bluuebunny/crossref_metadata_2025_split huggingface dataset:
Focus-tunable microscope for imaging small neuronal processes in freely moving animals
Authors: Bagramyan Arutyun , Tabourin Loïc , Rastqar Ali , Karimi Narges , Bretzner Frédéric , Galstian Tigran 
Published: November 2020

AbstractMiniature 1-photon microscopes have been widely used to image neuronal assemblies in the brain of freely moving animals over the last decade. However, these systems have important limitations for imaging in-depth fine neuronal structures. We present a novel subcellular imaging 1-photon device that uses an electrically tunable liquid crystal lens to enable a motion-free depth scan in the search of such structures. Our miniaturized microscope is compact (10 mm × 17 mm × 12 mm), lightweight (≈ 1.4 g), provides fast acquisition rate (30-50 frames/second), high magnification (8.7x) and high resolution (1.4 μm) that allow imaging of calcium activity of fine neuronal processes in deep brain regions during a wide range of behavioural tasks of freely moving mice.
Inflect: Optimizing Computational Workflows for Thermal Proteome Profiling Data Analysis
Authors: McCracken Neil A. , Peck Justice Sarah A. , Wijeratne Aruna B. , Mosley Amber L. 
Published: November 2020

ABSTRACTThe use of CETSA and Thermal Proteome Profiling (TPP) analytical methods are invaluable for the study of protein-ligand interactions and protein stability in a cellular context. These tools have increasingly been leveraged in work ranging from understanding signaling paradigms to drug discovery. Consequently, there is an important need to optimize the data analysis pipeline that is used to calculate protein melt temperatures (Tm) and relative melt shifts from proteomics abundance data. Here we report a user-friendly analysis of the melt shift calculation workflow where we describe the impact of each individual calculation step on the final output list of stabilized and destabilized proteins. This report also includes a description of how key steps in the analysis workflow quantitatively impacts the list of stabilized/destabilized proteins from an experiment. We applied our findings to develop a more optimized analysis workflow that illustrates the dramatic sensitivity of chosen calculation steps on the final list of reported proteins of interest in a study and will make the R based program Inflect available for research community use. Overall, this work provides an essential resource for scientists as they analyze data from TPP and CETSA experiments and implement their own analysis pipelines geared towards specific applications.
Discovery of new genetic determinants controlling the morphological plasticity in rice root and shoot under phosphate starvation using GWAS
Authors: Mai Nga T P , Mai Chung Duc , Van Nguyen Hiep , Le Khang Quoc , Duong Linh Viet , To Huong Thi Mai 
Published: November 2020

AbstractPhosphorus is an essential nutrient for plants that is often in short supply. In rice (Oryza sativaL.), phosphate (Pi) deficiency leads to various physiological disorders that consequently affect plant productivity. In this study, a large-scale phenotyping experiment of a set of 160 Vietnamese rice landraces was performed under greenhouse conditions by employing an alpha lattice design with three replicates to identify quantitative trait loci (QTLs) associated with plant growth inhibition by Pi deficiency. Rice plantlets were grown for six weeks in the PVC sand column (16 cm diameter × 80 cm height) supplied with Pi-deficient (10 µM P) medium or full Pi Yoshida (320 µM P) medium. The effects of Pi deficiency on the number of crown roots, root length, shoot length, root weight, shoot weight and total weight were studied. From 36 significant markers identified by using Genome-wide association study, a total of 21 QTLs associated with plant growth inhibition under Pi starvation conditions were defined. A list of 158 candidate genes co-located with defined QTLs was found. Interestingly, a QTL namelyqRST9.14were detected found common across three weight-traits. The co-located geneGLYCEROPHOSPHODIESTER PHOSPHODIESTERASE 13was found potentially involved in Pi transport. Understanding the molecular mechanisms of Pi starvation responses, and identifying potential QTLs responsible for low-Pi stress tolerance will provide valuable information for developing new varieties tolerant to low-Pi conditions.
Uncovering the mesendoderm gene regulatory network through multi-omic data integration
Authors: Jansen Camden , Paraiso Kitt D. , Zhou Jeff J. , Blitz Ira L. , Fish Margaret B. , Charney Rebekah M. , Cho Jin Sun , Yasuoka Yuuri , Sudou Norihiro , Bright Ann Rose , Wlizla Marcin , Veenstra Gert Jan C. , Taira Masanori , Zorn Aaron M. , Mortazavi Ali , Cho Ken W.Y. 
Published: November 2020

SummaryMesendodermal specification is one of the earliest events in embryogenesis, where cells first acquire distinct identities. Cell differentiation is a highly regulated process that involves the function of numerous transcription factors (TFs) and signaling molecules, which can be described with gene regulatory networks (GRNs). Cell differentiation GRNs are difficult to build because existing mechanistic methods are low-throughput, and high-throughput methods tend to be non-mechanistic. Additionally, integrating highly dimensional data comprised of more than two data types is challenging. Here, we use linked self-organizing maps to combine ChIP-seq/ATAC-seq with temporal, spatial and perturbation RNA-seq data fromXenopus tropicalismesendoderm development to build a high resolution genome scale mechanistic GRN. We recovered both known and previously unsuspected TF-DNA/TF-TF interactions and validated through reporter assays. Our analysis provides new insights into transcriptional regulation of early cell fate decisions and provides a general approach to building GRNs using highly-dimensional multi-omic data sets.HighlightsBuilt a generally applicable pipeline to creating GRNs using highly-dimensional multi-omic data setsPredicted new TF-DNA/TF-TF interactions during mesendoderm developmentGenerate the first genome scale GRN for vertebrate mesendoderm and expanded the core mesendodermal developmental network with high fidelityDeveloped a resource to visualize hundreds of RNA-seq and ChIP-seq data using 2D SOM metaclusters.
A New Comprehensive Catalog of the Human Virome Reveals Hidden Associations with Chronic Diseases
Authors: Tisza Michael J. , Buck Christopher B. 
Published: November 2020

AbstractWhile there have been remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This is despite the fact that many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases and all of them encompass large amounts of viral sequences. The lack of a comprehensive database for human-associated viruses, along with inadequate methods for high-throughput identification of highly divergent viruses in metagenomic data, has historically stymied efforts to characterize virus sequences in a comprehensive way. In this study, a new high-specificity and high-sensitivity bioinformatic tool, Cenote-Taker 2, was applied to thousands of human metagenome datasets, uncovering over 50,000 unique virus operational taxonomic units. Publicly available case-control studies were re-analyzed, and over 1,700 strong virus-disease associations were found.
The Genetic Architecture of Larval Aggregation Behavior in Drosophila
Authors: McKinney Ross M , Ben-Shahar Yehuda 
Published: November 2020

AbstractMany insect species exhibit basal social behaviors such as aggregation, which play important roles in their feeding and mating ecologies. However, the evolutionary, genetic, and physiological mechanisms that regulate insect aggregation remain unknown for most species. Here, we used natural populations of Drosophila melanogaster to identify the genetic architecture that drives larval aggregation feeding behavior. By using quantitative and reverse genetic approaches, we have identified a complex neurogenetic network that plays a role in regulating the decision of larvae to feed in either solitude or as a group. Results from single gene, RNAi-knockdown experiments show that several of the identified genes represent key nodes in the genetic network that determines the level of aggregation while feeding. Furthermore, we show that a single non-coding SNP in the gene CG14205, a putative acyltransferase, is associated with both decreased mRNA expression and increased aggregate formation, which suggests that it has a specific role in inhibiting aggregation behavior. Our results identify, for the first time, the genetic components which interact to regulate naturally occurring levels of aggregation in D. melanogaster larvae.
Sclerostin depletion induces inflammation in the bone marrow of mice
Authors: Donham Cristine , Chicana Betsabel , Robling Alexander , Mohamed Asmaa , Elizaldi Sonny , Chi Michael , Freeman Brian , Millan Alberto , Murguesh Deepa , Loots Gabriela G. , Manilay Jennifer O. 
Published: November 2020

ABSTRACTRomosozumab, a humanized monoclonal antibody specific for sclerostin, has been approved for treatment of post-menopausal women with osteoporosis at high risk for fracture. In several Phase III clinical trials, romosozumab decreased the risk of vertebral fractures up to 73% and increased total hip area bone mineral density by 3.2%. Previous work in 12 to 15-week-old sclerostin-knockout (Sost-/-) mice indicated that changes in immune cell development occur in the bone marrow (BM), which could be a possible side effect to follow in human patients. Our overall goal was to define the mechanisms that guide behavior of long-term hematopoietic stem cells (LT-HSCs) after exposure to an irregular BM microenvironment. SOST plays an important role in maintaining bone homeostasis, as demonstrated by the increased ratio of bone volume to total volume observed inSost-/-mice. Here, we examined the effects of short-term sclerostin depletion in the BM on hematopoiesis in young (8 week-old) mice receiving sclerostin-antibody (Scl-Ab) treatment for 6 weeks, and the effects of long-term Sost-deficiency on wild-type (WT) LT-HSCs transplanted into older (16-22 week-old) cohorts ofSost-/-mice. Our analyses revealed an increased frequency of granulocytes and decreased frequency of lymphocytes in the BM of Scl-Ab treated mice and WT→Sost-/-hematopoietic chimeras, indicating myeloid-biased differentiation inSost-deficient BM microenvironments. This myeloid bias extended to extramedullary hematopoiesis in the spleen and was correlated with an increase in inflammatory cytokines TNFα, IL-1α and MCP-1 in the serum of theSost-/-BM. Additionally, we observed alterations in erythrocyte differentiation in the BM and spleen ofSost-/-mice. Taken together, our current study indicates novel roles forSostin the regulation of myelopoiesis and control of inflammation in the BM. Our animal studies strongly recommend tracking of hematopoietic function in patients treated with romosozumab.
CD4+ T cell subsets present stable relationships in their T cell receptor repertoires
Authors: Wang Shiyu , Wang Longlong , Liu Ya 
Published: November 2020

AbstractCD4+ T cells are key components of adaptive immunity. The cell differentiation equips CD4+ T cells with new functions. However, the effect of cell differentiation on T cell receptor (TCR) repertoire is not investigated. Here, we examined the features of TCR beta (TCRB) repertoire of the top clones within naïve, memory and regular T cell (Treg) subsets: repertoire structure, gene usage, length distribution and sequence composition. First, we found that memory subsets and Treg would be discriminated from naïve by the features of TCRB repertoire. Second, we found that the correlations between the features of memory subsets and naïve were positively related to differentiation levels of memory subsets. Third, we found that public clones presented a reduced proportion and a skewed sequence composition in differentiated subsets. Furthermore, we found that public clones led naïve to recognize a broader spectrum of antigens than other subsets. Our findings suggest that TCRB repertoire of CD4+ T cell subsets is skewed in a differentiation-depended manner. Our findings show that the variations of public clones contribute to these changes. Our findings indicate that the reduce of public clones in differentiation trim the antigen specificity of CD4+ T cells. The study unveils the physiological effect of memory formation and facilitates the selection of proper CD4+ subset for cellular therapy.
Orai1- and Orai2-, but not Orai3-mediated ICRACis regulated by intracellular pH
Authors: Rychkov Grigori Y. , Zhou Fiona H. , Adams Melissa K. , Brierley Stuart M. , Ma Linlin , Barritt Greg J. 
Published: November 2020

ABSTRACTThree Orai (Orai1, Orai2 and Orai3) and two STIM (STIM1 and STIM2;stromal interactionmolecule) mammalian protein homologues constitute major components of the store-operated Ca2+entry mechanism. When co-expressed with STIM1, Orai1, Orai2 and Orai3 form highly selective Ca2+channels with properties of Ca2+release activated Ca2+(CRAC) channels. Despite the high level of homology between Orai proteins, CRAC channels formed by different Orai isoforms have distinctive properties, particularly with regards to Ca2+dependent inactivation, inhibition/potentiation by 2-APB and sensitivity to reactive oxygen species. This study characterises and compares the regulation of Orai1, Orai2- and Orai3-mediated CRAC current (ICRAC) by intracellular pH. Using whole-cell patch clamping of HEK293T cells heterologously expressing Orai and STIM1 we show that ICRACformed by each Orai homologue has a unique sensitivity to changes in intracellular pH (pHi). Orai1-mediated ICRACexhibits a strong dependence on pHiof both current amplitude and the kinetics of Ca2+dependent inactivation. In contrast, Orai2 amplitude, but not kinetics, depends on pHi, whereas Orai3 shows no dependence on pHiat all. Investigation of different Orai1-Orai3 chimeras suggests that pHidependence of Orai1 resides in both, the N-terminus and intracellular loop 2, and may also involve pH-dependent interactions with STIM1.
Managing student and faculty expectations and the unexpected during the COVID-19 lockdown: role transformation
Authors: Othman Radiah 
Published: November 2020

PurposeThe purpose of this paper is to reflect teaching and learning practices, to highlight an educator’s new roles in the transformation when teaching online during the COVID-19 lockdown.Design/methodology/approachThe paper takes a transformative reflection approach, based on competencies and activity system analysis to connect theory and practical experience in managing the students, the teaching delivery and the assessments.FindingsThe transition to online teaching and assessments requires various considerations of the curriculum and instructional approaches and necessitates the transformation of the role of the subject-matter expert to that of designer and co-learner. Empathy and understanding of students’ conditions enable this role transformation.Practical implicationsThe paper highlights the importance of preparedness among faculty members and universities in dealing with uncertainties and the willingness to expand traditional roles and to upgrade the required skills, knowledge and attitudes to engender sustainable teaching and learning practices in response to future disruptions.Originality/valueThe paper reflects on the experience of a faculty who had adopted blended learning prior to the lockdown and how the teaching practice and roles transformed when fully transitioning to online delivery during the lockdown in New Zealand.
Immigrants’ disadvantage online: understanding the effects of immigration status, gender and country of origin on the e-government use in Israel
Authors: Rosenberg Dennis 
Published: November 2020

Purpose
Digital inequality studies claim that social inequalities tend to be replicated online. However, studies have not attempted so far to deeper understand such stratification in immigrant societies regarding the e-government use. This study aims to understand the role of immigration status, gender and country of origin in the e-government use, thereby reflecting what the literature on the sociology of migration refers to as immigrants’ “double” and “triple” disadvantage.

Design/methodology/approach
Israel was chosen as a case study because it is an immigration society in which immigrants’ socioeconomic status is usually inferior to that of the native population. The data were attained from the 2017 Israel Social Survey. The population of the study included internet users from the Jewish sector (N = 4,222). Logistic regression was used as the multivariate technique.

Findings
The results indicated that immigrant women are disadvantaged in terms of e-government use regardless of their year of immigration. Yet, when the data are segmented by country of origin, only female immigrants from the former Soviet Union show evidence of a triple disadvantage.

Research limitations/implications
The conclusion is that immigrants’ disadvantages in the offline sphere also exist in the online sphere.

Practical implications
Particular categories, which use e-government to a small extent, were identified, serving a call for action for the public officials. They should develop plans to make e-government more accessible to individuals belonging to these categories.

Originality/value
This study incorporates digital and immigrant sociology for the explanation of immigrants’ (online) social inclusion.
Namib Mills Group: managing talent in a Namibian food production business
Authors: Swart-Opperman Christina , Barnardo Claire , Boyd Sarah 
Published: November 2020

Learning outcomes
The learning outcomes are as follows: to understand why talent management is a vital component of a company’s broader strategy for long-term operational excellence; to understand the impact of generation, life stage and career stage on an employee’s professional needs, goals and expectations of their firm; to understand how organisational culture contributes, in this case, to ineffective people management practices; and to develop a talent management strategy: new policies, processes or practices that will address the identified issues and create a sustainable pipeline of talent.

Case overview/synopsis
This case finds the successful agro-processing firm Namib Mills in a state of internal tension in April 2019. As Namibia’s premier supplier of staple food products, Namib Mills is performing well in a struggling economy. Then yet, CEO Ian Collard is concerned that his senior management team is not exhibiting the kind of leadership and strategic management needed to take the company into the future. As Ian examines the issue further – with the aid of a report from an external consultant – he begins to see that the weaknesses of his senior managers, who are prone to micromanaging and poor communication, are part of a bigger issue of talent management in the firm. The junior employees, who are energetic and ready to innovate, are growing restless as they wait for career growth and promotion opportunities. The rising leaders in middle management are also struggling to break through. Ian must confront how organisational culture and generational diversity within this family-owned business have created talent management barriers and develop a strategy for sustainably developing employees into the leaders of the future.

Complexity academic level
This case is designed for a master’s level management program and is well-suited for courses that deal with organisational behaviour, people management or human resources management. Specifically, the case is aimed at students interested in talent management, generational diversity and organisational culture.

Subject code
CSS 6: Human Resource Management.
Managing cancer patients care during the COVID-19 outbreak: a literature investigate
Authors: Özyer Yasemın , Yanmış Safiye 
Published: November 2020

PurposeThis review, which was created specifically for cancer care by reviewing the literature, was prepared to provide suggestions for determining the current difficulties in cancer care during COVID-19 outbreak and managing these difficulties. It is thought that this review can contribute to the identification of deficiencies related to the subject, to create interest in this issue in our country and in the world and to guide patients in the care during the COVID-19 pandemic process.Design/methodology/approachThe literature search was carried out using the following electronic seven databases. Search terms used included: “COVID-19”, “management of cancer care” and “cancer care”. Articles meeting the following criteria were included in the current review: articles published in English, articles published in peer-reviewed journals and articles and guidelines published in 2020, articles suggesting management of cancer care during the COVID-19 outbreak.FindingsThe findings suggest that new guidelines need to be created to assess the level of problems in cancer treatment and in hospital, to respond appropriately with the best available resources during COVID-19 outbreak.Originality/valueThis paper seeks to provide suggestions for determining the current difficulties in cancer care during COVID-19 outbreak and managing these difficulties. By doing so, it is believed the suggestions presented will contribute significantly to the quality of cancer care during COVID-19 outbreak.
Empowering children to make and shape our digital futures – from adults creating technologies to children transforming cultures
Authors: Iivari Netta 
Published: November 2020

PurposeDigital technology education of children needs to be reconsidered. The purpose of this paper is to focus on empowering the young generation as regards digital technology. Digital technology education should reap the benefits of recent developments brought in by extensive, ongoing digitalization and prepare the young generation to manage and master in their technology rich future. The recent COVID 19 pandemic has made this particularly relevant and visible in the society. The young generation should adopt a proactive and critical stance toward digital technology and consider how design and technology can be used for making the world a better place.Design/methodology/approachThis commentary reviews literature on the complex concept of empowerment and suggests a model on the aspects to be considered when aiming at empowering the young generation as regards digital technology in the context of digital technology education.FindingsA model is proposed that comprehensively addresses empowerment of children as regards digital technology both at individual and collective levels and in mainstream sense as a relational and motivational construct as well as in critical sense in terms of collective empowerment, social responsibility and liberation of the oppressed.Research limitations/implicationsRadical renewal in the children's education is needed in the digital age. This model outlines aspects to be considered in such a transformation. The insights should be valuable for research communities addressing the topic of children's education in the digital age in general or the topic of children's digital technology education in particular.Practical implicationsThe model should also be of help for practitioners, i.e. teachers and facilitators working in informal learning spaces for developing children's digital education in practice.Social implicationsThe commentary addresses significant societal issues. It is actually not only children who should be empowered to engage in making and shaping our digital futures, but people in general. The model provides novel and valuable insights on what aspects to consider in such a significant endeavor.Originality/valueThe model proposed is novel and clearly needed in the research addressing this topic.