bluuebunny/crossref_metadata_2025_split huggingface dataset:
Derivation of macaque trophoblast stem cells
Authors: Schmidt Jenna Kropp , Meyer Michael G. , Wiepz Gregory J. , Block Lindsey N. , Dusek Brittany M. , Kroner Kamryn M. , Bertogliat Mario J. , Keding Logan T. , Koenig Michelle R. , Mean Katherine D. , Golos Thaddeus G. 
Published: March 2020

AbstractNonhuman primates are excellent models for studying human placentation as experimental manipulationsin vitrocan be translated toin vivopregnancy. Our objective was to develop macaque trophoblast stem cells (TSC) as anin vitroplatform for future assessment of primate trophoblast development and function. Macaque TSC lines were generated by isolating first trimester placental villous cytotrophoblasts followed by culture in TSC medium to “reprogram” the cells to a proliferative state. TSCs grew as mononuclear colonies, whereas upon induction of syncytiotrophoblast (ST) differentiation multinuclear structures appeared, indicative of syncytium formation. Chorionic gonadotropin secretion was >4,000-fold higher in ST culture media compared to TSC media. Characteristic trophoblast hallmarks were defined in TSCs and ST including expression of C19MC miRNAs and macaque placental nonclassical MHC class I molecule, Mamu-AG. TSC differentiation to extravillous trophoblasts (EVTs) with or without the ALK-5 inhibitor A83-01 resulted in differing morphologies but similar expression of Mamu-AG and CD56 as assessed by flow cytometry, hence further refinement of relevant EVT markers is needed. Our preliminary characterization of macaque TSCs suggests that these cells represent a proliferative, self-renewing TSC population capable of differentiating to STsin vitrothereby establishing an experimental model of primate placentation.
dom2vec: Unsupervised protein domain embeddings capture domains structure and function providing data-driven insights into collocations in domain architectures
Authors: Melidis Damianos P. , Malone Brandon , Nejdl Wolfgang 
Published: March 2020

AbstractMotivationWord embedding approaches have revolutionized Natural Language Processing NLP research. These approaches aim to map words to a low-dimensional vector space in which words with similar linguistic features are close in the vector space. These NLP approaches also preserve local linguistic features, such as analogy. Embedding-based approaches have also been developed for proteins. To date, such approaches treat amino acids as words, and proteins are treated as sentences of amino acids. These approaches have been evaluated either qualitatively, via visual inspection of the embedding space, or extrinsically, via performance on a downstream task. However, it is difficult to directly assess the intrinsic quality of the learned embeddings.ResultsIn this paper, we introduce dom2vec, an approach for learning protein domain embeddings. We also present fourintrinsicevaluation strategies which directly assess the quality of protein domain embeddings. We leverage the hierarchy relationship of InterPro domains, known secondary structure classes, Enzyme Commission class information, and Gene Ontology annotations in these assessments. These evaluations allow us to assess the quality of learned embeddings independently of a particular downstream task. Importantly, allow us to draw an analog between the local linguistic features in nature languages and the domain structure and function information in domain architectures, thus providing data-driven insights into the context found in thelanguageof domain architectures. We also show that dom2vec embeddings outperform, or are comparable with, state-of-the-art approaches on downstream tasks.AvailabilityThe protein domain embeddings vectors and the entire code to reproduce the results are available athttps://github.com/damianosmel/dom2vec.Contactmelidis@l3s.uni-hannover.de
Repurposing Old Antibodies for New Diseases by Exploiting Cross Reactivity and Multicolored Nanoparticles
Authors: Rodriguez-Quijada Cristina , Gomez-Marquez Jose , Hamad-Schifferli Kimberly 
Published: March 2020

ABSTRACTWe exploit the cross-reactivity of dengue (DENV) and zika (ZIKV) virus polyclonal antibodies for nonstructural protein 1 (NS1) to construct a selective sensor that can detect yellow fever virus (YFV) NS1 in a manner similar to chemical olfaction. DENV and ZIKV antibodies were screened for their ability to bind to DENV, ZIKV, and YFV NS1 by ELISA and in pairs in paper immunoassays. A strategic arrangement of antibodies immobilized on paper and conjugated to different colored gold NPs was used to distinguish the three biomarkers. Machine learning of test area RGB values showed that with two spots, readout accuracies of 100% and 87% were obtained for both pure NS1 and DENV/YFV mixtures, respectively. Additional image pre-processing allowed differentiation between all 4 DENV serotypes with 92% accuracy. The technique was extended to hack a commercial DENV test to detect YFV and ZIKV by augmentation with DENV and ZIKV polyclonal antibodies.TOC GRAPHIC
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network
Authors: Wu Tianqi , Guo Zhiye , Hou Jie , Cheng Jianlin 
Published: March 2020

AbstractMotivationDriven by deep learning techniques, inter-residue contact/distance prediction has been significantly improved and substantially enhancedab initioprotein structure prediction. Currently all the distance prediction methods classify inter-residue distances into multiple distance intervals (i.e. a multi-classification problem) instead of directly predicting real-value distances (i.e. a regression problem). The output of the former has to be converted into real-value distances in order to be used in tertiary structure prediction.ResultsTo explore the potentials of predicting real-value inter-residue distances, we develop a multi-task deep learning distance predictor (DeepDist) based on new residual convolutional network architectures to simultaneously predict real-value inter-residue distances and classify them into multiple distance intervals. We demonstrate that predicting the real-value distance map and multi-class distance map at the same time performs better than predicting real-value distances alone, indicating their complementarity. On 43 CASP13 hard domains, the average mean square error (MSE) of DeepDist’s real-value distance predictions is 0.896 Å when filtering out the predicted distance >=16 Å, which is lower than 1.003 Å of DeepDist’s multi-class distance predictions. When the predicted real-value distances are converted to binary contact predictions at 8Å threshold, the precisions of top L/5 and L/2 contact predictions are 78.6% and 64.5%, respectively, higher than the best results reported in the CASP13 experiment. These results demonstrate that the real-value distance prediction can predict inter-residue distances well and improve binary contact prediction over the existing state-of-the-art methods. Moreover, the predicted real-value distances can be directly used to reconstruct protein tertiary structures better than multi-class distance predictions due to the lower MSE.
Loss of SUV420H2 promotes EGFR inhibitor resistance in NSCLC through upregulation of MET via LINC01510
Authors: Pal A.S. , Agredo A.M. , Lanman N.A. , Clingerman J. , Gates K , Kasinski A.L. 
Published: March 2020

AbstractEpidermal growth factor receptor inhibitors (EGFRi) are standard-of-care treatments administered to patients with non-small cell lung cancer (NSCLC) that harbor EGFR alterations. However, development of resistance within a year post-treatment remains a major challenge. Multiple mechanisms can promote survival of EGFRi treated NSCLC cells, including secondary mutations in EGFR and activation of bypass tracks that circumvent the requirement for EGFR signaling. Nevertheless, mechanisms involved in bypass track activation are understudied, and in a subset of cases the mechanisms are unknown. The findings from this study identified an epigenetic factor, SUV420H2 that when lost drives resistance of NSCLC to multiple EGFRi, including erlotinib, gefitinib, afatinib, and osimertinib. SUV420H2 catalyzes trimethylation of histone H4 lysine-20, a modification required for gene repression and maintenance of heterochromatin. Here we show that loss of SUV420H2 leads to upregulation of an oncogenic long non-coding RNA,LINC01510that promotes transcription of the oncogene MET, a component of a major bypass track involved in EGFRi resistance.SignificanceDue to an incomplete understanding of the mechanisms involved in promoting resistance to EGFRi, patients often succumb to their disease. Here we identified a global mediator of EGFRi resistance, SUV420H2 that helps to uncover an additional mechanism involved in resistance driven via a major bypass track involving the protooncogene MET.
Cryo-EM structure of catalytic ribonucleoprotein complex RNase MRP
Authors: Perederina Anna , Li Di , Lee Hyunwook , Bator Carol , Berezin Igor , Hafenstein Susan L. , Krasilnikov Andrey S. 
Published: March 2020

AbstractRNase MRP is an essential eukaryotic ribonucleoprotein complex involved in the maturation of rRNA and the regulation of the cell cycle. RNase MRP is related to the ribozyme-based RNase P, but it has evolved to have distinct cellular roles. We report a cryo-EM structure of theS. cerevisiaeRNase MRP holoenzyme solved to 3.0 Å. We describe the structure of this 450 kDa complex, interactions between its components, and the organization of its catalytic RNA. We show that while the catalytic center of RNase MRP is inherited from the ancestral enzyme RNase P, the substrate binding pocket of RNase MRP is significantly altered by the addition of unique RNA and protein elements, as well as by RNA-driven protein remodeling.One Sentence SummaryChanges in peripheral RNA elements and RNA-driven protein remodeling result in diversification of related catalytic RNPs
Microbial resource management forex situbiomethanation of hydrogen at alkaline pH
Authors: Logroño Washington , Popp Denny , Kleinsteuber Sabine , Sträuber Heike , Harms Hauke , Nikolausz Marcell 
Published: March 2020

AbstractBiomethanation is a promising solution to convert H2produced from surplus electricity and CO2to CH4by using hydrogenotrophic methanogens. Inex situbiomethanation with mixed cultures, homoacetogens and methanogens compete for H2/CO2. We enriched a hydrogenotrophic microbiota on CO2and H2as sole carbon and energy sources, respectively, to investigate these competing reactions. Microbial community structure and dynamics of bacteria and methanogenic archaea were evaluated through 16S rRNA andmcrAgene amplicon sequencing, respectively. Hydrogenotrophic methanogens and homoacetogens were enriched as acetate was concomitantly produced along with CH4. By controlling the media composition, especially changing the reducing agent, the formation of acetate was lowered and grid quality CH4(≥ 97%) was obtained. Formate was identified as an intermediate that was produced and consumed during the bioprocess. Stirring intensities ≥1000 rpm were detrimental, probably due to shear force stress. The predominating methanogens belonged to the generaMethanobacteriumandMethanoculleus. The bacterial community was dominated byLutispora. The methanogenic community was stable, whereas the bacterial community was more dynamic. Our results suggest that hydrogenotrophic communities can be steered towards selective production of CH4from H2/CO2by adapting the media composition, the reducing agent and the stirring intensity.
Image matters: Development of a novel staining method, the RGB-trichrome, as a reliable tool for the study of the musculoskeletal system
Authors: Gaytan Francisco , Morales Concepción , Reymundo Carlos , Tena-Sempere Manuel 
Published: March 2020

AbstractMorphometry and histology are essential approaches for investigation and diagnosis of musculo-skeletal disorders. Despite the advent of revolutionary methods of image analysis and high resolution three-dimensional imaging technology, basic conventional light microscopy still provides an incisive overview of the structure and tissue dynamics of the musculoskeletal system. This is crucial to both preclinical and clinical research, since several clinically relevant processes, such as bone repair, osteoarthritis, and metabolic bone diseases, display distinct, if not pathognomonic, histological features. Due to the particular characteristics of the skeletal tissues (i.e., the existence of mineralized extracellular matrices), a large number of staining methods applicable to either decalcified or undecalcified tissues are available. However, it is usually the case that several staining methods need to be sequentially applied in order to achieve the different endpoints required to fully assess skeletal tissue structure and dynamics, and to allow morphometric quantification. We describe herein a novel staining method, the RGB trichrome, amenable for application to decalcified, paraffin embedded human musculoskeletal tissues. The acronym RGB corresponds to the three primary dyes used: picrosiriusRed, fastGreen, and alcianBlue. Although these individual pigments are commonly used either isolated, in binary combinations, or as part of more complex polychrome staining methods, when merged in the RGB trichrome staining produce high-quality/high-contrast images, permitting not only clear identification of different tissues (i.e., the different types of cartilage, bone and fibrous connective tissue), but also discrimination between calcified and uncalcified bone and cartilage, as well as an unexpected diversity of shades of color, while displaying singular properties among polychrome staining methods, such as the unveiling of the bone osteocyte dendritic/canalicular network. Hence, we propose the RGB trichrome as simple but highly-reliable tool for the preclinical and clinical study of the musculoskeletal system.
Simulation of Ca2+oscillations in astrocytes mediated by amyloid beta in Alzheimer’s disease
Authors: Gao Huayi , Liu Langzhou , Chen Shangbin 
Published: March 2020

AbstractDisruptions of astrocyte Ca2+signaling is important in Alzheimer’s disease (AD) with the unclear mechanism of amyloid beta peptide (Aβ). We have modified our previous computational model of spontaneous Ca2+oscillations in astrocytes to investigate the effects of Aβ on intracellular Ca2+dynamics. The simulation results have shown consistence with the previous experiments. Aβ can increase the resting concentration of intracellular Ca2+and change the regime of Ca2+oscillations by activating L-type voltage-gated calcium channels and the metabolic glutamate receptors, or by increasing ryanodine receptors sensitivity and Ca2+leakage, respectively. This work have provided a toolkit to study the influence of Aβ on intracellular Ca2+dynamics in AD. It is helpful for understanding the toxic role of Aβ during the progression of AD.Statement of SignificanceAlzheimer’s disease (AD) is the most common neurodegenerative disease with the unclear mechanism of amyloid beta peptide (Aβ). This work have implemented a computational model to address the Ca2+dynamics of astrocyte mediated by Aβ with the four different pathways: voltage-gated calcium channels, metabotropic glutamate receptors 5, ryanodine receptor channels and membrane leak. The Ca2+oscillations and bifurcation diagram indicate that astrocytes exhibit ionic excitability mediated by Aβ and become the potential targets of Aβ neurotoxicity. We expect this shared computational model would advance the understanding of AD.
Measurement and compensation of misalignment in double-sided hard X-ray Fresnel zone plates
Authors: Yurgens Viktoria , Koch Frieder , Scheel Mario , Weitkamp Timm , David Christian 
Published: March 2020

Double-sided Fresnel zone plates are diffractive lenses used for high-resolution hard X-ray microscopy. The double-sided structures have significantly higher aspect ratios compared with single-sided components and hence enable more efficient imaging. The zone plates discussed in this paper are fabricated on each side of a thin support membrane, and the alignment of the zone plates with respect to each other is critical. Here, a simple and reliable way of quantifying misalignments by recording efficiency maps and measuring the absolute diffraction efficiency of the zone plates as a function of tilting angle in two directions is presented. The measurements are performed in a setup based on a tungsten-anode microfocus X-ray tube, providing an X-ray energy of 8.4 keV through differential measurements with a Cu and an Ni filter. This study investigates the sources of the misalignments and concludes that they can be avoided by decreasing the structure heights on both sides of the membrane and by pre-programming size differences between the front- and back-side zone plates.
Behind the scenes: spotlight on the entrepreneurship educator
Authors: Wraae Birgitte , Walmsley Andreas 
Published: March 2020

PurposeExplores the role of the entrepreneurship educator and their place in the entrepreneurship education landscape.Design/methodology/approachThe paper uses an adapted version of Jones and Matlay's (2011) conceptual framework that describes the context of entrepreneurship education to explore the entrepreneurship educator's role. In-depth interviews were conducted with eleven entrepreneurship educators from five universities/university colleges in Denmark.FindingsIllustrates the situated nature of entrepreneurship education. The entrepreneurship educator is embedded in a system of dialogic relationships with a range of stakeholders. This paper provides insights into how the entrepreneurship educator navigates these relationships and the influence these relationships have in determining the scope and nature of the entrepreneurship educator's role.Research limitations/implicationsProvides a framework and findings upon which further studies can build in an area that has hitherto received limited attention. Findings could be compared with those in other geographical contexts, for example. The dialogic relationships themselves could be explored either holistically or individually with other stakeholders (e.g. students, institutions, communities).Originality/valueResearch on the role of the entrepreneurship educator is extremely limited in an area that has otherwise seen a proliferation of research. The adaptation and application of Jones and Matlay's (2011) framework provides a novel way of understanding how this role is shaped. Where most studies focus either on course content or the students, this study proposes another way to gain insight into the complex world of delivering entrepreneurship education.
“The NOSCA Mafia”: overseas student activism in Australia, 1985–1994
Authors: Briedis Tim 
Published: March 2020

PurposeThe purpose of the paper is to explore and analyse the history of the predominantly Malaysian Network of Overseas Students Collectives in Australia (NOSCA), that existed from 1985–1994.Design/methodology/approachThe paper is based on extensive archival research in the State Library of New South Wales, the National Library of Australia and the University of New South Wales (UNSW) Archives. It makes particular use of the UNSW student newspaper Tharunka and the NOSCA publications Truganini and Default. It also draws upon nine oral history interviews with former members of NOSCA.FindingsThe NOSCA was particularly prominent at the UNSW, building a base there and engaging substantially in the student union. Informed by anarchism, its activists were interested in an array of issues–especially opposition to student fees and in solidarity with struggles for democracy and national liberation in Southeast Asia, especially around East Timor. Moreover, the group would serve as a training ground for a layer of activists, dissidents and opposition politicians throughout Southeast Asia, with a milieu of ex-NOSCA figures sometimes disparagingly referred to as “the NOSCA Mafia.”Originality/valueWhile there has been much research on overseas students, there has been far less on overseas students as protestors and activists. This paper is the first case study to specifically hone in on NOSCA, one of the most substantial and left wing overseas student groups. Tracing the group's history helps us to reframe and rethink the landscape of student activism in Australia, as less white, less middle class and less privileged.
Impostor phenomenon: considerations for leadership practice
Authors: Downing Megan S. , Arthur-Mensah Nana , Zimmerman Jeffrey 
Published: March 2020

PurposeThe impostor phenomenon (IP) is a psychological cycle experienced by individuals who, despite successes, are plagued by self-doubt and a concern of being identified as fraudulent. IP research is typically focused on the psychological well-being of those who experience IP, examining antecedents and outcomes of IP. Research on organizational impact is limited with few studies examining IP’s influence on leadership practices. The purpose of this paper is to discuss IP and explore the value of mitigating IP’s negative effects with a view to developing a conceptual model that illustrates IP in context with leaders.Design/methodology/approachUsing a scoping literature review methodology, this paper draws on identity theory to explore and discuss the relevance of IP to organizations and leadership practice.FindingsFollowing a review of relevant literature, the authors propose a conceptual model that illustrates IP’s impact on organizational leaders’ capacity to practice leadership due to conflicting identity standards and diminished self-efficacy. Implications for organizational leadership development as well as leadership practice, theory, and research are discussed.Research limitations/implicationsThis paper is a theoretical analysis, not an empirical study, however, it presents a conceptual model that provides perspective on IP and its relevance to leadership as well as the organizational value of and suggestions for mitigating IP.Originality/valueA greater understanding of IP and IP’s potential consequences on leadership in the workplace may contribute to organizational interventions that mitigate IP's impact on leaders and the organizations they serve.
Gender effects on odor-induced taste enhancement and subsequent food consumption
Authors: Koubaa Yamen , Eleuch Amira 
Published: March 2020

PurposeThe purpose of this paper is to test for gender-specific effects on odor-induced taste enhancement and subsequent food consumption in olfactory food marketing.Design/methodology/approachLab experiments conducted among female and male participants using vanillin as a stimulus and ratings of sweetness, taste pleasantness and eating of sugar-free food as measures.FindingsOdor-induced taste enhancement is gender-specific. Female consumers outperform male consumers in olfactory reaction and sweetness perception. While men outperform women in food consumption.Research limitations/implicationsOdor intensity was set to the concentration level of 0.00005per cent according to the findings from (Fujimaru and Lim, 2013). The authors believe that this intensity level is appropriate for both men and women. Still, there may be some gender effects on intensity levels, which are not explored here. The author’s test for the effects of one personal factor, gender and odor-induced taste enhancement of sugar-free food. The authors think that investigating the combined effects of more personal factors such as age, culture and so on adds to the accuracy of the results.Practical implicationsIt seems that the stronger sensory capacities of women in terms of odor detection and recognition already confirmed in the literature extends to the cross-modal effects of this sensory detection and recognition on taste enhancement. It seems appropriate to tailor olfactory food advertising according to the gender of the target audience.Originality/valueOdor-induced taste enhancement is still a novel subject in marketing. While most of the research has investigated the effects of smelling congruent odors on taste perception and food consumption among mixed groups of men and women, the value of this paper lies in the investigation of the potential moderating effects of gender on this relationship.