bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subcellular structure segmentation from cryo-electron tomograms via machine learning
Authors: Zhou Li , Yang Chao , Gao Weiguo , Perciano Talita , Davies Karen M. , Sauter Nicholas K. 
Published: April 2020

AbstractWe describe how to use several machine learning techniques organized in a learning pipeline to segment and identify subcellular structures from cryo electron tomograms. These tomograms are difficult to analyze with traditional segmentation tools. The learning pipeline in our approach starts from supervised learning via a special convolutional neural network trained with simulated data. It continues with semi-supervised reinforcement learning and/or a region merging techniques that try to piece together disconnected components that should belong to the same subcellular structure. A parametric or non-parametric fitting procedure is then used to enhance the segmentation results and quantify uncertainties in the fitting. Domain knowledge is used in generating the training data for the neural network and in guiding the fitting procedure through the use of appropriately chosen priors and constraints. We demonstrate that the approach proposed here work well for extracting membrane surfaces of protein reconstituted liposomes in a cellular environment that contains other artifacts.
Robust survival-based RNAi using in tandem silencing of adenine phosphoribosyltransferase
Authors: Orr Robert G. , Foley Stephen J. , Galotto Giulia , Liu Boyuan , Vidali Luis 
Published: April 2020

AbstractRNA interference (RNAi) enables flexible and dynamic interrogation of entire gene families or essential genes without the need for exogenous proteins, unlike CRISPR-Cas technology. Unfortunately, isolation of plants undergoing potent gene silencing requires laborious design, visual screening, and physical separation for downstream characterization. Here, we developed a novel APT-based RNAi technology (APTi) inPhyscomitrella patensthat simultaneously improves upon the multiple limitations of current RNAi techniques. APTi exploits the pro-survival output of transiently silencing the APT gene in the presence of 2-fluoradenine, thereby establishing survival itself as a reporter of RNAi. To maximize silencing efficacy of gene targets we created vectors that facilitate insertion of any gene target sequence in tandem with the APT silencing motif. The APTi approach resulted in a homogenous population ofP. patensmutants specific for our gene target, with zero surviving background plants within 8 days. The observed mutants directly corresponded to a maximal 93% reduction of the tested target protein, substantially exceeding previous dsRNA methods. The positive selection nature of APTi represents a fundamental improvement in RNAi technology and will contribute to the growing demand for technologies amenable to high-throughput phenotyping.One-sentence summaryGeneration of dsRNA targeting theAPTgene in tandem with a target gene enables positive selection of strongly silencing plants.
The coordinated localization of mRNA to centrosomes facilitates error-free mitosis
Authors: Ryder Pearl V. , Fang Junnan , Lerit Dorothy A. 
Published: April 2020

AbstractCentrosomes are microtubule-organizing centers required for error-free mitosis and embryonic development. The microtubule-nucleating activity of centrosomes is conferred by the pericentriolar material (PCM), a composite of numerous proteins subject to cell cycle-dependent oscillations in levels and organization. In diverse cell types, mRNAs localize to centrosomes and may contribute to changes in PCM abundance. Here, we investigate the regulation of mRNA localization to centrosomes in the rapidly cyclingDrosophila melanogasterembryo. We find that RNA localization to centrosomes is regulated during the cell cycle and developmentally. We identify a novel role for the fragile-X mental retardation protein (FMRP), which localizes to pericentrosomal RNA granules, in the post-transcriptional regulation of centrosomal RNA. Further, the mis-targeting of a model centrosomal mRNA,centrocortin(cen), is sufficient to alter cognate protein localization to centrosomes and impair spindle morphogenesis and genome stability.
Comparative secretome ofMagnaporthe oryzaeidentified proteins involved in virulence and cell wall integrity
Authors: Liu Ning , Qi Linlu , Huang Manna , Chen Deng , Yin Changfa , Zhang Yiying , Wang Xingbin , Yuan Guixin , Wang Rui-Jin , Yang Jun , Peng You-Liang , Lu Xunli 
Published: April 2020

AbstractPlant fungal pathogens secrete numerous proteins into the apoplast at the plant–fungus contact sites to facilitate colonization. Only a few secreted proteins were functionally characterized inMagnaporthe oryzae, the fungal pathogen causing rice blast disease worldwide. ALG3 is an α-1, 3-mannosyltransferase function in N-glycan synthesis for secreted N-glycosylated proteins, and the Δalg3mutants show strong defects in cell wall integrity and fungal virulence, indicating a potential effect on the secretion of multiple proteins. In this study, we compared the secretome of wild type and Δalg3mutants, and identified 51 proteins that require ALG3 for proper secretion. These are predicted to be involved in metabolic processes, interspecies interactions, cell wall organization, and response to chemicals. The tested secreted proteins localized at the apoplast region surrounding the fungal infection hyphae. Moreover, theN-glycosylation of candidate proteins was significantly changed in the Δalg3mutant, leading to the reduction of protein secretion and abnormal protein localization. Furthermore, we tested the function of two genes, one is a previously reported M. oryzae geneInvertase 1(INV1) encoding a secreted invertase, and the other one is a gene encoding an Acid mammalian chinitase (AMCase). The fungal virulence was significantly reduced and the cell wall integrity was altered in the Δinv1and Δamcasemutant strains. Elucidation of the comparative secretome ofM. oryzaeimproves our understanding of the proteins that require ALG3 for secretion, and of their function in fungal virulence and cell wall integrity.
sTAM: An Online Tool for the Discovery of miRNA-set Level Disease Biomarkers
Authors: Shi Jiangcheng , Cui Qinghua 
Published: April 2020

AbstractmicroRNAs (miRNAs) are one class of important small noncoding RNA molecules, which have shown their excellent ability as biomarkers of various diseases. However, current miRNA biomarkers including those comprised of multiple miRNAs work at a single-miRNA level but not at a miRNA set level. Given the rapidly accumulated miRNA omics data, it is believed that miRNA set level analysis could be an important supplement to the single miRNA level analysis. For doing so, here we presented a computational method for single-sample miRNA set enrichment analysis and developed the sTAM tool (http://mir.rnanut.net/stam). Moreover, we demonstrated the usefulness of sTAM scores in discovering miRNA-set level biomarkers through two case studies. We conducted pan-cancer analysis of the sTAM scores of “tumor suppressor miRNA set” on 15 types of cancers from TCGA and 14 types of cancers from GEO, finding that the scores show a good performance in distinguishing the cancers from the controls. Moreover, we revealed that the sTAM score of “brain development” miRNA set can effectively predict cerebrovascular disorder (CVD). Finally, we believe sTAM can be used in discovering disease-related biomarkers at a miRNA-set level.
Analysis of new nosological models from disease similarities using clustering
Authors: Santamaría Lucía Prieto , García del Valle Eduardo P. , García Gerardo Lagunes , Zanin Massimiliano , González Alejandro Rodríguez , Ruiz Ernestina Menasalvas , Gallardo Yuliana Pérez , Chan Gandhi Samuel Hernández 
Published: April 2020

AbstractWhile classical disease nosology is based on phenotypical characteristics, the increasing availability of biological and molecular data is providing new understanding of diseases and their underlying relationships, that could lead to a more comprehensive paradigm for modern medicine. In the present work, similarities between diseases are used to study the generation of new possible disease nosologic models that include both phenotypical and biological information. To this aim, disease similarity is measured in terms of disease feature vectors, that stood for genes, proteins, metabolic pathways and PPIs in the case of biological similarity, and for symptoms in the case of phenotypical similarity. An improvement in similarity computation is proposed, considering weighted instead of Booleans feature vectors. Unsupervised learning methods were applied to these data, specifically, density-based DBSCAN clustering algorithm. As evaluation metricsilhouettecoefficient was chosen, even though the number of clusters and the number of outliers were also considered. As a results validation, a comparison with randomly distributed data was performed. Results suggest that weighted biological similarities based on proteins, and computed according to cosine index, may provide a good starting point to rearrange disease taxonomy and nosology.
The neutrophil antimicrobial peptide cathelicidin promotes Th17 differentiation
Authors: Minns Danielle , Smith Katie J , Alessandrini Virginia , Hardisty Gareth , Melrose Lauren , Jackson-Jones Lucy , MacDonald Andrew S. , Davidson Donald J , Findlay Emily Gwyer 
Published: April 2020

ABSTRACTThe host defence peptide cathelicidin (LL-37 in humans, mCRAMP in mice) is released from neutrophils by de-granulation, NETosis and necrotic cell death; it has potent antibacterial, antiviral and antifungal activity as well as being a powerful immunomodulator. It is released in proximity to CD4+T cells during inflammatory and infectious disease but its impact on T cell phenotype is scarcely understood. Here we demonstrate that cathelicidin is a powerful Th17 potentiating factor which increases expression of the aryl hydrocarbon receptor (AHR) and the RORγt transcription factor, in a TGF-β1-dependent manner. We show that cathelicidin induces IL-17F production in particular, and that its induction of IL-17A+F+ double producing cells is dependent on AHR while its induction of IL-17F single producing cells is not. In the presence of TGF-β1, cathelicidin profoundly suppressed IL-2 and down-regulated T-bet, specifically directing T cells away from Th1 and into a Th17 phenotype. Strikingly, Th17, but not Th1 cells were protected from apoptotic death by cathelicidin, in the first example of a neutrophil-released mediator inducing survival of a T cell subset. Finally, we show that cathelicidin is released by neutrophils in mouse lymph nodes following inoculation of heat-killedSalmonella typhimuriumand that cathelicidin-deficient mice have suppressed Th17 responses during inflammation, but not at steady state. We propose that the release of cathelicidin by neutrophils is required for maximal Th17 differentiation and IL-17 production by CD4+T cells, and that this is one method by which early neutrophilia directs subsequent adaptive immune responses with some sophistication.
Sustainability reporting and bank performance after financial crisis
Authors: Buallay Amina , Fadel Sayed M. , Alajmi Jasim , Saudagaran Shahrokh 
Published: April 2020

PurposeThis study aims to examine the relationship between sustainability reporting and bank performance after financial crisis in developed and developing countries.Design/methodology/approachThis study examines 882 banks from developed and developing countries covering 11 years after the 2008 financial crisis. The independent variable is environmental, social and governance (ESG) scores. The dependent variables are return on assets, return on equity and Tobin’s Q. This study uses bank- and country-specific control variables to measure the relationship between sustainability reporting and bank performance.FindingsThe findings deduced from the empirical results demonstrate that ESG improves banks’ accounting and market-based performance in developed countries, supporting value creation theory. Using pooling regression and instrumental variable – generalized method of moments, this study finds that ESG weakens banks’ performance in developed and developing countries.Originality/valueTo the best of the author’s knowledge, this is the first study to investigate and compare the impact of sustainability reporting on banks’ performance in developed and developing countries. The study found similarities in the impact of sustainability reporting and the improvement of banks’ current and future performance.
Competitiveness of sharing economy companies in emerging markets
Authors: Maalouf Jamal T. , Abi Aad Amine , El Masri Karam 
Published: April 2020

Purpose
This paper aims to explore the competitiveness of the sharing economy in emerging markets from the perspective of actual and potential consumers.

Design/methodology/approach
It is not surprising that most sharing economy businesses may not follow traditional competitiveness approaches. Consequently, their entry strategies and competitiveness methods might face modern, unique and unexpected challenges vis-à-vis securing sufficient consumer willingness to purchase goods and services.

Findings
A novel theoretical research model is developed which posits that people’s willingness to use the sharing economy is negatively related to liabilities of newness and positively related to consumer innovativeness and interpersonal trust. The relationship between cost and willingness to use is likely to vary on a case-by-case basis depending on the nature and extent of substitutes available or, in other words, the novelty or lack thereof embedded in the particular good or service. Other potential determinants are also best viewed as case-specific such as ethical/sustainability concerns, which vary as a function of target consumers’ preferences for ameliorating social and environmental externalities.

Originality/value
Sharing economy businesses have expanded to numerous countries around the world. There is growing evidence to suggest that this diffusion will most likely be maintained. The competitiveness of these businesses in emerging markets may depend on several variables but there is a dearth of literature in this domain which this paper seeks to address while concomitantly highlighting important avenues for future research.
Knowledge sharing: an innovative organizational approach to engage volunteers
Authors: Fait Monica , Sakka Georgia 
Published: April 2020

PurposeA profound managerial transformation approach is increasingly designed to unleash the energy and creativity of employees. The purpose of this paper is to observe as the organizations in this sector can use the knowledge sharing to derive maximum efficiency from such crucial volunteers, creating an environment suitable for stimulating the psychological well-being that is the basis of engagement.Design/methodology/approachThis exploratory study proposes a model to account the intrinsic and extrinsic motivations to exchange knowledge related to factors that stimulate volunteer's engagement.FindingsThe results of a survey of 301 volunteers operating in European organizations indicate that influencers of volunteers in a specific domain activated by knowledge sharing can act as sources of creation and can reinforce their identity, sense of belonging and trust in the organization.Research limitations/implicationsDespite results cannot be generalized because of the samples of convenience, exploratory factor analysis was used to identify the elements for which nonprofit organizations should activate a knowledge-sharing strategy so that engaged volunteers feel like cocreators of values and therefore act as true competitive assets.Originality/valueThis paper contributes to the expansion of engagement studies through framing the motivations of volunteers in knowledge sharing as a process of social interaction that involves knowledge, experience and expertise and which is able to create an environment suitable to feeding the psychological well-being that is the basis of engagement.
Seasonal employee leadership in the hospitality industry: a scale development
Authors: Arasli Huseyin , Altinay Levent , Arici Hasan Evrim 
Published: April 2020

PurposeThe purpose of this paper is to examine the model of seasonal employee leadership (SEL) in a service management process and to create a multi-dimensional scale to gauge this construct. This is because very recent qualitative research by Arasli and Arici (2019), which is the first stage of this scale, recommended a multi-dimensional SEL model for the hospitality industry.Design/methodology/approachMaking use of data gathered from 1,343 seasonal hotel employees, the authors established a new scale to examine the SEL model. Two separate data sets were collected; the first set was used to perform an exploratory factor analysis, while the second set was processed to confirm the initial factor results using a confirmatory factor analysis.FindingsThe results show that the measurement scale developed in this research provides considerable reliability, as well as convergent and discriminant validities. In particular, the findings confirmed a four-dimensional measurement scale of the SEL: seasonal leader’s qualities, core influence, operational influence and terminal influence.Originality/valueThe paper is the first attempt to develop a new scale which measures the SEL approach in the hospitality literature. Therefore, this study contributes to the current literature through developing and testing the four-dimensional SEL scale and shedding light on the importance of an industry-specific leadership in managing seasonal hotel employees effectively.
NCSS notable trade book lesson plan: Joan Procter, dragon doctor: the woman who loved reptiles
Authors: Swain Holly Hilboldt 
Published: April 2020

PurposeJoan Procter, Dragon Doctor describes the life of Joan Beauchamp Procter, renowned herpetologist, zoologist, Curator of Reptiles at the British Museum and designer of the London Zoo Reptile House. In this lesson, students reframe initial viewpoints of scientists that are not representative of a broad understanding of who scientists are and what being a scientist means. Exploring understandings and expanding their view of science to include varied areas of social sciences provokes deep discussions among students as they prepare to teach others. Using content area skills, artwork, writing, literacy and technology, students explore diverse people and fields of the sciences.Design/methodology/approachStudents engage in collaborative efforts with peers to involve themselves with content knowledge and skills in the social studies, as they integrate other areas of the curriculum including science, art, writing, literacy, literature, technology, critical thinking, research skills and inquiry-based learning. Findings include students participating in meaningful learning individually and collectively through inquiry. As students learn with and from one another, they conceptualize their own ideas through their own work in exploring relevant resources. Students plan action to move learning outside the classroom in generating changes in museums and monuments to showcase broader cultural representation of scientists in their communities.FindingsStudents engage in inquiry learning using Joan Procter, Dragon Doctor as a key text. Students explore the text and related resources, while learning with one another about scientists. Students expand their content knowledge and apply critical thinking skills, noting similarities and differences in scientists, ultimately acknowledging that what scientists do through inquiry and exploration helps them identify as scientists. Varied fields and backgrounds of scientists are explored, and students examine cultural representation in museums commemorating scientists and scientific contributions. Students create action plans to consult with museums about these issues and curate exhibits, like Joan Procter, to share with others.Originality/valueThis lesson provides students multiple avenues to deepen learning while conceptualizing and formulating their own understandings. Further, students are required to use multiple skills in conveying their ideas for social change to reflect their new broader conceptualization of scientists and the many fields that science includes. Additionally, they have to understand the topics discussed fully in order to convey their research findings to another audience in their school or community as they create museum exhibits. Finally, while students learn, they begin to see themselves represented in fields through evident, inclusive demonstrations of contributions by diverse scientists.
Long‐term safety of brodalumab in Japanese patients with plaque psoriasis: An open‐label extension study
Authors: Yamaguchi Yukie , Takatsu Nobumichi , Ootaki Kenji , Nakagawa Hidemi 
Published: April 2020

AbstractBrodalumab, an interleukin‐17 receptor A inhibitor, demonstrated rapid and robust efficacy with a favorable safety profile in patients with moderate to severe plaque psoriasis. Here, we present data from a multicenter, open‐label extension study in patients with plaque psoriasis with/without psoriatic arthritis who completed 64 weeks of treatment with brodalumab (140 or 210 mg, every 2 weeks [Q2W]). Patients were enrolled to evaluate the long‐term safety and efficacy of a modified dose of brodalumab. Eligible patients were switched to a reduced dose of brodalumab (140 mg every 4 weeks on day 1) in the extension study; the dose and dosing interval were modified sequentially at the physician’s discretion (minimum 140 mg every 8 weeks and maximum 210 mg Q2W) until drug approval, after which all patients were switched to 210 mg Q2W for postmarketing surveillance. Of the 129 patients enrolled, 107 (82.9%) completed the 108‐week or more extension study. All patients had psoriasis that was well controlled with brodalumab treatment on day 1. Improvement in psoriasis‐related symptoms, evaluated with the Psoriasis Area and Severity Index, Psoriasis Scalp Severity Index, Dermatology Life Quality Index, Nail Psoriasis Severity Index, and American College of Rheumatology 20, 50 and 70, was maintained during the 108‐week extension study. Brodalumab treatment was well tolerated throughout, and no new safety signals were identified. The most commonly reported treatment‐related adverse event was nasopharyngitis, followed by influenza and oral candidiasis. No cases of serious candida infection or Crohn’s disease were observed in this study. Serious treatment‐related adverse events, such as appendicitis, brain abscess, bacterial meningitis, colon cancer, immunoglobulin A nephropathy and tubulointerstitial nephritis, were reported in one patient each. No anti‐brodalumab‐binding antibodies or brodalumab‐neutralizing antibodies were detected in any patient throughout the extension study. Overall, the long‐term efficacy and safety of brodalumab were demonstrated over 108 weeks.