bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple Dimerizing Motifs Modulate the Dimerization of the Syndecan Transmembrane Domains
Authors: Chen J. , Wang F. , He C. , Luo S-Z. 
Published: January 2020

AbstractSyndecans(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

AbstractValue-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

AbstractThe 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

ABSTRACTPb2+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 MetallomicsSyt1, 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

AbstractEndothelial 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

AbstractClimate 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

AbstractDelivery 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

SummaryFaces 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.
Dorsal anterior cingulate cortex neurons only partially integrate determinants of value
Authors: Azab Habiba , Hayden Benjamin 
Published: January 2020

ABSTRACTEvaluation 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

AbstractWhile 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

ABSTRACTProtein 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.
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

PurposeThe 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/approachThe 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.FindingsThis 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/implicationsThe framework proposed in this research can be used for different industries and segments.Originality/valueThe 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

PurposeThe 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/approachApplying a sample of 594 valid responses, the authors analyzed the data according to linear regression models.FindingsThe 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 implicationsThis furthermore makes recommendations to regional governments and to HEIs in order to enable better encouragement of entrepreneurship in academia.Originality/valueThis 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.