bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sponge contribution to the silicon cycle of a diatom-rich shallow bay
Authors: López-Acosta María , Maldonado Manuel , Grall Jacques , Ehrhold Axel , Sitjà Cèlia , Galobart Cristina , Leynaert Aude 
Published: October 2021

AbstractIn coastal systems, planktonic and benthic silicifiers compete for the pool of dissolved silicon, a nutrient required to make their skeletons. The contribution of planktonic diatoms to the cycling of silicon in coastal systems is often well characterized, while that of benthic silicifiers such as sponges has rarely been quantified. Herein, silicon fluxes and stocks are quantified for the sponge fauna in the benthic communities of the Bay of Brest (France). A total of 45 siliceous sponge species living in the Bay account for a silicon standing stock of 1215 tons, while that of diatoms is only 27 tons. The silicon reservoir accumulated as sponge skeletons in the superficial sediments of the Bay rises to 1775 tons, while that of diatom skeletons is only 248 tons. These comparatively large stocks of sponge silicon were estimated to cycle two orders of magnitude slower than the diatom stocks. Sponge silicon stocks need years to decades to be renewed, while diatom turnover lasts only days. Although the sponge monitoring over the last 6 years indicates no major changes of the sponge stocks, our results do not allow to conclude if the silicon sponge budget of the Bay is at steady state, and potential scenarios are discussed. The findings buttress the idea that sponges and diatoms play contrasting roles in the marine silicon cycle. The budgets of these silicon major users need to be integrated and their connections revealed, if we aim to reach a full understanding of the silicon cycling in coastal ecosystems.
Systematic expression profiling of dprs and DIPs reveals cell surface codes in Drosophila larval peripheral neurons
Authors: Wang Yupu , Lobb-Rabe Meike , Ashley James , Chatterjee Purujit , Anand Veera , Bellen Hugo J. , Kanca Oguz , Carrillo Robert A. 
Published: October 2021

AbstractIn complex nervous systems, neurons must identify their correct partners to form synaptic connections. The prevailing model to ensure correct recognition posits that cell surface proteins (CSPs) in individual neurons act as identification tags. Thus, knowing what cells express which CSPs would provide insights into neural development, synaptic connectivity, and nervous system evolution. Here, we investigated expression of dprs and DIPs, two CSP subfamilies belonging to the immunoglobulin superfamily (IgSF), in Drosophila larval motor neurons (MNs), sensory neurons (SNs), peripheral glia and muscles using a collection of GAL4 driver lines. We found that dprs are more broadly expressed than DIPs in MNs and SNs, and each examined neuron expresses a unique combination of dprs and DIPs. Interestingly, many dprs and DIPs are not robustly expressed, but instead, are found in gradient and temporal expression patterns. Hierarchical clustering showed a similar expression pattern of dprs and DIPs in neurons from the same type and with shared synaptic partners, suggesting these CSPs may facilitate synaptic wiring. In addition, the unique expression patterns of dprs and DIPs revealed three uncharacterized MNs - MN23-Ib, MN6-Ib (A2) and MN7-Ib (A2). This study sets the stage for exploring the functions of dprs and DIPs in Drosophila MNs and SNs and provides genetic access to subsets of neurons.
Arabidopsis PROTODERMAL FACTOR2 binds lysophosphatidylcholines and transcriptionally regulates phospholipid metabolism
Authors: Wojciechowska Izabela , Mukherjee Thiya , Knox-Brown Patrick , Hu Xueyun , Khosla Aashima , Mathews Graham L. , Thompson Kyle A. , Peery Seth T. , Szlachetko Jagoda , Thalhammer Anja , Hincha Dirk K. , Skirycz Aleksandra , Schrick Kathrin 
Published: October 2021

ABSTRACTPlant homeodomain leucine-zipper IV (HD-Zip IV) transcription factors (TFs) contain an evolutionarily conserved steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain. The START domain is required for TF activity; however, its presumed role as a lipid sensor is not well understood. Here we used tandem affinity purification from Arabidopsis cell cultures to demonstrate that PROTODERMAL FACTOR2 (PDF2), a representative family member which controls epidermal differentiation, recruits lysophosphatidylcholines in a START-dependent manner. In vitro assays with recombinant protein verified that a missense mutation in a predicted ligand contact site reduces lysophospholipid binding. We additionally uncovered that PDF2 controls the expression of phospholipid-related target genes by binding to a palindromic octamer with consensus to a phosphate (Pi) response element. Phospholipid homeostasis and elongation growth were altered in pdf2 mutants according to Pi availability. Cycloheximide chase experiments further revealed a role for START in maintaining protein levels, and Pi limitation resulted in enhanced protein destabilization, suggesting a mechanism by which lipid binding controls TF activity. We propose that the START domain serves as a molecular sensor for membrane phospholipid status in the epidermis. Overall our data provide insights towards understanding how the lipid metabolome integrates Pi availability with gene expression.
Adrenergic signaling controls early transcriptional programs during CD8+ T cell responses to viral infection
Authors: Estrada Leonardo D. , Çobanoğlu Didem Ağaç , Wise Aaron , Maples Robert W. , Çobanoğlu Murat Can , Farrar J. David 
Published: October 2021

AbstractViral infections drive the expansion and differentiation of responding CD8+ T cells into variegated populations of cytolytic effector and memory cells. While pro-inflammatory cytokines and cell surface immune receptors play a key role in guiding T cell responses to infection, T cells are also markedly influenced by neurotransmitters. Norepinephrine is a key sympathetic neurotransmitter, which acts to suppress CD8 + T cell cytokine secretion and lytic activity by signaling through the β2-adrenergic receptor (ADRB2). Although ADRB2 signaling is considered generally immunosuppressive, its role in regulating differentiation of effector T cells in response to infection has not been investigated. Using an adoptive transfer approach, we compared the expansion and differentiation of wild type (WT) to Adrb2-/- CD8 + T cells throughout the primary response to vesicular stomatitis virus (VSV) infection in vivo. We measured the dynamic changes in transcriptome profiles of antigen-specific CD8 + T cells as they responded to VSV. Within the first 7 days of infection, WT cells out-paced the expansion of Adrb2-/- cells, which correlated with reduced expression of IL-2 and the IL-2Rα in the absence of ADRB2. RNASeq analysis identified over 300 differentially expressed genes that were both temporally regulated following infection and selectively regulated in WT vs Adrb2-/- cells. These genes contributed to major transcriptional pathways including cytokine receptor activation, signaling in cancer, immune deficiency, and neurotransmitter pathways. By parsing genes within groups that were either induced or repressed over time in response to infection, we identified three main branches of genes that were differentially regulated by the ADRB2. These gene sets were predicted to be regulated by specific transcription factors involved in effector T cell development, such as Tbx21 and Eomes. Collectively, these data demonstrate a significant role for ADRB2 signaling in regulating key transcriptional pathways during CD8 + T cells responses to infection that may dramatically impact their functional capabilities and downstream memory cell development.
Regulatory variants active in iPSC-derived pancreatic progenitor cells are associated with Type 2 Diabetes in adults
Authors: Nguyen Jennifer P. , D’Antonio-Chronowska Agnieszka , Fujita Kyohei , Salgado Bianca M. , Matsui Hiroko , Arthur Timothy D. ,   iPSCORE Consortium, Donovan Margaret K.R. , D’Antonio Matteo , Frazer Kelly A. 
Published: October 2021

AbstractPancreatic progenitor cells (PPC) are an early developmental multipotent cell type that give rise to mature endocrine, exocrine, and ductal cells. To investigate the extent to which regulatory variants active in PPC contribute to pancreatic complex traits and disease in the adult, we derived PPC from induced pluripotent stem cells (iPSCs) of nine unrelated individuals and generated single cell profiles of chromatin accessibility (snATAC- seq) and transcriptome (scRNA-seq). While iPSC-PPC differentiation was asynchronous and included cell types from early to late developmental stages, we found that the predominant cell type consisted of NKX6-1+ progenitors. Genetic characterization using snATAC-seq identified 86,261 regulatory variants that either displayed chromatin allelic bias and/or were predicted to affect active transcription factor (TF) binding sites. Integration of these regulatory variants with 380 fine-mapped type 2 diabetes (T2D) risk loci identified regulatory variants in 209 of these loci that are functional in iPSC-PPC, either by affecting transcription factor binding or through association with allelic effects on chromatin accessibility. The PPC active regulatory variants in 65 of these loci showed strong evidence of causally underlying the association with T2D. Our study shows that studying the functional associations of regulatory variation in iPSC-PPC enables the identification and characterization of causal SNPs for adult Type 2 Diabetes.
Microplastic pollution of commercial fishes from coastal and offshore waters, Japan
Authors: Yagi Mitsuharu , Kobayashi Tsunefumi , Maruyama Yutaka , Hoshina Sota , Masumi Satoshi , Aizawa Itaru , Uchida Jun , Kinoshita Tsukasa , Yamawaki Nobuhiro , Aoshima Takashi , Morii Yasuhiro , Shimizu Kenichi 
Published: October 2021

ABSTRACTMicroplastics (MPs) pollution is a worldwide issue in the marine environment. There is growing concern of consuming MPs through fish, yet the current contamination status of fish collected from the deep sea surrounding Japan remains limited. We present baseline data on MPs in commercially important fishes from the coastal and offshore waters near Kyushu, Japan (East China Sea). We examined the MPs in the digestive tracts of two pelagic (n = 150 in total) and five demersal species (n = 235 in total). The fish were caught by pole and line, and bottom trawl at different geographical positions. The MPs in pelagic fish (39.1 %) were higher than demersal fish (10.3 %) and of larger sizes. The MPs correlated with habitat depth and type. There was species variation in the shape and polymer composition of MPs. These results increase our understanding of the heterogeneous uptake of MPs by fishes.
Unravelling the Graded Millisecond Allosteric Activation Mechanism of Imidazole Glycerol Phosphate Synthase
Authors: Calvó-Tusell Carla , Maria-Solano Miguel A. , Osuna Sílvia , Feixas Ferran 
Published: October 2021

ABSTRACTDeciphering the molecular mechanisms of enzymatic allosteric regulation requires the structural characterization of key functional states and also their time evolution toward the formation of the allosterically activated ternary complex. The transient nature and usually slow millisecond timescale interconversion between these functional states hamper their detailed experimental and computational characterization. Here, we design a computational strategy tailored to reconstruct millisecond timescale events to describe the graded allosteric activation of imidazole glycerol phosphate synthase (IGPS) in the ternary complex. IGPS is a heterodimeric bienzyme complex responsible for the hydrolysis of glutamine to glutamate in the HisH subunit and delivering ammonia for the cyclase activity in HisF. Despite significant advances in understanding the underlying allosteric mechanism, essential molecular details of the long-range millisecond allosteric activation pathway of wild-type IGPS remain hidden. Without using a priori information of the active state, our simulations uncover how IGPS, with the allosteric effector bound in HisF, spontaneously captures glutamine in a catalytically inactive HisH conformation, subsequently attains a closed HisF:HisH interface, and finally forms the oxyanion hole in HisH for efficient glutamine hydrolysis. We show that effector binding in HisF dramatically decreases the conformational barrier associated with the oxyanion hole formation in HisH, in line with the experimentally observed 4500-fold activity increase in glutamine production. The formation of the allosterically active state is controlled by time-evolving dynamic communication networks connecting the effector and substrate binding sites. This computational strategy can be generalized to study other unrelated enzymes undergoing millisecond timescale allosteric transitions.
Aerodynamic coefficients modeling using Levenberg–Marquardt algorithm and network
Authors: Wang Zhigang , Li Aijun , Wang Lihao , Zhou Xiangchen , Wu Boning 
Published: October 2021

PurposeThe purpose of this paper is to propose a new aerodynamic parameter estimation methodology based on neural network and output error method, while the output error method is improved based on particle swarm algorithm.Design/methodology/approachFirstly, the algorithm approximates the dynamic characteristics of aircraft based on feedforward neural network. Neural network is trained by extreme learning machine, and the trained network can predict the aircraft response at (k + 1)th instant given the measured flight data atkth instant. Secondly, particle swarm optimization is used to enhance the convergence of Levenberg–Marquardt (LM) algorithm, and the improved LM method is used to substitute for the Gauss Newton algorithm in output error method. Finally, the trained neural network is combined with the improved output error method to estimate aerodynamic derivatives.FindingsNeither depending on the initial guess of the parameters to be estimated nor requiring numerical integration of the aircraft motion equation, the proposed algorithm can be used for unstable aircraft and is successfully applied to extract aerodynamic derivatives from both simulated and real flight data.Research limitations/implicationsThe proposed method requires iterative calculation and can only identify parameters offline.Practical implicationsThe proposed method is successfully applied to estimate aircraft aerodynamic parameters and can also be used as a new algorithm for other optimization problems.Originality/valueIn this study, the output error method is improved to reduce the dependence on the initial value of parameters and expand its application scope. It is applied in aircraft aerodynamic parameter identification together with neural network.
Determination of fuel consumption and pollutant emissions with the real-time engine running data of aircrafts in the taxi-out period
Authors: Akyüz Mehmet Kadri 
Published: October 2021

Purpose
The purpose of this paper is to calculate the fuel consumption and emissions of carbon monoxide (CO), nitrogen oxide (NOx) and hydrocarbons (HC) in the taxi-out period of aircraft at the International Diyarbakir Airport in 2018 and 2019.

Design/methodology/approach
Calculations were performed by determining the engine operating times in the taxi-out period with the flight data obtained from the airport authority. In the analyses, aircraft series and aircraft engine types were determined, and the Engine Exhaust Emission Databank of the International Civil Aviation Authority (ICAO) were used for the calculation.

Findings
Total fuel consumption in the taxi-out period in 2018 and 2019 was calculated as 525.64 and 463.69 tons, respectively. In 2018, HC, CO and NOx emissions caused by fuel consumption were found to be 1,109, 10,668 and 2,339 kg, respectively. In 2019, the total HC, CO and NOx emissions released to the atmosphere during the taxi-out phase are 966, 9,391 and 2,126 kg, respectively. B737 Series aircraft have the largest share in total fuel consumption and pollutant emissions.

Practical implications
This study explains the importance of determining fuel consumption and pollutant emissions by considering engine operating times in the taxi-out period. The study provides aviation authorities with scientific methods to follow in calculating fuel consumption and emissions from aircraft operations.

Originality/value
The originality of this study is the calculation of fuel consumption and pollutant emissions by determining real-time engine running times in the taxi-out period. In addition, calculations were made with real engine operating times determined in the taxi-out period using real flight data.
Research productivity of management faculty: job demands-resources approach
Authors: Barney Chet E. , Clark Brent B. , da Motta Veiga Serge P. 
Published: October 2021

PurposeThe main purpose of this study was to examine which job resources are most valuable for research productivity, depending on varying teaching demands.Design/methodology/approachData was collected from 324 management faculty at research, balanced and teaching (i.e. respectively low-, moderate- and high-teaching demands) public universities in the United States.FindingsResults showed that no single job resource predicted research productivity across all three types of schools. At research schools (i.e. low-teaching demands), productivity was positively associated with job resources including summer compensation, level of protection for untenured faculty and number of research assistant hours, while negatively associated with travel funding. At balanced schools (i.e. moderate-teaching demands), research output was positively associated with time allocated to research, grant money, travel funding and conference attendance, while negatively associated with amount of consulting hours. At teaching schools (i.e. high-teaching demands), the only significant resource was time allocated to research.Practical implicationsThis paper can help management faculty and business school leaders understand what resources are most appropriate given the teaching demands associated with the specific institution, and by further helping these institutions attract and retain the best possible faculty.Originality/valueThis study extends prior work on academic research performance by identifying resources that can help faculty publish given different levels of teaching demands. This is important as teaching demands tend to be relatively stable within an institution, while they can vary greatly across types of institutions.
Risk perception, health stressors and reduction in sharing cannabis products during the COVID-19 outbreak: a cross-sectional study
Authors: Rosenberg Dennis , Sznitman Sharon 
Published: October 2021

Purpose
This study aimed to understand the extent to which cannabis-related risk perception and COVID-19-related health worries were associated with the reported reduction in sharing cannabis smoking products to mitigate the risk of the coronavirus transmission or infection. This association was tested in two different periods in terms of toughness of national lockdown policy imposed in the first months of the pandemic in Israel.

Design/methodology/approach
The study population included adult recreational cannabis users who completed one of the two online cross-sectional surveys dedicated to COVID-19 and the cannabis use situation in Israel in the first half of the 2020. The two surveys were conducted six weeks apart. One survey was conducted in the period when strict lockdown measures were in place (N1 = 376). The other survey was conducted in the period when many lockdown measures were lifted (N2 = 284). Differences between the samples regarding risk perception, health stressors and reduction in sharing cannabis products were assessed using t-test. Regression analysis was used to test the independent correlates of reported reduction in sharing cannabis products.

Findings
Means of risk perception, health stressors and reported reduction in sharing cannabis products were higher in the sample surveyed in the period of the strict lockdown measures than in the sample surveyed in the period of eased lockdown measures. Risk perception was associated with reported reduction in sharing cannabis products only in the sample surveyed in the period of strict lockdown measures. In contrast, health stressors were related to reported reduction in sharing cannabis products in both samples.

Social implications
Health stressors may represent a more stable mechanism by which cannabis users engage in protective behavior during the pandemic than risk perceptions.

Originality/value
To the best of the authors’ knowledge, the current research is one of the first studies that examine the associations among risk perception, primary stressors and protective behavior in recreational cannabis users while referring to cannabis-related behavior other than use.
Ethical considerations of disaster research in conflict-affected areas
Authors: Mena Rodrigo , Hilhorst Dorothea 
Published: October 2021

PurposeDebates on the ethics of disaster and humanitarian studies concern unequal relations in research (among research institutes/researchers/stakeholders); the physical and psychological well-being of research participants and researchers; and the imposition of western methods, frameworks and epistemologies to the study of disasters. This paper focuses on everyday ethics: how they need to be translated throughout the everyday practices of research and how researchers can deal with the ethical dilemmas that inevitably occur.Design/methodology/approachThis paper analyses the process of addressing ethics-related dilemmas from the first author's experiences researching disaster governance in high-intensity conflict settings, in particular drawing from 4 to 6 months of fieldwork in South Sudan and Afghanistan. In addition, ethical issues around remote research are discussed, drawing on the example of research conducted in Yemen. It is based on the personal notes taken by the first author and on the experience of both authors translating guidelines for research in remote and hazardous areas into research practices.FindingsThe paper concerns translating ethics into the everyday practices of research planning, implementation and communication. It argues for the importance of adaptive research processes with space for continuous reflection in order to advance disaster studies based on (1) equitable collaboration; (2) participatory methodologies wherever possible; (3) safety and security for all involved; (4) ethical approaches of remote research and (5) responsible and inclusive research communication and research-uptake. Openness about gaps and limitations of ethical standards, discussions with peers about dilemmas and reporting on these in research outcomes should be embedded in everyday ethics.Originality/valueThe paper contributes to discussions on everyday ethics, where ethics are integral to the epistemologies and everyday practices of research.