bluuebunny/crossref_metadata_2025_split huggingface dataset:
How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates
Authors: Fogarty CA , Harbison AM , Dugdale AR , Fadda E 
Published: May 2020

AbstractN-glycosylation is one of the most abundant and diverse post-translational modifications of proteins, implicated in protein folding and structural stability, and mediating interactions with receptors and with the environment. All N-glycans share a common core from which linear or branched arms stem from, with functionalization specific to different species and to the cells’ health and disease state. This diversity generates a rich collection of structures, all diversely able to trigger molecular cascades and to activate pathways, which also include adverse immunogenic responses. These events are inherently linked to the N-glycans 3D architecture and dynamics, which remain for the large part unresolved and undetected because of their intrinsic structural disorder. In this work we use molecular dynamics (MD) simulations to provide insight into N-glycans 3D structure by analysing the effects of a set of very specific modifications found in plants and invertebrate N-glycans, which are immunogenic in humans. We also compare these structural motifs and combine them with mammalian N-glycans motifs to devise strategies for the control of the N-glycan 3D structure through sequence. Our results suggest that the N-glycans architecture can be described in terms of the local spatial environment of groups of monosaccharides. We define these “glycoblocks” as self-contained 3D units, uniquely identified by the nature of the residues they comprise, their linkages and structural/dynamic features. This alternative description of glycans 3D architecture can potentially lead to an easier prediction of sequence-to-structure relationships in complex carbohydrates, with important implications in glycoengineering design.
Golgi-Dependent Copper Homeostasis Sustains Synaptic Development and Mitochondrial Content
Authors: Hartwig Cortnie , Macías Méndez Gretchen , Bhattacharjee Shatabdi , Vrailas-Mortimer Alysia D. , Zlatic Stephanie A. , Freeman Amanda A. H. , Gokhale Avanti , Concilli Mafalda , Savas Christie Sapp , Rudin-Rush Samantha , Palmer Laura , Shearing Nicole , Margewich Lindsey , McArthy Jacob , Taylor Savanah , Roberts Blaine , Lupashin Vladimir , Polishchuk Roman S. , Cox Daniel N. , Jorquera Ramon A. , Faundez Victor 
Published: May 2020

AbstractRare genetic diseases preponderantly affect the nervous system with phenotypes spanning from neurodegeneration to neurodevelopmental disorders. This is the case for both Menkes and Wilson disease, arising from mutations in ATP7A and ATP7B, respectively. The ATP7A and ATP7B proteins localize to the Golgi and regulate copper homeostasis. We demonstrate conserved interactions between ATP7 paralogs with the COG complex, a Golgi complex tether. Disruption ofDrosophilacopper homeostasis by ATP7 tissue-specific transgenic expression caused alterations in epidermis, catecholaminergic, sensory, and motor neurons. Prominent among neuronal phenotypes was a decreased mitochondrial content at synapses, a phenotype that paralleled with alterations of synaptic morphology, transmission, and plasticity. These neuronal and synaptic phenotypes caused by transgenic expression of ATP7 were rescued by downregulation or haploinsufficiency of COG complex subunits. We conclude that the integrity of Golgi-dependent copper homeostasis mechanisms, requiring ATP7 and COG, are necessary to maintain mitochondria functional integrity and localization to synapses.Significance StatementMenkes and Wilson disease affect copper homeostasis and characteristically afflict the nervous system. However, their molecular neuropathology mechanisms remain mostly unexplored. We demonstrate that copper homeostasis in neurons is maintained by two factors that localize to the Golgi apparatus, ATP7 and the COG complex. Disruption of these mechanisms affect mitochondrial function and localization to synapses as well as neurotransmission and synaptic plasticity. These findings suggest a new principle of interorganelle communication whereby the Golgi apparatus and mitochondria are functionally coupled through homeostatically controlled cellular copper levels.
Chromosome-scale genome assembly ofFusarium oxysporumstrain Fo47, a fungal endophyte and biocontrol agent
Authors: Wang Bo , Yu Houlin , Jia Yanyan , Dong Quanbin , Steinberg Christian , Alabouvette Claude , Edel-Hermann Veronique , Kistler H. Corby , Ye Kai , Ma Li-Jun , Guo Li 
Published: May 2020

AbstractHere, we report a chromosome-level genome assembly ofFusarium oxysporumstrain Fo47 (12 pseudomolecules; contig N50: 4.52Mb), generated using a combination of PacBio long-read, Illumina pair-ended and Hi-C sequencing data. AlthoughF. oxysporumcauses vascular wilt to over 100 plant species, the strain Fo47 is classified as an endophyte and widely used as a biocontrol agent for plant disease control. The Fo47 genome carries a single accessory chromosome of 4.23 Mb, compared to the reference genome ofF. oxysporumf.sp.lycopersicistrain Fol4287. The high-quality assembly and annotation of the Fo47 genome will be a valuable resource for studying the mechanisms underlying the endophytic interactions betweenF. oxysporumand plants, as well as deciphering the genome evolution of theF. oxysporumspecies complex.
A functional screen for optimization of short hairpin RNA biogenesis and RISC loading
Authors: Sons Robert L , Kaufmann Kyle W , Hammond Scott M 
Published: May 2020

AbstractGene silencing via short hairpin mediated RNAi (shRNA) is a valuable experimental tool and has promise as a therapeutic strategy. Several shRNA platforms make use of the loop and flanking sequences from the endogenous microRNA (miRNAs) miR-30a or other miRNAs to provide an RNA structure for efficient and accurate biogenesis of the RNA trigger. However, the stem regions of these shRNAs are typically designed as perfect duplex structures which is an uncommon feature for endogenous miRNA precursors. A limitation of these designs is that shRNAs with perfect duplex stems undergo extensive stem cleavage analogous to the Dicer independent miRNA miR-451, destroying the shRNA trigger sequence that is present in the 3P arm. We employed an unbiased screen of > 9000 shRNA structures to identify features that prevent stem cleavage and promote canonical biogenesis and loading into the effector complex RISC. We find that a central stem bulge or kink reduces central stem cleavage and improves accuracy of Dicer processing. Furthermore, 9 - 10 GC nucleotides in the guide strand improves shRNA efficiency. These design rules enable more effective shRNA tools and are compatible with existing sets of optimized guide/target sequences.
Convolutional Neural Networks for Classifying Melanoma Images
Authors: Sagar Abhinav , Jacob Dheeba 
Published: May 2020

AbstractIn this work, we address the problem of skin cancer classification using convolutional neural networks. A lot of cancer cases early on are misdiagnosed leading to severe consequences including the death of patient. Also there are cases in which patients have other problems and doctors interpret it as skin cancer. This leads to unnecessary time and money spent for further diagnosis. In this work, we address both of the above problems using deep neural networks and transfer learning architecture. We have used publicly available ISIC databases for both training and testing our network. Our model achieves an accuracy of 0.935, precision 0.94, recall 0.77, F1 score 0.85 and ROC-AUC 0.861 which is better than the previous state of the art approaches.
Epithelial Cell-like Elasticity Modulates E-cadherin Adhesion Organization
Authors: Eftekharjoo Mohamad , Chatterji Siddharth , Maruthamuthu Venkat 
Published: May 2020

AbstractE-cadherin adhesions are essential for cell-to-cell cohesion and mechanical coupling between epithelial cells and reside in a micro-environment that comprises the adjoining epithelial cells. While E-cadherin has been shown to be a mechanosensor, it is unknown if E-cadherin adhesions can differentially sense stiffness within the range of that of epithelial cells. A survey of literature shows that epithelial cells’ Young’s moduli of elasticity lie predominantly in the sub kPa to few kPa range, with cancer cells often being softer than non-cancerous ones. Here, we devised oriented E-cadherin-coated soft silicone substrates with sub kPa or few kPa elasticity, but with similar viscous moduli, and found that E-cadherin adhesions differentially organize depending on the magnitude of epithelial cell-like elasticity. Linearly shaped E-cadherin adhesions associated with radially oriented actin, but not irregularly shaped E-cadherin adhesions associated with circumferential actin foci, were much more numerous on 2.4 kPa E-cadherin substrates compared to 0.3 kPa E-cadherin substrates. However, the total amount of E-cadherin in both types of adhesions taken together was similar on the 0.3 kPa and 2.4 kPa E-cadherin substrates, across many cells. Furthermore, while the average extent of nuclear recruitment of the mechanoresponsive transcription factor YAP on the 0.3 kPa E-cadherin substrate was undiminished relative to that on the 2.4 kPa substrate, a fraction of cells on the softer substrate displayed relatively high levels of YAP nuclear recruitment. Our results show that E-cadherin adhesions can be regulated by epithelial cell-like elasticity and have significant implications for disease states like carcinomas characterized by altered epithelial cell elasticity.
Lipopolysaccharide preconditioning augments phagocytosis of malaria-parasitized red blood cells through induced bone marrow-derived macrophages in the liver, thereby increasing the murine survival afterPlasmodium yoeliiinfection
Authors: Ono Takeshi , Yamaguchi Yoko , Nakashima Hiroyuki , Nakashima Masahiro , Ishikiriyama Takuya , Seki Shuhji , Kinoshita Manabu 
Published: May 2020

AbstractMalaria remains a grave concern for humans, as effective medical countermeasures for malaria infection have yet to be developed. Phagocytic clearance of parasitized red blood cells (pRBCs) by macrophages is an important front-line innate host defense against malaria infection. We previously showed that repeated injections of low-dose lipopolysaccharide (LPS) prior to bacterial infection, called LPS preconditioning, strongly augmented phagocytic/bactericidal activity in murine macrophages. However, how LPS preconditioning prevents murine malaria infection is unclear. We investigated the protective effects of LPS preconditioning against lethal murine malaria infection, focusing on CD11bhighF4/80lowliver macrophages, which are increased by LPS preconditioning. Mice were subjected to LPS preconditioning by intraperitoneal injections of low-dose LPS for 3 consecutive days, and 24 h later, they were intravenously infected with pRBCs ofPlasmodium yoelii17XL. LPS preconditioning markedly increased the murine survival and reduced parasitemia, while it did not reduce TNF secretions, only delaying the peak of plasma IFN-γ after malaria infection in mice. Anin vitrophagocytic clearance assay of pRBCs showed that the CD11bhighF4/80lowliver macrophages of the LPS-preconditioned mice had significantly augmented phagocytic activity against pRBCs. The adoptive transfer of CD11bhighF4/80lowliver macrophages from LPS-preconditioned mice to control mice significantly improved the survival after malaria infection. We conclude that LPS preconditioning stimulated CD11bhighF4/80lowliver macrophages to augment the phagocytic clearance of pRBCs, which may play a central role in resistance against malaria infection. LPS preconditioning may be an effective tool for preventing malaria infection.
Disclosure of corporate social responsibility (CSR) and its implications on company value as a result of the impact of corporate governance and profitability
Authors: Kamaliah Kamaliah 
Published: May 2020

Purpose
The purpose of this study is to examine the effect of corporate governance and corporate profitability on firm value with corporate social responsibility (CSR) disclosure as the intervening variable.

Design/methodology/approach
The population of this study was all companies listed in the LQ 45 Index group in the Indonesia Stock Exchange in 2013-2014. The inferential statistics used in this study applied the partial least square (PLS) based structural equation model (SEM) method with the assistance of SmartPLS 2.0. The PLS method was selected based on the consideration that there was a construct formed with reflective indicators in this study.

Findings
From the results of this study, it can be concluded that corporate governance does not have any effect on CSR disclosure, profitability of company has an effect on CSR disclosure, CSR disclosure has an effect on firm value. In addition, CSR disclosure does not mediate the effect of on firm value. These results showed that corporate governance can have an effect on firm value directly, and there is no role of CSR disclosure in mediating the effect of corporate governance on firm value, and profitability of company has an effect on firm value through CSR disclosure.

Originality/value
The originality of this research is on the reason that many studies that have been conducted still indicated the inconsistency in the results and diversity of the indicators, so that a similar research was conducted by involving the indicators used for measuring the corporate governance variable, which were the proportion of independent commissioners and audit committee. Meanwhile, for the profitability variable, return on assets and return on equity were used as the indicators.
In pursuit of corporate sustainability: factors contributing to employees' workplace behavior
Authors: Lee Stacy H. , Ha-Brookshire Jung E. 
Published: May 2020

PurposeAchieving sustainability is imperative for all businesses but perhaps even so more in fashion retail. As a vital group of stakeholders, employees interact with all other stakeholders and play a critical role in the sustainability of an organization.Design/methodology/approachThis study is to investigate internal and external factors that influence employees' harmful or useful behaviors based on the Social Cognitive Theory (SCT) of morality.FindingsThe findings show that employees' perceptions of the moral responsibility of achieving corporate sustainability both as an internal corporate ethical value and as an external factor influenced their organizational citizenship behavior, as well as their propensity toward displaying counterproductive workplace behavior. Higher quality relationships with managers were found to strengthen the relationship between corporate ethical values (CEVs) and organizational citizenship behaviors.Research limitations/implicationsThe objective of this study focused exclusively on the US fashion retail employees. Therefore, it is suggested that future research compares the cultural influences on employees as related to the moral responsibility of corporate sustainability.Originality/valueThis study is one of few studies which have explored the level of employees' perceived moral responsibility toward the notion of how corporate sustainability should be accomplished.
How outward investment from emerging markets affects economic development at home: using the eclectic paradigm to synthesize two IB literatures
Authors: Hendriks Guus 
Published: May 2020

PurposeThis paper aims to use the eclectic paradigm as a broad organizing framework to bring together two somewhat parallel international business (IB) literatures, one on the development effects of multinational enterprise activity and the other on the internationalization of emerging market multinationals (EMNEs). The author does so to better understand how outward foreign investment shapes economic development in firms’ home countries.Design/methodology/approachConsidering that the characteristics of foreign investment by EMNEs likely differ from that of their developed economy counterparts and that such characteristics may have unique development consequences, the author revisits one of IB’s overarching theories to rethink how ownership, location and internalization advantages take shape and stimulate diverse development outcomes.FindingsMy narrative review and conceptual analysis indicate that the eclectic paradigm is a valuable framework that can be used to shed light on underexplored phenomena and thereby inform important policy debates. The analysis suggests that unique characteristics of EMNE investment simultaneously have positive and negative development consequences in their home countries.Practical implicationsThe author sets out a research agenda that revolves around six propositions that separately relate one of these three distinct characteristics of EMNE investment to two development outcomes, namely, spillovers and direct effects on home-country employment. My propositions suggest that important policy dilemmas potentially apply, in that each of the three characteristics positively affects one of the aspects of development, but negatively the other.Originality/valueMy research agenda presents international business scholars with new opportunities to build on a history of policymaking impact, now geared toward resolving society’s grand challenge of underdevelopment.
Spatial variation in diet–microbe associations across populations of a generalist North American carnivore
Authors: Colborn A. Shawn , Kuntze Corbin C. , Gadsden Gabriel I. , Harris Nyeema C. 
Published: May 2020

Abstract

Generalist species, by definition, exhibit variation in niche attributes that promote survival in changing environments. Increasingly, phenotypes previously associated with a species, particularly those with wide or expanding ranges, are dissolving and compelling greater emphasis on population‐level characteristics.

In the present study, we assessed spatial variation in diet characteristics, gut microbiome and associations between these two ecological traits across populations of coyotes Canis latrans. We highlight the influence of the carnivore community in shaping these relationships, as the coyote varied from being an apex predator to a subordinate, mesopredator across sampled populations.

We implemented a scat survey across three distinct coyote populations in Michigan, USA. We used carbon (δ13C) and nitrogen (δ15N) isotopic values to reflect consumption patterns and trophic level, respectively. Corresponding samples were also paired with 16S rRNA sequencing to describe the microbial community and correlate with isotopic values.

Although consumption patterns were comparable, we found spatial variation in trophic level among coyote populations. Specifically, δ15N was highest where coyotes were the apex predator and lowest where coyotes co‐occurred with grey wolves Canis lupus.

The gut microbial community exhibited marked spatial variation across populations with the lowest operational taxonomic units diversity found where coyotes occurred at their lowest trophic level. Bacteriodes and Fusobacterium dominated the microbiome and were positively correlated across all populations. We found no correlation between δ13C and microbial community attributes. However, positive associations between δ15N and specific microbial genera increased as coyotes ascended trophic levels.

Coyotes provide a model for exploring implications of niche plasticity because they are a highly adaptable, wide‐ranging omnivore. As coyotes continue to vary in trophic position and expand their geographic range, we might expect increased divergence within their microbial community, changes in physiology and alterations in behaviour.
Scented nectar and the challenge of measuring honest signals in pollination
Authors: Burdon Rosalie C. F. , Raguso Robert A. , Gegear Robert J. , Pierce Ellen C. , Kessler André , Parachnowitsch Amy L. 
Published: May 2020

Abstract

Nectar scents are thought to function as honest signals of reward used by pollinators, but this hypothesis has rarely been tested.

Using Penstemon digitalis, we examined honest signalling of the nectar volatile (S)‐(+)‐linalool and pollinator responses to linalool in both field and laboratory settings. Because our previous work showed that linalool emission was associated with higher female fitness and that nectar is scented with linalool, we hypothesized that linalool was an honest signal of nectar reward. To assess honesty, we measured linalool–nectar associations including nectar volume, sugar amount, concentration and production rate for inflorescences and flowers in several populations. We also assessed whether Bombus impatiens, the main pollinator of P. digitalis at our sites, can use linalool as a foraging signal. We supplemented real or artificial flowers in the field and laboratory with varying linalool–nectar combinations to measure pollinator behavioural responses.

We found that an inflorescence's linalool emissions could be used to predict nectar rewards in P. digitalis, but this was driven by indirect associations with display size rather than directly advertising more profitable flowers. For flowers within inflorescences there was also no evidence for an association between signal and reward. Field tests of bumblebee behaviour were inconclusive. However, in laboratory assays, bumblebees generally used variation in linalool emissions to choose more profitable flowers, demonstrating they can detect differences in linalool emitted by P. digitalis and associate them with reward profitability. These results suggest experiments that decouple display size, scent and reward are necessary to assess whether (and when) bees prefer higher linalool emissions. Bees preferred nectars with lower linalool concentrations when linalool flavoured the nectar solution, suggesting the potential for conflicting pressures on scent emission in the field.

Synthesis. Our results highlight the challenges of assessing function for traits important to fitness and suggest that the perception of floral signalling honesty may depend on whether pollinators use inflorescences or flowers within inflorescences when making foraging decisions. We conclude that future research on honest signalling in flowering plants, as well as its connection to phenotypic selection, should explicitly define honesty, in theoretical and experimental contexts.