bluuebunny/crossref_metadata_2025 huggingface dataset:
Interprofessional Learning in Immediate Life Support training improves simulated patient related outcomes
Authors: Morse Jeremy Charles , Brown Craig William
Published: January 2020

Aim of the study

To assess team performance in implementing time critical key interventions during a simulated resuscitation after participating in either an interprofessional-learning (IPL) or uniprofessional-learning (UPL) Immediate Life Support training course (ILS).

Introduction

Much of the published work on team-based simulation training has measured the lower levels of Kirkpatrick’s hierarchy of evidence and effectiveness. This study aimed to ascertain if interprofessional team training could improve a higher level of outcome such as behaviour and patient outcomes.

Methods

A retrospective quantitative analysis of time critical points in a simulated cardiac arrest resuscitation, from a previous randomised study on the effects of Interprofessional Learning in ILS. The video recordings from the original study consisting of medical (n=48) and nursing (n=48) students were analysed to mark when either the IPL or UPL team performed a time critical intervention.

Results

Five time-critical points for interventions were identified; confirmation of cardiac arrest, commencement of initial CPR, rhythm check, time to 1st shock and delay in restarting CPR. Parametric testing of each of these time-based criteria were subjected to an independent sample t-test with statistically significant findings in three of the five criteria in favour of those who had undertaken the interprofessional learning.

Conclusion

Our results demonstrate that through an IPL approach in ILS there was a statistically different improvement in mean times to performing time-critical interventions, which if transferred to the clinical environment could improve and impact on both change of behaviour and patient outcomes in Kirkpatrick’s higher levels of evidence and effectiveness.

Though this study shows that team behaviour and performing time-critical interventions can improve in the short-term, we acknowledge that further longitudinal studies are required to ascertain the effect of such improvement over time. So that both as researchers and educators we can make healthcare teams work safer and more efficiently to improve patient outcomes.

What this paper adds

What is already known

Like simulation, intuitively we know that Interprofessional Learning and Team training should make a difference to clinical practice for those involved. The majority of research reported, is measured at the lower levels of Kirkpatrick’s hierarchy. This retrospective video analysis of a previous study aimed to look at the functioning between interprofessionally and uni-professionally trained teams in performing time-critical interventions in a simulated cardiac arrest.

What this study adds

Our study suggests that the use of Interprofessional Learning in resuscitation training does have an effect on performance during the management of a simulated cardiac arrest which could improve and impact on both change of behaviour and patient outcomes in Kirkpatrick’s higher levels of evidence and effectiveness.
A genomic epidemiology investigation of yaws re-emergence and bacterial drug resistance selection
Authors: Beale Mathew A , Noguera-Julian Marc , Godornes Charmie , Casadella Maria , Gonzalez-Beiras Camila , Parera Mariona , Corbacho-Monne Marc , Paredes Roger , Gonzalez-Candelas Fernando , Marks Michael , Lukehart Sheila A , Thomson Nicholas R , Mitja Oriol
Published: January 2020

Background: In a longitudinal study assessing the WHO strategy for yaws eradication using mass azithromycin treatment, we observed resurgence of yaws cases with dominance of a single JG8 sequence type and emergence of azithromycin-resistant Treponema pallidum. Here, we analyse genomic changes in the bacterial population using samples collected during the study.
Methods: We performed whole bacterial genome sequencing directly on DNA extracted from 37 lesion swabs collected from patients on Lihir Island, Papua New Guinea, between 2013 and 2016. We produced phylogenies and correlated these with temporo-spatial information to investigate the source of new cases and the emergence of five macrolide-resistant cases. We used deep amplicon sequencing of surveillance samples to assess the presence of minority macrolide resistance populations.
Findings: We recovered 20 whole Treponema genomes, and phylogenetic analysis showed that the re-emerging JG8 sequence type was composed of three bacterial sub-lineages characterised by distinct temporo-spatial patterns. Of five patients with resistant Treponema, all epidemiologically linked, we recovered genomes from three and found no variants. Deep sequencing showed that pre-treatment, the index patient harboured fixed macrolide-sensitive Treponema, while the post-treatment sample harboured a fixed resistant genotype, as did three of four contact cases. We also found no evidence of pre-existing minority Treponema drug-resistance variants in the general population.
Interpretation: In this study, re-emergence of yaws cases was polyphyletic, indicating multiple epidemiological sources. However, given the genomic and epidemiological linkage of resistant cases and the rarity of resistance alleles in the general population, it is likely that azithromycin resistance evolved only once in this study, followed by onward dissemination.
A new incidence peak of childhood narcolepsy type 1 in 2013: a new perspective on the role of influenza virus?
Authors: Zhang Zhongxing , Gool Jari , Fronczek Rolf , Bassetti Claudio L. , Dauvilliers Yves , Mayer Geert , Plazzi Giuseppe , Pizza Fabio , Santamaria Joan , Partinen Markku , Overeem Sebastiaan , Peraita-Adrados Rosa , da Silva Antonio Martins , Sonka Karel , Rio-Villegas Rafael del , Heinzer Raphael , Wierzbicka Aleksandra , Young Peter , Högl Birgit , Manconi Mauro , Feketeova Eva , Mathis Johannes , Paiva Teresa , Canellas Francesca , Lecendreux Michel , Baumann Christian R. , Barateau Lucie , Pesenti Carole , Antelmi Elena , Gaig Carles , Iranzo Alex , Lillo-Triguero Laura , Medrano-Martínez Pablo , Haba-Rubio José , Gorban Corina , Lammers Gert-Jan , Khatami Ramin
Published: January 2020

Increased incidence rates of narcolepsy type 1 (NT1) after the 2009-2010 H1N1 influenza pandemic (pH1N1) have been reported world-wide. While some European countries found an association between the NT1 increase and H1N1 vaccination Pandemrix, reports from Asian countries suggested the H1N1 virus rather than Pandemrix to be linked with the increase of new NT1 cases. We analyzed the number of de-novo NT1 cases in the last two decades until 2016 using the European Narcolepsy Network (EU-NN) database. Using robust data-driven modelling approaches we confirmed the peak of NT1 incidence in 2009-2010 pH1N1 and identified a new peak in 2013 that is age-specific for children/adolescents. Most of these de-novo cases showed a subacute disease onset consistent with an immune-mediated type of narcolepsy, which is most likely not related to Pandemrix vaccination that was used in 2009-2010, but may have been triggered by some new epidemiological event in Europe. Our finding of an unexpected peak in de-novo children narcolepsy in 2013 provides a unique opportunity to develop new hypotheses, such as considering other (influenza) viruses to further investigate the pathophysiology of immune-mediated narcolepsy.
Molecular Diversity Among Adult Human Hippocampal and Entorhinal Cells
Authors: Franjic Daniel , Choi Jinmyung , Skarica Mario , Xu Chuan , Li Qian , Ma Shaojie , Tebbenkamp Andrew T. N. , Santpere Gabriel , Arellano Jon I. , Gudelj Ivan , Jankovic-Rapan Lucija , Sousa Andre M. M. , Rakic Pasko , Sestan Nenad
Published: January 2020

The hippocampal-entorhinal system is comprised of functionally distinct subregions collectively critical for cognition, and selectively vulnerable to aging and pathological processes. To gain insights into neuronal and non-neuronal populations within this system, we performed single-nucleus transcriptional profiling from five human hippocampal-entorhinal subregions. We found that transcriptomic diversity of excitatory neurons across these subregions reflected the molecular transition from three-layered archicortex to six-layered neocortex. Additionally, mRNA and protein for DCX, an immature neuron marker, were clearly detected in some cells, but not in dentate granule cells, the cell-type predicted to be generated in adult neurogenesis. We also found that previously functionally uncharacterized METTL7B was enriched in human and non-human primate neuronal subtypes less vulnerable to initial Alzheimer’s disease pathology. Proteomic and biochemical assays revealed METTL7B interacts with Alzheimer’s disease-related proteins, including APP, and its overexpression reduced amyloid-beta generation. These results reveal cell type-specific molecular properties relevant for hippocampal-entorhinal physiology and dysfunction.
GeneMark-EP and -EP+: eukaryotic gene prediction with self-training in the space of genes and proteins
Authors: Brůna Tomáš , Lomsadze Alexandre , Borodovsky Mark
Published: January 2020

We have made several steps towards creating a fast and accurate algorithm for gene prediction in eukaryotic genomes. First, we introduced an automated method for efficientab initiogene finding, GeneMark-ES, with parameters trained in iterativeunsupervisedmode. Next, in GeneMark-ET we proposed a method of integration of unsupervised training with information on intron positions revealed by mapping short RNA reads.

Now we describe GeneMark-EP, a tool that utilizes another source of external information, a protein database, readily available prior to a start of a sequencing project. A new specialized pipeline, ProtHint, initiates massive protein mapping to genome and extracts hints to splice sites and translation start and stop sites of potential genes. GeneMark-EP uses the hints to improve estimation of model parameters as well as to adjust co-ordinates of predicted genes if they disagree with the most reliable hints (the -EP+ mode).

Tests of GeneMark-EP and -EP+ demonstrated improvements in gene prediction accuracy in comparison with GeneMark-ES, while the GeneMark-EP+ showed higher accuracy than GeneMark-ET. We have observed that the most pronounced improvements in gene prediction accuracy happened in large eukaryotic genomes.
Tau avoids the GTP cap at growing microtubule plus ends
Authors: Castle Brian T. , McKibben Kristen M. , Rhoades Elizabeth , Odde David J.
Published: January 2020

Plus-end tracking proteins (+TIPs) are a group of proteins that associate with the growing end of microtubules and mediate important cellular functions including neural development and cell division. Work in recent years has shown that the majority of +TIPs are directed to the plus-end through a family of end binding proteins (EBs), which preferentially bind the stabilizing cap of GTP-tubulin present during microtubule growth, versus weaker binding to GDP-tubulin in the proximal microtubule. One question yet to be addressed is whether there may exist other microtubule associated proteins (MAPs) that preferentially bind specific nucleotide states of tubulin. Here we report that the neuronal MAP tau, which is enriched in axons where it promotes microtubule growth and bundling, preferentially binds GDP-tubulin (KD= 0.26 µM) over GMPCPP-tubulin (KD= 1.1 µM)in vitroas well as GTP-tubulin at the tips of growing microtubulesin vitroandin vivo. This nucleotide preference causes tau binding to lag behind the growing microtubule plus-end by about 100-200 nm bothin vitroand in live cells. Thus, tau is a microtubule tip avoiding protein, establishing a new class of tip avoiding MAPs, and acts primarily by suppressing microtubule shortening rather than promoting growth. We speculate that neurological disease-relevant tau mutations may exert their phenotype by their failure to properly recognize GDP-tubulin, thus displacing +TIPs, such as EB3, and their associated activities into abnormal locations in the neuron.
Differences in Characteristics of Medicare Patients Treated by Ophthalmologists and Optometrists
Authors: Miller Darby D. , Stewart Michael W. , Gagne Joshua J. , Wagner Alan L. , Lee Aaron Y.
Published: January 2020

Purpose

To quantify differences in the age, gender, race, and clinical complexity of Medicare beneficiaries treated by ophthalmologists and optometrists in each of the United States.

Design

Cross-sectional study based on publicly accessible Medicare payment and utilization data from 2012 to 2017.

Methods

For each ophthalmic and optometric provider, demographic information of treated Medicare beneficiaries was obtained from the Medicare Provider Utilization and Payment Data from the Centers for Medicare and Medicaid Services (CMS) for the years 2012 to 2017. Clinical complexity was defined using Hierarchical Condition Category (HCC) coding.

Results

From 2012 to 2017, ophthalmologists in every state treated significantly older beneficiaries, with the greatest difference (4.99 years in 2014) between provider groups seen in Rhode Island. In most states, there was no gender difference among patients treated by the providers, but in 46 states ophthalmologists saw significantly more racially diverse groups of beneficiaries. HCC risk score analysis demonstrated that ophthalmologists in all 50 states saw more medically complex beneficiaries and the differences were statistically significant in 47 states throughout all six years.

Conclusions

Although there are regional variations in the characteristics of patients treated by ophthalmologists and optometrists, ophthalmologists throughout the United States manage older, more racially diverse, and more medically complex Medicare beneficiaries.
Hyaluronic Acid on the Urokinase Sustained Release with a Hydrogel System Composed of Poloxamer 407
Authors: Hsieh Hao-Ying , Lin Wei-Yang , Lee An Li , Li Yi-Chen , Chen Yi-Jane , Chen Ke-Cheng , Young Tai-Horng
Published: January 2020

Pleural empyema is an inflammatory condition characterized by accumulation of pus inside the pleural cavity, which is usually followed by bacterial pneumonia. During the disease process, the pro-inflammatory and pro-fibrotic cytokines in the purulent pleural effusion cause proliferation of fibroblasts and deposition of extracellular matrix, which lead to fibrin deposition and fibrothorax. Urokinase instillation therapy through a chest drainage tube is frequently used for fibrinolysis in patients with empyema. However, urokinase treatment requires multiple instillation (2-3 times per day, for 4-8 days) and easily flows out from the chest drainage tube due to its high water solubility. In this in vitro study, we developed a thermo-responsive hydrogel based on poloxamer 407 (P407) combined with hyaluronic acid (HA) for optimal loading and release of urokinase. Our results show that the addition of HA to poloxamer gels provides a significantly more compact microstructure, with smaller pore sizes (**p < 0.001). The differential scanning calorimetry (DSC) profile revealed no influence on the micellization intensity of poloxamer gel by HA. The 25% poloxamer-based gel was significantly superior to the 23% poloxamer-based gel, with slower gel erosion when comparing the 16th hour residual gel weight of both gels (*p < 0.05; **p < 0.001). The 25% poloxamer-HA gel also exhibited a superior urokinase release profile and longer release time. A Fourier-transform infrared spectroscopy (FT-IR) study of the P407/HA hydrogel showed no chemical interactions between P407 and HA in the hydrogel system. The thermoresponsive P407/HA hydrogel may have a promising potential in the loading and delivery of hydrophilic drugs. On top of that, in vitro toxicity test of this combination demonstrates a lower toxicity.
Consensus Features Nested Cross-Validation
Authors: Parvandeh Saeid , Yeh Hung-Wen , Paulus Martin P. , McKinney Brett A.
Published: January 2020

Motivation

Feature selection can improve the accuracy of machine learning models, but appropriate steps must be taken to avoid overfitting. Nested cross-validation (nCV) is a common approach that chooses the classification model and features to represent a given outer fold based on features that give the maximum inner-fold accuracy. Differential privacy is a related technique to avoid overfitting that uses a privacy preserving noise mechanism to identify features that are stable between training and holdout sets.

Methods

We develop consensus nested CV (cnCV) that combines the idea of feature stability from differential privacy with nested CV. Feature selection is applied in each inner fold and the consensus of top features across folds is a used as a measure of feature stability or reliability instead of classification accuracy, which is used in standard nCV. We use simulated data with main effects, correlation, and interactions to compare the classification accuracy and feature selection performance of the new cnCV with standard nCV, Elastic Net optimized by CV, differential privacy, and private Evaporative Cooling (pEC). We also compare these methods using real RNA-Seq data from a study of major depressive disorder.

Results

The cnCV method has similar training and validation accuracy to nCV, but cnCV has much shorter run times because it does not construct classifiers in the inner folds. The cnCV method chooses a more parsimonious set of features with fewer false positives than nCV. The cnCV method has similar accuracy to pEC and cnCV selects stable features between folds without the need to specify a privacy threshold. We show that cnCV is an effective and efficient approach for combining feature selection with classification.

Availability

Code available athttps://github.com/insilico/cncv.

Contact

brett.mckinney@utulsa.edu

Supplementary information:
Multiple Dimerizing Motifs Modulate the Dimerization of the Syndecan Transmembrane Domains
Authors: Chen J. , Wang F. , He C. , Luo S-Z.
Published: January 2020

Syndecans(SDCs) are a family of four members of integral membrane proteins, which play important roles in cell-cell interactions. Dimerization/oligomerization generated by transmembrane domains (TMDs) appear to crucially regulate several functional behaviors of all syndecan members. The distinct hierarchy of protein-protein interactions mediated by the syndecan TMDs may give rise to considerable complexity in the functions of syndecans. The molecular mechanism of the different dimerization tendencies in each type of SDCs remains unclear. Here, the self-assembly process of syndecan TMD homodimers and heterodimers was studied in molecular details by molecular dynamics simulations. Our computational results showed that the SDC2 forms the most stable homodimer while the SDC1 TMD dimerizes weakly, which is consistent with previous experimental results. Detailed analysis suggests that instead of the conserved dimerizing motif G8XXXG12 in all four SDCs involved in homo- and hetero-dimerization of SDCs, the G3XXXA7 motif in SDC1 competes with the interface of G8XXXG12 and thus disturbs the SDC1 involved dimerization. The SDC3 which contains a G9XXXA13 motif, however, forms a more stable dimer than SDC1, indicating the complexity of the competing effect of the GXXXA motif. As GXXXG and GXXXA are two common sequence motifs in the dimerization of helices, our results shed light on the competing effect of multiple dimerizing motifs on the dimerization of transmembrane domains.
Value and choice as separable, stable representations in orbitofrontal cortex
Authors: Kimmel Daniel L. , Elsayed Gamaleldin F. , Cunningham John P. , Newsome William T.
Published: January 2020

Value-based decision-making operates on multiple variables—including offer value, choice, expected outcome, and recent history—each functioning at different times in the decision process. Orbitofrontal cortex (OFC) has long been implicated in value-based decision-making, but it is unclear how downstream circuits might read out complex OFC responses into separate representations of the relevant variables to support different cognitive functions at specific times. We recorded from single neurons in OFC while macaque monkeys made cost-benefit decisions to juice offers. Using a novel analysis—optimal targeted dimensionality reduction—we discovered orthogonal, static dimensions (i.e. linear combinations of neurons) that selectively represented the value, choice, and expected reward of the present and, separately, previous offers. The neural composition of most representations was stable over discrete time periods that aligned to concurrent cognitive demands. We applied a new set of statistical methods to determine that the sensitivity, specificity and stability of the representations were greater than expected from the low-level features—dimensionality and temporal smoothness—of the responses alone. The separability and stability of OFC representations suggest a mechanism by which downstream circuits can read out specific task-relevant variables at appropriate times.
Zooplankters in an oligotrophic ocean: contrasts in the niches of the foraminifersGlobigerinoides ruberandTrilobatus sacculiferin the tropical South Pacific
Authors: Scott George H.
Published: January 2020

The distributions of two morphologically similar planktonic foraminifera (Globigerinoides ruberandTrilobus sacculifer) that are major taxa in the mixed layer of the tropical South Pacific Ocean are related to environmental variables (sea surface temperature, chlorophyll-a, nitrate, phosphate, salinity, oxygen) to determine the extent to which their niches overlap. Their distributions in ForCenS, a database of species in seafloor sediment are studied as a proxy for upper ocean data and are analysed as occurrences using MaxEnt, and as relative abundances via non-parametric regression (Random Forests). Their distributions are similar and their co-occurrences are high but relations between their abundances and the environmental variables are complex and non-linear. In the occurrence analysis sea surface temperature is the strongest predictor of niche suitability, followed by chlorophyll-a; environments between 0 – 20° S are mapped as the most suitable for both species. To the contrary, predicted species distributions are strongly differentiated by the abundance analysis. Nitrate and chlorophyll-a are primary variables in the map of predicted relative abundances ofGlobigerinoides ruber, with maxima in the hyper-oligotrophic zone of the subtropical gyre. In contrast, sea surface temperature and chlorophyll-a are primary variables in the map forTrilobatus sacculiferand predicted maxima are at the margins of the hyper-oligotrophic zone and near the West Pacific Warm Pool. The high relative abundance ofGlobigerinoides ruberin the hyper-oligotrophic zone is attributed to its close photosymbiotic relation with on-board dinoflagellates; this compensates for the low primary productivity in the zone. It is clearly identified as the best-adapted planktonic foraminifer in this huge marine ‘desert’ and might serve as a useful proxy. The photosymbiotic relation is less apparent inTrilobatus sacculiferwhich, asin vitroresearch suggests, primarily depends on particulate nutrition. The study shows the value of abundance over occurrence data for analysing the trophic resources of these zooplankters.
Interference of pH buffer with Pb2+-peripheral domain interactions: obstacle or opportunity?
Authors: Katti Sachin , Igumenova Tatyana I.
Published: January 2020

Pb2+is a xenobiotic metal ion that competes for Ca2+-binding sites in proteins. Using the peripheral Ca2+-sensing domains of Syt1, we show that the chelating pH buffer Bis-Tris enables identification and functional characterization of high-affinity Pb2+sites that are likely to be targeted by bioavailable Pb2+.

Significance to Metallomics

Syt1, a key regulator of Ca2+-evoked neurotransmitter release, is a putative molecular target of Pb2+. We demonstrate that the use of a chelating pH buffer Bis-Tris enables identification of Ca2+-binding sites that would be most susceptible to Pb2+attack in the cellular environment. In addition, experiments conducted in Bis-Tris revealed the differences between the membrane-binding responses of two Ca2+-sensing domains of Syt1, C2A and C2B. This work advances the understanding of how Pb2+interacts with multipartite Ca2+-binding sites, and illustrates that conducting the experiments under both chelating and non-chelating conditions could provide valuable insight into the mechanism of metallosensory proteins.
Single-cell RNA-seq reveals endoimmune cells in zebrafish
Authors: Shi Yunwei , Qian Peipei , Sheng Jiajing , Zhang Xu , Wang Xiaoning , Zhao Jingxiang , Wei Guanyun , Liu Xia , Xie Gangcai , Liu Dong
Published: January 2020

Endothelial cells (ECs) constitute a monolayer that covers the interior surface of blood vessels and participates in various processes. Although vascular ECs share certain common properties, they differ in both structure and function. So far, the transcriptome profile and heterogeneity of the full repertoire of ECs in vertebrates remain poorly understood. The relatively small size of zebrafish embryos and larvae allows a feasible analysis of the broad spectrum of ECs within every tissue and organ of a whole organism. ECs have been suggested to be conditional innate immune cells. Whether ECs possess the comparable capacity of involvement in immune response is so far undetermined. Currently, through single-cell RNA sequencing analysis of total ECs of zebrafish we identified a fraction of endothelial cells expressing the marker genes of innate immune cells, named “endoimmune cells”. We found the percentage of these cells gradually increased along with the embryonic development. Then, we observed the patrolling mCherry+ cells displayed the morphology alike to the macrophages and neutrophils. Furthermore, we revealed that some of the kdrl:ras-mCherry ECs were labelled with coro1a:EGFP as well. In addition, we demonstrated that the mCherry+ EC from intersegmental vessel could gradually present the expression of GFP inTg(kdrl:ras-mCherry∷coro1a:GFP)line, suggesting the endoimmune cells are derived from ECs. Importantly, we showed the endoimmune cells are responsive to the inflammation in zebrafish. Taken together, these data suggested the existence of endoimmune cells, a novel type of subpopulations of ECs. It will provide novel insights for understanding endothelial roles in both normal physiological function and human diseases and enable endoimmune cells-based target therapies.
Rapid quantitative assessment of fish larvae community composition using metabarcoding
Authors: Ratcliffe Frances C. , Uren Webster Tamsyn M. , Rodriguez-Barreto Deiene , O’Rorke Richard , de Leaniz Carlos Garcia , Consuegra Sofia
Published: January 2020

Climate change stressors greatly impact the early life-stages of many organisms but their cryptic morphology often renders them difficult to monitor using morphological identification. High-throughput sequencing of DNA amplicons (metabarcoding) is potentially a rapid and cost-effective method to monitor early life-stages for management and environmental impact assessment purposes. Yet, there is conflicting information about the quantitative capability of metabarcoding. We compared metabarcoding with traditional morphological identification to evaluate taxonomic precision and reliability of abundance estimates, using 332 fish larvae from multinet hauls (0-50m depth) collected at 14 offshore sampling sites in the Irish and Celtic seas. To improve relative abundance estimates, the amount of tissue for each specimen was standardised and mitochondrial primers with conserved binding sites were used. Family level correction factors for amplification bias and back-calculations were applied to estimate numbers of individuals of a given taxon in a sample. Estimates from metabarcoding reads and morphological assessment were positively correlated for relative family abundances as well as taxon richness (Rs=0.81, P=0.007) and diversity (Rs=0.88, P=0.003). After applying family level correction, back-estimates of the number of individuals per family within a sample were accurate to ± 2 individuals. Spatial patterns of community composition did not differ significantly between metabarcoding and morphological assessments.

Our results show that DNA metabarcoding of bulk tissue samples can be used to monitor changes in fish larvae abundance and community composition. This represents a feasible, efficient and faster alternative to morphological identification that can be applied to terrestrial and aquatic habitats.
Ultra-fast electroporation of giant unilamellar vesicles — Experimental validation of a molecular model
Authors: Sözer Esin B. , Haldar Sourav , Blank Paul S. , Castellani Federica , Vernier P. Thomas , Zimmerberg Joshua
Published: January 2020

Delivery of molecules to cells via electropermeabilization (electroporation) is a common procedure in laboratories and clinics. However, despite a long history of theoretical effort, electroporation protocols are still based on trial and error because the biomolecular structures and mechanisms underlying this phenomenon have not been established. Electroporation models, developed to explain observations of electrical breakdown of lipid membranes, describe the electric field-driven formation of pores in lipid bilayers. These transient pore models are consistent with molecular dynamics simulations, where field-stabilized lipid pores form within a few nanoseconds and collapse within tens of nanoseconds after the field is removed. Here we experimentally validate this nanoscale restructuring of bio-membranes by measuring the kinetics of transport of the impermeant fluorescent dye calcein into lipid vesicles exposed to ultrashort electric fields (6 ns and 2 ns), and by comparing these results to molecular simulations. Molecular transport after vesicle permeabilization induced by multiple pulses is additive for interpulse intervals as short as 50 ns, while the additive property of transport is no longer observed when the interval is reduced to 0 ns, consistent with the lifetimes of lipid electropores in molecular simulations. These results show that lipid vesicle responses to pulsed electric fields are significantly different from those of living cells where, for similar pulse properties, the uptake of fluorescent dye continues for several minutes.

Graphical abstract
Face recognition depends on specialized mechanisms tuned to view-invariant facial features: Insights from deep neural networks optimized for face or object recognition
Authors: Abudarham Naphtali , Yovel Galit
Published: January 2020

Faces are processed by specialized neural mechanisms in high-level visual cortex. How does this divergence to a face-specific and an object-general system contribute to face recognition? Recent advances in machine face recognition together with our understanding of how humans recognize faces enable us to address this fundamental question. We hypothesized that face recognition depends on a face-selective system that is tuned to view-invariant facial features, which cannot be accomplished by an object-general system. To test this hypothesis, we used deep convolutional neural networks (DCNNs) that were optimized for face or object recognition. Consistent with the hierarchical architecture of the visual system, results show that a human-like, view-invariant face representation emerges only at higher layers of a face-trained but not the object-trained neural network. Thus, by combining human psychophysics and computational modelling of the visual system, we revealed how the functional organization of the visual cortex may contribute to recognition.
Simultaneous analysis of neuroactive compounds in zebrafish
Authors: Myers-Turnbull Douglas , Taylor Jack C , Helsell Cole , McCarroll Matthew N , Ki Chris S , Tummino Tia A , Ravikumar Shreya , Kinser Reid , Gendelev Leo , Alexander Rebekah , Keiser Michael J , Kokel David
Published: January 2020

Neuroactive compounds are crucial tools in drug discovery and neuroscience, but it remains difficult to discover neuroactive compounds with new mechanisms of action. To address this need, researchers have developed mid-throughput phenotype-first approaches using zebrafish. This study introduces an open, non-commercial, and extensible hardware/software platform that captures and analyzes drugmodulated phenotypic responses larval zebrafish. We provide full specifications, computer-aided design (CAD) documents, and source code. Accompanying this study, we are also publicly depositing phenotypic data on 3.9 million animals and 34,000 compounds. The data include a high-replicate benchmark set on 14 compounds, a wellcontrolled reference set of 648 known neuroactive compounds, 20 specialized reference sets, a library of 1,520 FDA-approved drugs, 3 screening libraries. This open data resource is curated, structured, tied to extensive metadata, and available under a Creative Commons CC-BY license.
Dorsal anterior cingulate cortex neurons only partially integrate determinants of value
Authors: Azab Habiba , Hayden Benjamin
Published: January 2020

Evaluation often involves integrating multiple determinants of value, such as the different possible outcomes in risky choice. A brain region can be placed either before or after a presumed evaluation stage by measuring how responses of its neurons depend on multiple determinants of value. A brain region could also, in principle, show partial integration, which would indicate that it occupies a middle position between (pre-evaluative) non-integration and (post-evaluative) full integration. Existing mathematical techniques cannot distinguish full from partial integration and therefore risk misidentifying regional function. Here we use a new Bayesian regression-based approach to analyze responses of neurons in dorsal anterior cingulate cortex (dACC) to risky offers. We find that dACC neurons only partially integrate across outcome dimensions, indicating that dACC cannot be assigned to either a pre- or post-evaluative position. Neurons in dACC also show putative signatures of value comparison, thereby demonstrating that comparison does not require complete evaluation before proceeding.
ACSL3 is a novel GABARAPL2 interactor that links ufmylation and lipid droplet biogenesis
Authors: Eck Franziska , Kaulich Manuel , Behrends Christian
Published: January 2020

While studies of ATG genes in knockout models led to an explosion of knowledge about the functions of autophagy components, the exact roles of LC3/GABARAP proteins are still poorly understood. A major drawback for their understanding is that the available interactome data was largely acquired using overexpression systems. To overcome these limitations, we employed CRISPR/Cas9-based genome-editing to generate a panel of cells in which human ATG8 genes were tagged at their natural chromosomal locations with an N-terminal affinity epitope. This cellular resource was exemplarily employed to map endogenous GABARAPL2 protein complexes in response to autophagic modulation using interaction proteomics. This approach identified the ER transmembrane protein and lipid droplet biogenesis factor ACSL3 as a stabilizing GABARAPL2-binding partner. Through this interaction, the GABARAPL2-interacting protein and UFM1-activating enzyme UBA5 becomes anchored at the ER membrane. Functional analysis unveiled ACSL3 and lipid droplet formation as novel regulators of the enigmatic UFM1 conjugation pathway.
New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interaction data
Authors: Ronan Tom , Garnett Roman , Naegle Kristen
Published: January 2020

Protein domain interactions with short linear peptides, such as Src homology 2 (SH2) domain interactions with phosphotyrosine-containing peptide motifs (pTyr), are ubiquitous and important to many biochemical processes of the cell. The desire to map and quantify these interactions has resulted in the development of high-throughput (HTP) quantitative measurement techniques, such as microarray or fluorescence polarization assays. For example, in the last 15 years, experiments have progressed from measuring single interactions to covering 500,000 of the 5.5 million possible SH2-pTyr interactions in the human proteome. However, high variability in affinity measurements and disagreements about positive interactions between published datasets led us to re-evaluate the analysis methods and raw data of published SH2-pTyr HTP experiments. We identified several opportunities for improving the identification of positive and negative interactions, and the accuracy of affinity measurements. We implemented model fitting techniques that are more statistically appropriate for the non-linear SH2-pTyr interaction data. We developed a novel method to account for protein concentration errors due to impurities and degradation, as well as addressing protein inactivity and aggregation. Our revised analysis increases reported affinity accuracy, reduces the false negative rate, and results in an increase in useful data due to the addition of reliable true negative results. We demonstrate improvement in classification of binding vs non-binding when using machine learning techniques, suggesting improved coherence in the reanalyzed datasets. We present revised SH2-pTyr affinity results, and propose a new analysis pipeline for future HTP measurements of domain-peptide interactions.
Labeling Antibodies with N-Hydroxysuccinimide-Long Chain (NHS-LC)-Biotin
Authors: Berg Eric A. , Fishman Jordan B.
Published: January 2020

Labeling antibodies with biotin (biotinylation) is a useful and simple technique. Biotin's small size (244 Da) usually has little effect on the biological activity of the protein target. The most common way to biotinylate an antibody is to cross-link a biotin succinimidyl ester to a primary amine. There are many commercially available types of biotin analogs that can be used for labeling. They vary in reactive group chemistry as well as spacer length. For example, a common analog used for biotinylation is the succinimidyl ester of biotin with an aminohexanoic acid spacer (Long Chain or LC-Biotin), utilized here. A PEG spacer of varying length can also be used.
Purification of Total RNA from Mammalian Cells and Tissues
Authors: Green Michael R. , Sambrook Joseph
Published: January 2020

This protocol describes the use of a monophasic lysis reagent to isolate total RNA from mammalian cells (grown as either a monolayer or in suspension) or tissues. An alternative protocol for the isolation of RNA from a small quantity of cells (102–104) or tissue (1–10 mg) is also included. In the latter case, glycogen is added to the monophasic lysis reagent and is used as a carrier to increase the recovery of RNA.
In Vitro Transcription Systems
Authors: Green Michael R. , Sambrook Joseph
Published: January 2020

Virtually all in vitro transcription of DNA into RNA is performed with bacteriophage-encoded DNA-dependent RNA polymerases. These enzymes and their characteristics are introduced here.
Strategic drivers for product and process innovation
Authors: De Guimarães Julio Cesar Ferro , Severo Eliana Andréa , Campos Domingos Fernandes , El-Aouar Walid Abbas , Azevedo Fabiana Lucena Bezerra de
Published: January 2020

Purpose

The organizations need to use strategic drivers such as market orientation (MO) and knowledge management (KM) for the development of product and process innovations, which can become a major source of sustainable competitive advantage (SCA). However, there is a gap in the use of these precepts, specifically in Brazilian companies. The purpose of this paper is to measure the relationship among MO, KM orientation, innovation (product and process), SCA and organizational performance (OP).

Design/methodology/approach

The research was developed through a survey in 1,072 companies from the industrial manufacturing, commerce and services activity sectors. For the analysis of data, the study used the structural equation modeling method.

Findings

This study contributes to managerial decisions in the choice of investment in strategic drivers and innovation, to obtain competitive advantages and economic gains. The results highlight that companies that use market information have formal structures to support innovation processes achieving more successful results.

Research limitations/implications

The framework proposed in this research can be used for different industries and segments.

Originality/value

The theoretical value of this paper is the contribution to the literature with the provision of a framework to analyze the strategic drivers, which are antecedents of innovation in different sectors of activity and in different sizes of companies. It is highlighted as managerial contributions, that the study identified evidence that organizations seek a superior OP to the competitor, creating competitive differentials that result in SCA.
University entrepreneurial intentions: mainland and insular regions – are they different?
Authors: Lopes João , Teixeira Sergio Jesus , Ferreira João J.M. , Silveira Paulo , Farinha Luís , Lussuamo João
Published: January 2020

Purpose

The purpose of this paper is to involve the differences in the entrepreneurial intentions of student at higher education institutions (HEIs) in the Portuguese regions (mainland and insular).

Design/methodology/approach

Applying a sample of 594 valid responses, the authors analyzed the data according to linear regression models.

Findings

The results convey how HEI students generally do not intend to become entrepreneurs in both the mainland and the insular regions. Although HEI students broadly do not aim to launch their own businesses, the results show that students in mainland regions feel they have the skills to start a business and drive it to success. In insular regions, students feel encouraged by their friends and family to set up their own business. When comparing insular and mainland regions, the results demonstrate how in insular regions, there is a greater probability that HEI students become entrepreneurs than in the mainland regions. Furthermore, entrepreneurial intentions in the mainland regions develop in terms of “opportunities” while driven by necessity in the insular regions.

Practical implications

This furthermore makes recommendations to regional governments and to HEIs in order to enable better encouragement of entrepreneurship in academia.

Originality/value

This study is original and innovative due to its comparison of the entrepreneurial intentions prevailing in mainland and insular regions and may propose new highlights to the academic scientific literature.
Studies on effect of steel fiber and coarse aggregate on fracture properties of self compacting concrete using wedge splitting test
Authors: B. Raja Rajeshwari , M.V.N. Sivakumar
Published: January 2020

Purpose

Fracture properties depend on the type of material, method of testing and type of specimen. The purpose of this paper is to evaluate fracture properties by adopting a stable test method, i.e., wedge split test.

Design/methodology/approach

Coarse aggregate of three different sizes (20 mm, 16 mm and 12.5 mm), three ratios of coarse aggregate, fine aggregate (CA:FA) (50:50, 45:55, 40:60), presence of steel fibers, and specimens without and with guide notch were chosen as parameters of the study.

Findings

Load-crack mouth opening displacement curves indicate that for both fibrous and non-fibrous mixes, higher volume of aggregate and higher size of coarse aggregate have high fracture energy.

Originality/value

For all volumes of coarse aggregate, it was noticed that specimens with 12.5 mm aggregate size achieved highest peak load and abrupt drop post-peak. The decrease in coarseness of internal structure of concrete (λ) resulted in the increase of fracture energy.
Nurses’ emotions, emotional labor, and job satisfaction
Authors: Lee Mikyoung , Jang Keum-Seong
Published: January 2020

Purpose

The purpose of this paper is to examine the relationships between emotional labor, emotions, and job satisfaction among nurses, and explore the mediating role of emotions in the relationship between emotional labor and job satisfaction.

Design/methodology/approach

A cross-sectional study was designed with 168 nurses in Korea. Structural equation modeling and path analysis were performed to analyze data.

Findings

Surface acting correlated positively with anxiety and frustration. Deep acting correlated positively with enjoyment and pride but correlated negatively with anxiety, anger and frustration. Enjoyment and pride correlated positively with job satisfaction; anger correlated negatively with job satisfaction. Deep acting correlated positively with job satisfaction, while surface acting did not show a significant relationship. Enjoyment, pride and anger mediated the relationship between deep acting and job satisfaction.

Research limitations/implications

This research expands empirical findings on nurses’ emotional experiences, by considering their discrete emotions rather than general affect. It is the first study to empirically examine the relationships between emotional labor, discrete emotions and job satisfaction, as well as the mediating role of emotions in the relationship between emotional labor and job satisfaction in the nursing field. The mediating role of emotions suggests that not only nurses and nurse managers but also hospital administrators should take nurses’ emotions into account to increase nurses’ well-being and their job satisfaction. Finally, differential influences of surface acting and deep acting on nurses’ emotional experiences and job satisfaction highlight the need for practical interventions to promote the use of deep acting among nurses.

Originality/value

This study confirms the mediating role of emotions in the relationship between emotional labor and job satisfaction in the nursing field. It encourages future research to pay greater attention to nurses’ emotions themselves along with emotional labor. Findings add an interdisciplinary aspect to research on nursing by assimilating psychological perspectives of emotion and emotion management research to this field.
The motivating power of gamification
Authors: Lier Liesa Marie , Breuer Christopher
Published: January 2020

Purpose

An increasing number of firms have implemented workplace health promotion programmes (WHPPs). However, such programmes can only be effective and economically viable if employees actually engage. In an effort to uncover ways to promote employee engagement and, hence, WHPP effectiveness, the purpose of this paper is to assess the impact of the inclusion of a gamification element in a worksite health promotion programme on health outcomes.

Design/methodology/approach

Real-life data from a WHPP provider firm were analysed. Linear and logistic regression analyses were performed to assess the impact of participating in a step challenge on average daily step count and the likelihood of reaching the widely communicated goal of taking at least 10,000 steps per day.

Findings

It was found that the inclusion of gamification elements was significantly positively related to physical activity outcomes: employees who participated in the step challenge took considerably more steps than employees who did not participate (β=1,139.36, p<0.005). Participation increased the likelihood of fulfilling the recommended goal of 10,000 steps per day significantly vs non-participants (β=1.81, p=0.005). Finally, the results indicate that challenge participation was associated with a considerably greater increase in steps for men than for women.

Originality/value

This research advances the scientific understanding of the modern types of WHPPs that build on digital solutions and gamification. As an increasing number of firms face the challenge of designing a programme that actually works, the finding that the inclusion of gamification considerably increases programme effectiveness in terms of health outcomes is highly valuable.