bluuebunny/crossref_metadata_2025_split huggingface dataset:
A single-cell analysis of the molecular lineage of chordate embryogenesis
Authors: Zhang Tengjiao , Xu Yichi , Imai Kaoru , Fei Teng , Wang Guilin , Dong Bo , Yu Tianwei , Satou Yutaka , Shi Weiyang , Bao Zhirong 
Published: March 2020

SummaryIn multicellular organisms, a single zygote develops along divergent lineages to produce distinct cell types. What governs these processes is central to the understanding of cell fate specification and stem cell engineering. Here we used the protochordate modelCiona savignyito determine gene expression profiles of every cell of single embryos from fertilization through the onset of gastrulation and provided a comprehensive map of chordate early embryonic lineage specification. We identified 47 cell types across 8 developmental stages up to the 110-cell stage in wild type embryos and 8 fate transformations at the 64-cell stage upon FGF-MAPK inhibition. The identities of all cell types were evidenced byin situexpression pattern of marker genes and expected number of cells based on the invariant lineage. We found that, for the majority of asymmetrical cell divisions, the bipotent mother cell shows predominantly the gene signature of one of the daughter fates, with the other daughter being induced by subsequent signaling. Our data further indicated that the asymmetric segregation of mitochondria in some of these divisions does not depend on the concurrent fate inducing FGF-MAPK signaling. In the notochord, which is an evolutionary novelty of chordates, the convergence of cell fate from two disparate lineages revealed modular structure in the gene regulatory network beyond the known master regulator T/Brachyury. Comparison to single cell transcriptomes of the early mouse embryo showed a clear match of cell types at the tissue level and supported the hypothesis of developmental-genetic toolkit. This study provides a high-resolution single cell dataset to understand chordate embryogenesis and the relationship between fate trajectories and the cell lineage.HighlightsTranscriptome profiles of 47 cell types across 8 stages in early chordate embryoBipotent mother in asymmetric division shows the default daughter fateModular structure of the notochord GRN beyond the known function of TInvariant lineage and manual cell isolation provide truth to trajectory analysis
RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors
Authors: Munawar Mustafa , Martin Frank , Toljamo Anna , Kokko Harri , Oksanen Elina 
Published: March 2020

ABSTRACTPlant diseases are often diagnosed by the method of DNA extraction followed by PCR. DNA extraction from plant tissue can be a recalcitrant and lengthy process, and sometimes ends up with inhibitors that reduce PCR amplification efficiency. Here we present a unique approach, ‘RPA-PCR couple’, to exclude the DNA extraction step from the standard plant diagnostic process. The process crudely macerates plant tissue in water for a few minutes, and then transfers the macerate supernatant to a Recombinase Polymerase Amplification (RPA) reaction. Following an incubation of 20 minutes at 39 °C, the RPA reaction can be directly utilized in PCR amplification. In RPA-PCR couple, the RPA reaction is run at slower reaction kinetics to promotes amplification of long amplicons and the slower reaction kinetics are achieved by lowering RPA components concentrations. In this proof of concept study, we targetedPhytophthoraintergenic mitochondrial spacer betweenatp9andnad9genes and the two commonPhytophthorapathogens of strawberry:P. fragariaeandP. cactorum. We presented coupling of RPA with real time TaqMan and SYBR Green PCR assays, and conventional PCR amplification aimed at Sanger sequencing. We found the RPA-PCR couple specific and capable of detecting as low as 10 fg ofPhytophthoragenomic DNA. Moreover, comparing RPA-PCR couple with the routine method of DNA extraction followed by PCR generated comparable results for the field samples. The idea of RPA-PCR couple to exclude DNA extraction may have vast application in different fields such as clinical diagnostics, food inspection and soil sciences.
MicroRNA-214 prevents pulmonary angiogenesis and alveolarization in neonatal rats with hyperoxia-mediated impairment of lung development by blocking PlGF-dependent STAT3 signaling pathway
Authors: Zhang Zhi-Qun , Li Xiao-Xia , Li Jing , Hong Hui , Huang Xian-Mei 
Published: March 2020

AbstractIn recent years, the roles of microRNAs (miRNAs) in pulmonary diseases have been widely studied and researched. However, the molecular mechanism by which miR-214 affects bronchopulmonary dysplasia (BPD) remains elusive and merits further exploration. Hence, this study aims to clarify the function of miR-214 in pulmonary angiogenesis and alveolarization in preterm infants with BPD. BPD neonatal rat model was induced by hyperoxia, and pulmonary epithelial cells were isolated from rats and exposed to hyperoxia. Gain- or loss-of-function experiments were performed in BPD neonatal rats and hyperoxic pulmonary epithelial cells. MiR-214 and PlGF expression in BPD neonatal rats, and eNOS, Bcl-2, c-myc, Survivin, α-SMA and E-cadherin expression in hyperoxic pulmonary epithelial cells were detected using RT-qPCR and western blot analysis. The interaction between PlGF and miR-214 was identified using dual luciferase reporter gene assay and RIP assay. ELISA was adopted to assess IL-1β, TNF-a, IL-6, ICAM-1 and Flt-1 expression in rats. Decreased miR-214 expression and elevated PlGF expression were evident in the lung tissues of neonatal rats with BPD. PlGF was a target of miR-214, and miR-214 downregulated PlGF to inactivate the STAT3 signaling pathway. miR-214 overexpression or PlGF silencing decreased apoptosis of hyperoxic pulmonary epithelial cells and declined pulmonary angiogenesis and alveolarization in BPD neonatal rats. Collectively, miR-214 can protects against pulmonary angiogenesis and alveolarization in preterm infants with BPD by suppressing PlGF and blocking STAT3 signaling pathway.
Evidence from combined analysis of single cell RNA-Seq and ATAC-Seq data of regulatory toggles operating in native and iPS-derived murine retina
Authors: Georges Anouk , Lavergne Arnaud , Mandai Michiko , Lepiemme Fanny , Karim Latifa , Demeulenaere Loic , Aguilar Diego , Schyns Michael , Dupont Sébastien , Nguyen Laurent , Rakic Jean-Marie , Takahashi Masayo , Georges Michel , Takeda Haruko 
Published: March 2020

AbstractWe report the generation and analysis of single-cell RNA-Seq data (> 38,000 cells) from native and iPSC-derived murine retina at four matched developmental stages spanning the emergence of the major retinal cell types. We combine information from temporal sampling, visualization of 3D UMAP manifolds, pseudo-time and RNA velocity analyses, to show that iPSC-derived 3D retinal aggregates broadly recapitulate the native developmental trajectories. However, we show relaxation of spatial and temporal transcriptome control, premature emergence and dominance of photoreceptor precursor cells, and susceptibility of dynamically regulated pathways and transcription factors to culture conditions in iPSC-derived retina. We generate bulk ATAC-Seq data for native and iPSC-derived murine retina identifying ∼125,000 peaks. We combine single-cell RNA-Seq with ATAC-Seq information and obtain evidence that approximately half the transcription factors that are dynamically regulated during retinal development may act as repressors rather than activators. We propose that sets of activators and repressors with cell-type specific expression constitute “regulatory toggles” that lock cells in distinct transcriptome states underlying differentiation. We provide evidence supporting our hypothesis from the analysis of publicly available single-cell ATAC-Seq data for adult mouse retina. We identify subtle but noteworthy differences in the operation of such toggles between native and iPSC-derived retina particularly for the Etv1, Etv5, Hes1 and Zbtb7a group of transcription factors.
Ultrasonic Spatial Target Localization Using Artificial Pinnae of Brown Long-eared Bat
Authors: Zhang Sen , Ma Xin , Dong Zheng , Zhou Weidong 
Published: March 2020

AbstractEcholocating bats locate a target by echolocation and their performance is related to the shape of the binaural conformation in bats. In this study, we developed an artificial sonar system based on the vertical sound localization characteristics of the brown long-eared bat (Plecotus auritus). First, using the finite element method, we found that the beam of the first side lobe formed by a pinna constructed according to that in the brown long-eared bat shifted in an almost linear manner in the vertical direction as the frequency changed from 30 kHz to 60 kHz. We established a model of the relationship between the time-frequency features of the echo emitted by brown long-eared bats and the spatial direction by using the pre-trained neural network. We also developed a majority vote-based method called sliding window cumulative peak estimation (SWCPE) to optimize the outputs from the neural network. In addition, an L-shaped pinna structure was designed to simultaneously estimate the azimuth and elevation. Our field experiments indicated that the binaural conformation and relative binaural orientation both played vital roles in spatial target localization by these bats. Accurate echolocation can be achieved using a simple binaural sonar device even without binaural time difference information.
Calcium-Binding Proteins are Altered in the Cerebellum in Schizophrenia
Authors: Vidal-Domènech Francisco , Riquelme Gemma , Pinacho Raquel , Rodriguez-Mias Ricard , Vera América , Monje Alfonso , Ferrer Isidre , Callado Luis F. , Meana J. Javier , Villén Judit , Ramos Belén 
Published: March 2020

AbstractAlterations in the cortico-cerebellar-thalamic-cortical circuit might underlie the diversity of symptoms in schizophrenia. However, molecular changes in cerebellar neuronal circuits, part of this network, have not yet been fully determined. Using LC-MS/MS, we screened altered candidates in pooled grey matter of cerebellum from schizophrenia subjects who committed suicide (n=4) and healthy individuals (n=4). Further validation by immunoblotting of three selected candidates was performed in two cohorts comprising schizophrenia (n=20), non-schizophrenia suicide (n=6) and healthy controls (n=21). We found 99 significantly altered proteins, 31 of them previously reported in other brain areas by proteomic studies. Transport function was the most enriched category, while cell communication was the most prevalent function. For validation, we selected the vacuolar proton pump subunit 1 (VPP1), from transport, and two EF-hand calcium-binding proteins, calmodulin and parvalbumin from cell communication. All candidates showed significant changes in schizophrenia (n=7) compared to controls (n=7). VPP1 was altered in the non-schizophrenia suicide group and increased levels of parvalbumin were linked to antipsychotics. Further validation in an independent cohort of non-suicidal chronic schizophrenia subjects (n=13) and non-psychiatric controls (n=14) showed that parvalbumin was increased while calmodulin was decrease in schizophrenia. Our findings provide evidence of an dysregulation of calcium-binding proteins in the cerebellum in schizophrenia, suggesting an impact on normal calcium-dependent synaptic functioning of cerebellar circuits. Our study also links VPP1 to suicide behaviours, suggesting a possible impairment in vesicle neurotransmitter refilling and release in these phenotypes.
Shark movements in the Revillagigedo Archipelago and connectivity with the Eastern Tropical Pacific
Authors: Lara-Lizardi Frida , Hoyos-Padilla Mauricio , Hearn Alex , Klimley A. Peter , Galván-Magaña Felipe , Arauz Randall , Bessudo Sandra , Castro Eleazar , Clua Eric , Espinoza Eduardo , Fischer Chris , Peñaherrera-Palma César , Steiner Todd , Ketchum James T. 
Published: March 2020

AbstractLong-distance movements of sharks within and between islands pose substantial challenges for resource managers working with highly migratory species. When no-take zones do not cover the critical areas that sharks use as part of their lifecycle, exposure to fishing activities can be significant. Shark movements between the Marine Protected Areas (MPAs) of the Eastern Tropical Pacific (ETP) have been studied for several years, however little is known about the strength of connectivity between these islands. We analyzed the extensive MigraMar ultrasonic telemetry dataset to assess how Galapagos sharks (Carcharhinus galapagensis) and silky sharks (Carcharhinus falciformis) use different islands as stepping-stones during their migrations within the Revillagigedo National Park and other ETP islands. Of the 66 sharks monitored, 63.5% moved within the same island, 25.4% between two islands or more and only 10.1% across different MPAs. AC. falciformistagged in Roca Partida Island, Revillagigedo, travelled to Clipperton Atoll and another one tagged in Darwin Island travelled to the atoll on two different years. The largest movement ofC. galapagensiswas accomplished by a shark tagged at Socorro Island, Revillagigedo, later detected at Clipperton and finally recorded in Darwin Island, Galapagos. This last path was in fact, one of the longest movements ever recorded for the species. Although long-distance dispersion was not common, our results highlight the need for co-operation between different countries to ensure adequate protection for sharks in the form of swimways and other conservation tools in the ETP.
Podocyte-specific knockout of the neonatal Fc receptor (FcRn) results in differential protection depending on the model of immune-mediated kidney disease
Authors: Dylewski James , Tonsawan Pantipa , Garcia Gabriela , Lewis Linda , Blaine Judith 
Published: March 2020

AbstractPodocytes have been proposed to be antigen presenting cells (APCs). In traditional APCs, the neonatal Fc receptor (FcRn) is required for antigen presentation and global knockout of FcRn protects against immune-mediated kidney disease. Since podocytes express FcRn, we sought to determine whether the absence of podocyte FcRn ameliorates immune-mediated disease. We examined MHCII and costimulatory markers expression in cultured wild type (WT) and FcRn knockout (KO) podocytes. Interferon gamma (IFNγ) induced MHCII expression in both WT and KO podocytes but did not change CD80 expression. Neither WT nor KO expressed CD86 or inducible costimulatory ligand (ICOSL) at baseline or with IFNγ. Using an antigen presentation assay, WT podocytes but not KO treated with immune complexes induced a modest increase in IL-2. Induction of the anti-glomerular basement membrane (anti-GBM) model resulted in a significant decrease in glomerular crescents in podocyte-specific FcRn knockout mouse (podFcRn KO) versus controls but the overall percentage of crescents was low. To examine the effects of the podocyte-specific FcRn knockout in a model with a longer autologous phase, we used the nephrotoxic serum nephritis (NTS) model. We found that the podFcRn KO mice had significantly reduced crescent formation and glomerulosclerosis compared to control mice. This study demonstrates that lack of podocyte FcRn is protective in immune mediated kidney disease that is dependent on an autologous phase. This study also highlights the difference between the anti-GBM model and NTS model of disease.
Time-controlled Multichannel Dynamic Traction Imaging of Biaxially Stretched Adherent Cells
Authors: Horvath Aron N. , Ziegler Andreas A. , Gerhard Stephan , Holenstein Claude N. , Beyeler Benjamin , Snedeker Jess G. , Silvan Unai 
Published: March 2020

AbstractHere, a dynamic traction force microscopy method is described which enables sub-second temporal resolution imaging of transient subcellular events secondary to extrinsic stretch of adherent single cells. The system employs a novel tracking approach with minimal computational overhead to compensate substrate-based stretch-induced motion/drift of stretched single cells in real time, allowing capture of biophysical phenomena on multiple channels by fluorescent multichannel imaging on a single camera, thus avoiding the need for beam splitting with associated loss of light. The potential impact of the technique is demonstrated by characterizing transient subcellular forces and corresponding nuclear deformations in equibiaxial stretching experiments, uncovering a high frequency strain-rate dependent response in the transfer of substrate strains to the nucleus.
Robust differentiation of human pluripotent stem cells into endothelial cells via temporal modulation of ETV2 with modified mRNA
Authors: Wang Kai , Lin Ruei-Zeng , Hong Xuechong , Ng Alex H. , Lee Chin Nien , Neumeyer Joseph , Wang Gang , Wang Xi , Ma Minglin , Pu William T. , Church George M. , Melero-Martin Juan M. 
Published: March 2020

ABSTRACTHuman induced pluripotent stem cell (h-iPSC)–derived endothelial cells (h-iECs) have become a valuable tool in regenerative medicine. However, current differentiation protocols remain inefficient and lack reliability. Here, we describe a method for rapid, consistent, and highly efficient generation of h-iECs. The protocol entails the delivery of modified mRNA encoding the transcription factorETV2at the intermediate mesodermal stage of differentiation. This approach reproducibly differentiated thirteen diverse h-iPSC lines into h-iECs with exceedingly high efficiency. In contrast, standard differentiation methods that relied on endogenousETV2were inefficient and notably inconsistent. Our h-iECs were functionally competent in many respects, including the ability to form perfused vascular networksin vivo. Importantly, timely activation ofETV2was critical, and bypassing the mesodermal stage produced putative h-iECs with reduced expansion potential and inability to form functional vessels. Our protocol has broad applications and could reliably provide an unlimited number of h-iECs for vascular therapies.
Dissection of theFgf8regulatory landscape byin vivoCRISPR-editing reveals extensive inter- and intra-enhancer redundancy
Authors: Hörnblad A. , Langenfeld K. , Bastide S. , Langa Vives F. , Spitz F. 
Published: March 2020

AbstractDevelopmental genes are often regulated by multiple elements with overlapping activity. Yet, in most cases, the relative function of those elements and their contribution to endogenous gene expression remain uncharacterized. Illustrating this situation, distinct sets of enhancers have been proposed to directFgf8in the limb apical ectodermal ridge (AER) and the midbrain-hindbrain boundary (MHB). Usingin vivoCRISPR/Cas9 genome engineering, we functionally dissect this complex regulatory ensemble and demonstrate two distinct regulatory logics. In the AER, the control ofFgf8expression appears extremely distributed between different enhancers. In contrast, in the MHB, one of the three active enhancers is essential while the other two are dispensable. Further dissection of the essential MHB enhancer revealed another layer of redundancy and identified two sub-parts required independently forFgf8expression and formation of midbrain and cerebellar structures. Interestingly, cross-species transgenic analysis of this enhancer suggests changes of the organisation of this essential regulatory node in the vertebrate lineage.
Framing sustainable development challenges: accounting for SDG-15 in the UK
Authors: Sobkowiak Madlen , Cuckston Thomas , Thomson Ian 
Published: March 2020

PurposeThis research seeks to explain how a national government becomes capable of constructing an account of its biodiversity performance that is aimed at enabling formulation of policy in pursuit of SDG 15: Life on Land.Design/methodology/approachThe research examines a case study of the construction of the UK government's annual biodiversity report. The case is analysed to explain the process of framing a space in which the SDG-15 challenge of halting biodiversity loss is rendered calculable, such that the government can see and understand its own performance in relation to this challenge.FindingsThe construction of UK government's annual biodiversity report relies upon data collected through non-governmental conservation efforts, statistical expertise of a small project group within the government and a governmental structure that drives ongoing evolution of the indicators as actors strive to make these useful for policy formulation.Originality/valueThe analysis problematises the SDG approach to accounting for sustainable development, whereby performance indicators have been centrally agreed and universally imposed upon all signatory governments. The analysis suggests that capacity-building efforts for national governments may need to be broader than that envisaged by the 2030 Agenda for Sustainable Development.
Exploring experiential indicators in flight training organization: a case study
Authors: Atasoy Vehbi Emrah , Ekici Selcuk 
Published: March 2020

Purpose
The purpose of this paper is to introduce an approach to evaluate the establishment requirements of an flight training organization (FTO) through indicators that are not included in the regulations from the viewpoint of “acquired indicators from FTO experience” (AIs-FTOE).

Design/methodology/approach
Although the establishment requirements of an FTO can be determined through regulations, it was realized that the pilot training process can be achieved in a safe, sustainable and economical manner through indicators that are not included in the regulations. These indicators were obtained through experience in the operation process of the FTOs. In this study, the indicators (obtained from the regulations and experiences) affecting the efficiency of FTOs, that were or would be operational, were determined, and the effects of the indicators on the organization were examined and presented in detail. The case study was carried out in the Department of Flight Training (ETU-P) of Eskişehir Technical University which has an FTO.

Findings
In accordance with the results, the necessity indicators were defined, and the indicators that were not included in the regulations were called as AIs-FTOE. Identified AIs-FTOEs were classified into three main headings: natural and artificial obstacles, meteorological conditions and physical and technological resources. Detailed indicator data results were presented after examinations.

Practical implications
When literature on FTOs was examined, it was seen that there is a need to identify and classify indicators that affect the efficiency of FTOs. To the authors’ knowledge, this study will be the first in the literature that presented information based on an active FTO in detail. Thus, the AIs-FTOEs identified in this study will serve as a roadmap for the FTOs to be established and are to be used as parameters to evaluate efficiency for the established ones.

Originality/value
To the best of authors’ knowledge, this paper will be the first paper in the literature describing the indicators that can be evaluated in terms of efficiency, sustainability and economy of FTOs.