpose of this study is to show that corporations may resort to legal compliance instead of acting voluntarily towards abatement of environmental damages as a strategy for improving their reputation.

Design/methodology/approach

Based on the natural philosophy and postulate of business, theoretical models have been developed to justify the purpose of this paper. Financial impacts of Indian revenue law on environmental damage prevention by the polluting firms have been gauged mathematically.

Findings

Corporate environmental responsibilities have seemed to be more reputation-led than innovation-led or efficiency-led. Reputation-led environmental responsibilities can have ways to bypass innovations and some firms can simply comply with regulations at the society’s cost (may be to a sizeable extent). If penalty is imposed on companies in the form of taxation for damaging the environment, then companies get chances to pass the financial burden to the shareholders in the form of lower dividend pay-outs. Unless the capital market supports corporate green initiatives, there may be destruction of shareholder wealth.

Research limitations/implications

Extensive empirical analysis have not been conducted as the paper concentrates on developing theoretical understanding of the models of “green cost”.

Practical implications

The exploration and outcomes of this paper can offer several directions to the government, business and social activists in articulating green economic policy for the benefits of all.

Social implications

The civil society will understand better what the corporate environmental responsibility really means for them.

Originality/value

This paper has made a modest endeavour to develop theoretical models of both “green cost internalisation” and “green cost externalisation”. It has paved the path for further deliberations and research.
Can all sectors of the hospitality and tourism industry be influenced by the innovation of Blockchain technology?
Authors: Willie Paul
Published: May 2019

Purpose

This paper aims to provide a general introduction to Blockchain technology and how it can be used within the global hospitality industry. In particular, this paper speaks to three industry sectors where Blockchain technology is currently in use.

Design/methodology/approach

This paper draws on the perspective of an academic who also continues to serve as an industry practitioner within the field of hospitality technology. To this end, the paper provides several examples as to how Blockchain technology can be used to further advance the hospitality profession within a number of different industry sectors.

Findings

Blockchain technology is being used now within the hospitality industry for both practical and strategic purposes. It can be used in most sectors of the profession and will continue to be used within the hospitality industry for many years ahead. The technology is still relatively new and will continue to become more advanced and sophisticated with the passage of time.

Practical implications

Many hospitality industry examples are provided as to how Blockchain technology can be used to improve operational effectiveness, efficiencies and overall profitability.

Originality/value

This paper adds value and contributes to the literature relating to Blockchain technology applications in the international hospitality industry. It represents current and future use that can and should be taken into consideration by both the hospitality industry and academia.
Development of nickel bi-porous wicks for miniature loop heat pipe applications
Authors: Mahulkar Yogesh , Sedani Chetankumar
Published: May 2019

Purpose

Miniature loop heat pipes (MLHPs) are highly efficient passive heat transfer devices, which have considerable advantages over conventional heat pipes. Currently, miniature LHPs with ammonia and water as working fluids have been developed and utilized in electronics cooling within temperature range of 50°C-70°C at any orientation in 1-g conditions.

Design/methodology/approach

The authors studied the standard procedure for the development of bi-porous nickel wicks and their characterization. Three different shaped nickel powders were studied, and best fitting nickel powder for electronics cooling application was reported. The manufacturing of bi-porous wick structures was analyzed with parameters such as porosity, permeability, capillary pressure and effective thermal conductivity for efficient performance of MLHP.

Findings

The study investigated the sintering process for number of samples to identify effective sample for the particular application. It is found that carbonyl nickel powder (type 287) with particle size of 2.6-3.3 µm gives promising results. Permeability and porosity were found to be highest in this case.

Originality/value

It is found that carbonyl nickel powder type with particle size gives promising results. Permeability and porosity was found to be highest in this case.