bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function
Authors: Ravichandran Mirunalini , Rafalski Dominik , Ortega-Recalde Oscar , Davies Claudia I. , Glanfield Cassandra R. , Kotter Annika , Misztal Katarzyna , Wang Andrew H. , Wojciechowski Marek , Rażew Michał , Mayyas Issam M. , Kardailsky Olga , Schwarz Uwe , Zembrzycki Krzysztof , Morison Ian M. , Helm Mark , Weichenhan Dieter , Jurkowska Renata Z. , Krueger Felix , Plass Christoph , Zacharias Martin , Bochtler Matthias , Hore Timothy A. , Jurkowski Tomasz P. 
Published: December 2021

AbstractTET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic cores of mammalian TET enzymes favor CpGs embedded within bHLH and bZIP transcription factor binding sites, with 250-fold preference in vitro. Crystal structures and molecular dynamics calculations show that sequence preference is caused by intra-substrate interactions and CpG flanking sequence indirectly affecting enzyme conformation. TET sequence preferences are physiologically relevant as they explain the rates of DNA demethylation in TET-rescue experiments in culture and in vivo within the zygote and germline. Most and least favorable TET motifs represent DNA sites that are bound by methylation-sensitive immediate-early transcription factors and OCT4, respectively, illuminating TET function in transcriptional responses and pluripotency support.One-Sentence SummaryThe catalytic domains of the enzymes that facilitate passive and drive active DNA demethylation have intrinsic sequence preferences that target DNA demethylation to bHLH and bZIP transcription factor binding sites.
High density single-unit human cortical recordings using the Neuropixels probe
Authors: Chung JE , Sellers KK , Leonard MK , Gwilliams L , Xu D , Dougherty M , Kharazia V , Welkenhuysen M , Dutta B , Chang EF 
Published: December 2021

SummaryA fundamental unit of neural computation is the action potential. While significant advances have been made in the ability to sample action potentials of large numbers of individual neurons in animal models, translation of these methodologies to humans has been lacking due to clinical time constraints, electrical noise in the operating room, and reliability of the methodology. Here we present a reliable method for intraoperative recording of dozens of neurons in humans using the Neuropixels probe, yielding up to ∼100 simultaneously-recorded single-units (n=596 across 11 recordings in 8 participants). Most single-units were active within 1 minute of reaching target depth, compatible with clinical time constraints. Cell pairs active close in time were spatially closer in most recordings, demonstrating the power to resolve complex cortical dynamics. Altogether, this approach provides access to population single-unit activity across the depth of human neocortex at scales previously only accessible in animal models.HighlightsSingle units in 8 patients, yielding 596 putative single units across 11 recordingsThe majority of putative neurons fire at least 1 spike within one minute after reaching target depthPutative neurons take longer to fire at least one spike in anesthetized compared to awake participantsCell-pairs that fire action potentials close in time are spatially closer together than those fire further apart in time
TXNRD3 supports male fertility via the redox control of spermatogenesis
Authors: Dou Qianhui , Turanov Anton A. , Mariotti Marco , Hwang Jae Yeon , Wang Huafeng , Lee Sang-Goo , Paulo Joao A. , Yim Sun Hee , Gygi Stephen P. , Chung Jean-Ju , Gladyshev Vadim N. 
Published: December 2021

AbstractThioredoxin/glutathione reductase (TGR, TXNRD3) is a thiol oxidoreductase of unknown function composed of thioredoxin reductase and glutaredoxin domains. This NADPH-dependent enzyme evolved by gene duplication within the Txnrd family, is expressed in the testes and can reduce both thioredoxin and glutathione in vitro. To characterize the function of TXNRD3 in vivo, we generated a strain of mice with the deletion of Txnrd3 gene. We show that Txnrd3 knockout mice are viable and without discernable gross phenotypes, but TXNRD3 deficiency leads to fertility impairment in male mice. Txnrd3 knockout animals exhibit a lower fertilization rate in vitro, a sperm movement phenotype and an altered redox status of thiols. Proteomic analyses revealed a broad range of substrates reduced by TXNRD3 during sperm maturation, presumably as a part of quality control. The results show that TXNRD3 plays a critical role in male reproduction via the thiol redox control of spermatogenesis.
Kinetics Of Interferon-λ And Receptor Expression In Response To In Vitro Respiratory Viral Infection
Authors: Lozhkov Alexey A , Yolshin Nikita D , Baranovskaya Irina L , Plotnikova Marina A , Sergeeva Mariia V. , Gyulikhandanova Natalia E , Klotchenko Sergey A , Vasin Andrey V 
Published: December 2021

AbstractThe major protective immune response against viruses is production of type I and III interferons (IFNs). IFNs induce the expression of hundreds of IFN-stimulated genes (ISGs) that block viral replication and further viral spread. The ability of respiratory viruses to suppress induction of IFN-mediated antiviral defenses in infected epithelial cells may be a factor contributing to the particular pathogenicity of several strains. In this report, we analyzed expression of IFNs and some ISGs in an alveolar epithelial cell subtype (A549) in response to infection with: influenza A viruses (A/California/07/09pdm (H1N1), A/Texas/50/12 (H3N2)); influenza B virus (B/Phuket/3073/13); adenovirus type 5 and 6; or respiratory syncytial virus (strain A2). IFNL and ISGs expression significantly increased in response to infection with all RNA viruses 24 hpi. Nevertheless, only IBV led to early increase in IFNL and ISGs mRNA level. IBV and H1N1 infection led to elevated proinflammatory cytokine production. We speculate that augmented IFN-α, IFN-β, IL-6 levels negatively correlate to SOCS1 expression. Importantly, we showed a decrease in IFNLR1 mRNA in case of IBV infection that implies the existence of negative ISGs expression regulation at IFNλR level. It could be either a specific feature of IBV or a consequence of early IFNL expression.
Work and oxygen consumption of isolated right ventricular papillary muscle in experimental pulmonary hypertension
Authors: van der Laarse Willem J. , Bogaards Sylvia J.P. , Schalij Ingrid , Noordegraaf Anton Vonk , Vaz Frédéric M. , van Groen Duncan 
Published: December 2021

SummaryRight-sided myocardial mechanical efficiency (work output/metabolic energy input) in pulmonary hypertension can be severely reduced. We determined the contribution of intrinsic myocardial determinants of efficiency using papillary muscle preparations from monocrotaline-induced pulmonary hypertensive (MCT-PH) rats. The hypothesis was tested that efficiency is reduced by mitochondrial dysfunction in addition to increased activation heat reported previously. Right ventricular (RV) muscle preparations were subjected to 5 Hz sinusoidal length changes at 37°C. Work and suprabasal oxygen consumption (VO2) were measured before and after cross-bridge inhibition by blebbistatin. Cytosolic cytochrome c concentration, myocyte cross-sectional area, proton permeability of the inner mitochondrial membrane (PP IMM), and monoamine oxidase (MAO)-A and glucose 6-phosphate dehydrogenase (G-6-PDH) activities and phosphatidylglycerol (PG) and cardiolipin (CL) contents were determined. Mechanical efficiency ranged from 23 to 11% in control (n = 6) and from 22 to 1% in MCT-PH (n = 15) and correlated with work (r2 = 0.68, P < 0.0001) but not with VO2 (r2 = 0.004, P = 0.7919). VO2 for cross-bridge cycling was proportional to work (r2 = 0.56, P = 0.0005). Blebbistatin-resistant VO2 (r2 = 0.32, P = 0.0167) and IMM PP (r2 = 0.36, P = 0.0110) correlated inversely with efficiency. Together, these variables explained the variance of efficiency (coefficient of multiple determination R2 = 0.79, P = 0.0001). Cytosolic cytochrome c correlated inversely with work (r2 = 0.28, P = 0.0391), but not with efficiency (r2 = 0.20, P = 0.0867). G-6-PDH, MAO-A and PG/CL increased in the RV wall of MCT-PH but did not correlate with efficiency. Reduced myocardial efficiency in MCT-PH is due to activation processes and mitochondrial dysfunction. The variance of work and the ratio of activation heat reported previously and blebbistatin-resistant VO2 are discussed.Key pointsMechanical efficiency of right ventricular myocardium is reduced in pulmonary hypertension. Increased energy use for activation processes has been demonstrated previously, but the contribution of mitochondrial dysfunction is unknown.Work and oxygen consumption is determined during work loops. Oxygen consumption for activation and cross-bridge cycling confirm the previous heat measurements.Cytosolic cytochrome c concentration, proton permeability of the mitochondrial inner membrane and phosphatidylglycerol/cardiolipin are increased in experimental pulmonary hypertension.Mitochondrial dysfunction in right ventricular myocytes is related to reduced work and mechanical efficiency in experimental pulmonary hypertension.Upregulation of the pentose phosphate pathway and a potential gap in the energy balance suggest mitochondrial dysfunction in right ventricular overload is due to excessive production of reactive oxygen species.
Diffusion of small molecule drugs is affected by surface interactions and crowder proteins
Authors: Dey Debabrata , Nunes-Alves Ariane , Wade Rebecca C , Schreiber Gideon 
Published: December 2021

AbstractCrowded environments are known to affect the diffusion of macromolecules but their effects on the diffusion of small molecules, such as drugs, are largely uncharacterized. Here, we investigate how three macromolecular protein crowders, bovine serum albumin (BSA), hen egg-white lysozyme and myoglobin, influence the translational diffusion rates and interactions of four low molecular-weight compounds: the diagnostic marker fluorescein, and three drugs, doxorubicin, glycogen synthase kinase-3 inhibitor SB216763 and quinacrine. Using Fluorescence Recovery After Photo-bleaching in Line mode (Line- FRAP), Brownian dynamics simulations and molecular docking, we find that the diffusive behavior of the small molecules is highly affected by self-aggregation, interactions with the proteins, and surface adhesion. The diffusion of fluorescein is decreased by protein crowders due to its interactions with the proteins and their surface adsorption. In contrast, the presence of protein crowders increases the diffusion rate of doxorubicin by reducing surface interactions. SB216763 shows a third scenario, where BSA, but not lysozyme or myoglobin , reduces self-aggregation, resulting in faster diffusion. Quinacrine was the only compound whose diffusion was not affected by the presence of protein crowders. The mechanistic insights gained here into the effects of interactions of small molecules with proteins and surfaces on the translational diffusion of small molecules can assist in optimizing the design of compounds for higher mobility and lower occlusion in complex macromolecular environments.
Bioprinting the Tumor Microenvironment with an Upgraded Consumer Stereolithographic 3D Printer
Authors: Breideband Louise , Wächtershäuser Kaja N. , Hafa Levin , Wieland Konstantin , Frangakis Achilleas , Stelzer Ernst H. K. , Pampaloni Francesco 
Published: December 2021

AbstractA widespread application of three-dimensional (3D) bioprinting in basic and translational research requires the accessibility to affordable printers able to produce physiologically relevant tissue models. To facilitate the use of bioprinting as a standard technique in biology, an open-source device based on a consumer-grade 3D stereolithographic (SL) printer was developed. This SL bioprinter can produce complex constructs that preserve cell viability and recapitulate the physiology of tissues. The detailed documentation of the modifications apported to the printer as well as a throughout performance analysis allow for a straightforward adoption of the device in other labs and its customization for specific applications. Given the low cost, several modified bioprinters could be simultaneously operated for a highly parallelized tissue production.To showcase the capability of the bioprinter, we produced constructs consisting of patient-derived cholangiocarcinoma organoids encapsulated in a gelatin methacrylate (GelMA)/polyethylene glycol diacrylate (PEGDA) hydrogel. A thorough characterization of different GelMA/PEGDA ratios revealed that the mechanical properties of the bioprinted tumor model can be accurately fine-tuned to mimic a specific tumor micro-environment. Immunofluorescence and gene expression analyses of tumor markers confirmed that the bioprinted synthetic hydrogel provides a flexible and adequate replacement of animal-derived reconstituted extracellular matrix.
A nanopore interface for high bandwidth DNA computing
Authors: Zhang Karen , Chen Yuan-Jyue , Doroschak Kathryn , Strauss Karin , Ceze Luis , Seelig Georg , Nivala Jeff 
Published: December 2021

AbstractDNA has emerged as a powerful substrate for programming information processing machines at the nanoscale. Among the DNA computing primitives used today, DNA strand displacement (DSD) is arguably the most popular, with DSD-based circuit applications ranging from disease diagnostics to molecular artificial neural networks. The outputs of DSD circuits are generally read using fluorescence spectroscopy. However, due to the spectral overlap of typical small-molecule fluorescent reporters, the number of unique outputs that can be detected in parallel is limited, requiring complex optical setups or spatial isolation of reactions to make output bandwidths scalable. Here, we present a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies’ MinION device). We show that engineered reporter probes can be detected and classified with high accuracy at the single-molecule level directly from raw nanopore signals using deep learning. We then demonstrate this method’s utility in multiplexed detection of clinically relevant microRNA sequences. These results increase DSD output bandwidth by an order of magnitude over what is possible with fluorescence spectroscopy, laying the foundations for a new paradigm in DNA circuit readout and programmable multiplexed molecular diagnostics using portable nanopore devices.
Farm diversification efforts, (open) innovation networks and performance: what is the connection?
Authors: Dias Claudia , Rodrigues Ricardo Gouveia , Ferreira João J. 
Published: December 2021

PurposeBased on farm diversification's conventional and unconventional nature, the study intends to discriminate different profiles of farm diversification businesses. Furthermore, this study analyses the links between farm diversification efforts, (open) innovation networks as well as the environmental performance (EP) and financial performance (FP) of farms.Design/methodology/approachA questionnaire was administered through personal interviews with 160 fresh fruit farmers in an inland Portuguese region. Linear regression, latent class analysis (LCA) and multinomial logistic regression were used.FindingsThere are significant differences between the levels of diversification, performance and participation in (open) innovation networks of the three classes of farmers discriminated. Different types of diversification efforts and (open) innovation networks influence EP and FP, while FP and R&D projects are associated with the likelihood of being part of a farm diversification class. Moreover, this study shows that innovation networks, promoted by specialized agricultural advisors and R&D projects, are important forms of open innovation in the agricultural sector.Research limitations/implicationsThe study contributes to understanding the agricultural sector's diversification efforts and (open) innovation networks and their association with EP and FP. The conventional or unconventional nature of farm diversification was self-reported.Practical implicationsEuropean and local institutions are advised to develop more R&D programs directed to farmers, including environmental and financial issues, besides comprising agricultural and non-agricultural diversification.Originality/valueThis study provides new insights to understand the association between diversification efforts, (open) innovation networks and agricultural businesses' performance.
Review of Tsunami early warning system and coastal resilience with a focus on Indian Ocean
Authors: Pal Indrajit , Ghosh Subhajit , Dash Itesh , Mukhopadhyay Anirban 
Published: December 2021

Purpose
This paper aims to provide a general overview of the international Tsunami warning system mandated by the United Nations, particularly on cataloging past studies and a strategic focus in the Indian Ocean, particularly on the Bay of Bengal region.

Design/methodology/approach
Present research assimilates the secondary non-classified data on the Tsunami warning system installed in the Indian Ocean. Qualitative review and exploratory research methodology have been followed to provide a holistic profile of the Tsunami rarly warning system (TEWS) and its role in coastal resilience.

Findings
The study finds the need for strategic focus to expand and interlink regional early warning cooperation mechanisms and partnerships to enhance capacities through cooperation and international assistance and mobilize resources necessary to maintain the TEWS in the Indian Ocean region. The enhanced capacity of the TEWS certainly improves the resilience of Indian Ocean coastal communities and infrastructures.

Originality/value
The study is original research and useful for policy planning and regional cooperation on data interlinkages for effective TEWS in the Indian Ocean region.
Pathways towards Green Banking adoption: moderating role of top management commitment
Authors: Bukhari Syed Asim Ali , Hashim Fathyah , Amran Azlan 
Published: December 2021

PurposeThe purpose of this study is to empirically examine the determinants and outcomes of Green Banking adoption and the moderating influence of top management commitment under the corporate environmental ethics ideology. External stakeholder pressures are analyzed as determinants of Green Banking adoption. Brand image and operational efficiency are examined as outcomes of this business ideology. Green Banking adoption is adapted as a second-order construct with four first-order reflective constructs to ensure in-depth conceptualization of the construct.Design/methodology/approachGreen Banking adoption is studied at the bank branch level in a developing country, i.e. Pakistan. The data is collected from the branch managers of 212 bank branches from five major cities of Pakistan through mails. Self-administered survey was used for the data collection. The data was analyzed through the application of partial least square-structured equation modeling in SMART PLS 3.2.9. The measurement model and the structural model of the research framework were analyzed through the two-stage approach of the second-order analysis.FindingsThe results indicate a positive relationship between customer and competitor pressure and Green Banking adoption among bank branches in Pakistan depicting an influence of various environmental ethical pressures on bank’s adoption practices. Community pressure was shown to have no significant influence on Green Banking adoption at the branch level. The moderator of top management commitment caused a positive influence on the relationship between all the studied stakeholder pressures and Green Banking adoption. Branch managers reported branch image and operational efficiency to be enhanced due to Green Banking adoption.Originality/valueThis study attempts to fill in the significant gap in Green Banking adoption literature through an empirical analysis of Green Banking’s second-order construct. Currently, limited literature exists on the various aspects of Green Banking adoption, and an empirical study has not been conducted at the bank branch level. The study contributes significant practical, theoretical and methodological contributions to the area of Green Banking.
Power, shared goals and supplier flexibility: a study of the HUB-and-spoke supply chain
Authors: Liu Gordon , Aroean Lukman , Ko Wai Wai 
Published: December 2021

PurposeSupplier flexibility reflects a supplier's operations-related decisions in responsively providing the necessary inputs to the focal firm. Drawing on resource-dependency theory and transaction cost economics, this study develops a conceptual framework to explain the differential effects of a focal firm's power over supplier flexibility in the context of the hub-and-spoke supply chain (SC). This study also considers the goals shared between the focal firm and its suppliers as an important contingency factor within the framework.Design/methodology/approachThis study tests the proposed conceptual framework using dyadic survey data from a hub-and-spoke SC consisting of a large construction contractor and its 100 suppliers in Indonesia.FindingsThe findings show that coercive power has an inverted U-shaped effect on supplier flexibility, while legal-legitimate power has a U-shaped effect. Furthermore, shared goals positively moderate the U-shaped effect between legal-legitimate power and supplier flexibility.Originality/valueThis study differentiates between the impacts of coercive power and legal-legitimate power on supplier flexibility in the hub-and-spoke SC. It also demonstrates that shared goals play a moderating role in affecting the impacts of legal-legitimate power on supplier flexibility. These findings also have important implications with regard to integrating resource-dependency theory and transaction cost economics to explain these associations.
The mediating effects of student satisfaction on technostress–performance expectancy relationship in university students
Authors: Abd Aziz Nurul Nadia , Aziz Mohd Amar , Abd Rahman Noor Amira Syazwani 
Published: December 2021

PurposeThis study aimed to explore the technostress effects on the students' expectancy in their academic performance. Three main factors were used as predictors, namely techno-complexity (TC), techno-insecurity (TIS) and techno-overload (TO), to measure the students' performance expectancy via the mediating effects of student satisfaction (SS).Design/methodology/approachA total of 234 survey-based online questionnaires were filled by students from Universiti Teknologi Mara (UiTM). Based on the data, the hypothetical model was tested statistically using the Partial Least Square–Structural Equation Modelling (PLS-SEM), specifically the Smart Partial Least Square (SmartPLS) version 3.3.2.FindingsThe results indicated that SS mediated the relationship between TC, TIS and performance expectancy. Nevertheless, the two predictors (TC and TIS) negatively affected SS, whereas SS positively affected the performance expectancy. The findings further revealed that reducing TC and TIS could increase SS and their expectancy to achieve better academic performance.Practical implicationsThis study proposed that higher learning institutions provide an innovative and user-friendly platform for the online learning environment. Consequently, this improvement could increase SS with the online learning experience and motivate them to expect better academic achievement.Originality/valueThis study also contributed to the existing literature by building and testing a technostress model and articulating the inter-relations between SS and performance expectancy.