bluuebunny/crossref_metadata_2025_split huggingface dataset:
WITHDRAWN: Multiplane Mesoscope reveals distinct cortical interactions following expectation violations
Authors: Orlova Natalia , Najafi Farzaneh , Tsyboulski Dmitri , Seid Sam , Kivikas Sara , Kato India , Griffin Fiona , Leon Arielle , Hytnen Ross D. , L’Heureux Quinn , North Kat , Swapp Jackie , Nayan Chelsea , Hancock Nicole , Ahmed Ruweida , Gelfand Emily , Cho Andrew , Mace Kyla , Howard Robert , Casal Linzy , Lambert Sophie , Lee Eric Kenji , Caldejon Shiella , Waughman Xana , Williford Allison , Garrett Marina , Ollerenshaw Doug , Olsen Shawn R. , Groblewski Peter A. , Saggau Peter , Lecoq Jérôme 
Published: October 2020

Withdrawal StatementThis manuscript has been withdrawn because it was posted without the consent of all authors. Therefore, this work should not be cited as reference for the project. If you have any questions, please contact the corresponding author.
Optimal Adaptive Electrode Selection to Maximize Simultaneously Recorded Neuron Yield
Authors: Choi John , Wingel Katie , Charles Adam , Kumar Krishan , Choudhury Mahdi , Pesaran Bijan , Khazali Mohammad 
Published: October 2020

AbstractNeural-Matrix style, high-density electrode arrays for brain-machine interfaces (BMIs) and neuroscientific research require the use of multiplexing: Each recording channel can be routed to one of several electrode sites on the array. This capability allows the user to flexibly distribute recording channels to the locations where the most desirable neural signals can be resolved. For example, in the Neuropixel probe, 960 electrodes can be addressed by 384 recording channels. However, currently no adaptive methods exist to use recorded neural data to optimize/customize the electrode selections per recording context. Here, we present an algorithm called classification-based selection (CBS) that optimizes the joint electrode selections for all recording channels so as to maximize isolation quality of detected neurons. We show, in experiments using Neuropixels in non-human primates, that this algorithm yields a similar number of isolated neurons as would be obtained if all electrodes were recorded simultaneously. Neuron counts were 41-85% improved over previously published electrode selection strategies. The neurons isolated from electrodes selected by CBS were a 73% match, by spike timing, to the complete set of recordable neurons around the probe. The electrodes selected by CBS exhibited higher average per-recording-channel signal-to-noise ratio. CBS, and selection optimization in general, could play an important role in development of neurotechnologies for BMI, as signal bandwidth becomes an increasingly limiting factor. Code and experimental data have been made available1.
Physiological synaptic activity and recognition memory are fueled by astroglial glutamine
Authors: Cheung Giselle , Bataveljic Danijela , Kumar Naresh , Moulard Julien , Dallérac Glenn , Visser Josien , Rollenhagen Astrid , Mongin Cédric , Chever Oana , Bemelmans Alexis-Pierre , Lübke Joachim , Leray Isabelle , Rouach Nathalie 
Published: October 2020

AbstractPresynaptic glutamate replenishment is fundamental to brain function. In high activity regimes, such as epileptic episodes, this process is thought to rely on the glutamate-glutamine cycle between neurons and astrocytes. However the presence of an astroglial glutamine supply, as well as its functional relevancein vivoin the healthy brain remain controversial, partly due to a lack of tools that can directly examine glutamine transfer. Here, we generated a novel fluorescent probe that tracks glutamine in live cells, which provided direct visual evidence of an activity-dependent glutamine supply from astroglial networks to presynaptic structures under physiological conditions. This mobilization is mediated by connexin43, an astroglial protein with both gap-junction and hemichannel functions, and is essential for synaptic transmission and object recognition memory. Our findings uncover an indispensable recruitment of astroglial glutamine in physiological synaptic activity and memory via an unconventional pathway, thus providing an astrocyte basis for cognitive processes.
Methyl-CpG binding domain protein 2 plays a causal role in breast cancer growth and metastasis
Authors: Mahmood Niaz , Arakelian Ani , Szyf Moshe , Rabbani Shafaat A. 
Published: October 2020

AbstractMethyl-CpG-binding domain protein 2 (Mbd2), a reader of DNA-methylation, has been implicated in the progression of several types of malignancies, including breast cancer. To test whether Mbd2, which is overexpressed in human breast cancer samples and in MMTV-PyMT mammary pads, plays a causal role in mammary tumor growth and metastasis we depleted Mbd2 in transgenic MMTV-PyMT model of breast cancer by cross-breeding with Mbd2 knockout mice to generate heterozygous (PyMT;Mbd2+/-) and homozygous (PyMT;Mbd2-/-) animals. We found thatMbd2depletion caused a gene dose-dependent delay in mammary tumor formation, reduced primary tumor burden, and lung metastasis at the experimental endpoint. In addition, animals from the PyMT;Mbd2-/-group survived significantly longer compared to the wildtype (PyMT;Mbd2+/+) and PyMT;Mbd2+/-arms. Transcriptomic and proteomic analyses of the primary tumors obtained from PyMT;Mbd2+/+and PyMT;Mbd2+/-groups revealed thatMbd2depletion alters several key determinants of the molecular signaling networks related to tumorigenesis and metastasis, which thereby demonstrate that Mbd2 is regulating transcriptional programs critical for breast cancer. To our knowledge, this is the first study demonstrating a causal role for a DNA-methylation reader in breast cancer. Results from this study will provide the rationale for further development of first-in-class targeted epigenetic therapies against Mbd2 to inhibit the progression of breast and other common cancers.
Meta-transcriptomic identification of divergentAmnoonviridaein fish
Authors: Turnbull Olivia M. H. , Ortiz-Baez Ayda Susana , Eden John-Sebastian , Shi Mang , Williamson Jane E. , Gaston Troy F. , Zhang Yong-Zhen , Holmes Edward C. , Geoghegan Jemma L. 
Published: October 2020

AbstractTilapia lake virus (TiLV) has caused mass mortalities in farmed and wild tilapia with serious economic and ecological consequences. Until recently, this virus was the sole member of theAmnoonviridae, a family within the orderArticulaviralescomprising segmented negative-sense RNA viruses. We sought to identify additional viruses within theAmnoonviridaethrough total RNA sequencing (meta-transcriptomics) and data mining of published transcriptomes. Accordingly, we sampled marine fish species from both Australia and China and discovered two new viruses within theAmnoonviridae, tentatively calledFlavolineata virusandPiscibus virus, respectively. In addition, by mining vertebrate transcriptome data we identified nine additional virus transcripts matching to multiple genomic segments of TiLV in both marine and freshwater fish. These new viruses retained sequence conservation with the distantly relatedOrthomyxoviridaein the RdRp subunit PB1, but formed a distinct and diverse phylogenetic group. These data suggest that theAmnoonviridaehave a broad host range within fish and that greater animal sampling will identify additional divergent members of theArticulavirales.
DeepFoci: Deep Learning-Based Algorithm for Fast Automatic Analysis of DNA Double Strand Break Ionizing Radiation-Induced Foci
Authors: Vicar Tomas , Gumulec Jaromir , Kolar Radim , Kopecna Olga , Pagáčová Eva , Falk Martin 
Published: October 2020

AbstractDNA double-strand breaks, marked by Ionizing Radiation-Induced (Repair) Foci (IRIF), are the most serious DNA lesions, dangerous to human health. IRIF quantification based on confocal microscopy represents the most sensitive and gold standard method in radiation biodosimetry and allows research of DSB induction and repair at the molecular and a single cell level. In this study, we introduce DeepFoci - a deep learning-based fully-automatic method for IRIF counting and its morphometric analysis. DeepFoci is designed to work with 3D multichannel data (trained for 53BP1 and γH2AX) and uses U-Net for the nucleus segmentation and IRIF detection, together with maximally stable extremal region-based IRIF segmentation.The proposed method was trained and tested on challenging datasets consisting of mixtures of non-irradiated and irradiated cells of different types and IRIF characteristics - permanent cell lines (NHDF, U-87) and cell primary cultures prepared from tumors and adjacent normal tissues of head and neck cancer patients. The cells were dosed with 1-4 Gy gamma-rays and fixed at multiple (0-24 h) post-irradiation times. Upon all circumstances, DeepFoci was able to quantify the number of IRIF foci with the highest accuracy among current advanced algorithms. Moreover, while the detection error of DeepFoci remained comparable to the variability between two experienced experts, the software kept its sensitivity and fidelity across dramatically different IRIF counts per nucleus. In addition, information was extracted on IRIF 3D morphometric features and repair protein colocalization within IRIFs. This allowed multiparameter IRIF categorization, thereby refining the analysis of DSB repair processes and classification of patient tumors with a potential to identify specific cell subclones.The developed software improves IRIF quantification for various practical applications (radiotherapy monitoring, biodosimetry, etc.) and opens the door to an advanced DSB focus analysis and, in turn, a better understanding of (radiation) DNA damaging and repair.HighlightsNew method for DSB repair focus (IRIF) detection and multi-parameter analysisTrainable deep learning-based methodFully automated analysis of multichannel 3D datasetsTrained and tested on extremely challenging datasets (tumor primary cultures)Comparable to an expert analysis and superb to available methodsGraphical Abstract
Interferon-gamma promotes iron export in human macrophages to limit intracellular bacterial replication
Authors: Abreu Rodrigo , Essler Lauren , Giri Pramod , Quinn Fred 
Published: October 2020

AbstractSalmonellosis and listeriosis together accounted for more than one third of foodborne illnesses in the United States and almost half the hospitalizations for gastrointestinal diseases in 2018 while tuberculosis afflicted over 10 million people worldwide causing almost 2 million deaths. Regardless of the intrinsic virulence differences amongListeria monocytogenes, Salmonella entericaandMycobacterium tuberculosis, these intracellular pathogens share the ability to survive and persist inside the macrophage and other cells and thrive in iron rich environments. Interferon-gamma (IFN-γ) is a central cytokine in host defense against intracellular pathogens and has been shown to promote iron export in macrophages. We hypothesize that IFN-γ decreases iron availability to intracellular pathogens consequently limiting replication in these cells. In this study, we show that IFN-γ regulates the expression of iron-related proteins hepcidin, ferroportin, and ferritin to induce iron export from macrophages.Listeria monocytogenes, S. enterica, andM. tuberculosisinfections significantly induce iron sequestration in human macrophages. In contrast, IFN-γ significantly reduces hepcidin secretion inS. entericaandM. tuberculosisinfected macrophages. Similarly, IFN-γ-activated macrophages express higher ferroportin levels than untreated controls even after infection withL. monocytogenesbacilli; bacterial infection greatly down-regulates ferroportin expression. Collectively, IFN-γ significantly inhibits pathogen-associated intracellular iron sequestration in macrophages and consequently retards the growth of intracellular bacterial pathogens by decreasing iron availability.
Genome-scale reconstructions to assess metabolic phylogeny and organism clustering
Authors: Schulz Christian , Almaas Eivind 
Published: October 2020

AbstractApproaches for systematizing information of relatedness between organisms is important in biology. Phylogenetic analyses based on sets of highly conserved genes are currently the basis for the Tree of Life. Genome-scale metabolic reconstructions contain high-quality information regarding the metabolic capability of an organism and are typically restricted to metabolically active enzyme-encoding genes. While there are many tools available to generate draft reconstructions, expert-level knowledge is still required to generate and manually curate high-quality genome-scale metabolic models and to fill gaps in their reaction networks. Here, we use the tool AutoKEGGRec to construct 975 genome-scale metabolic draft reconstructions encoded in the KEGG database without further curation. The organisms are selected across all three domains, and their metabolic networks serve as basis for generating phylogenetic trees.We find that using all reactions encoded, these metabolism-based comparisons give rise to a phylogenetic tree with close similarity to the Tree of Life. While this tree is quite robust to reasonable levels of noise in the metabolic reaction content of an organism, we find a significant heterogeneity in how much noise an organism may tolerate before it is incorrectly placed in the tree. Furthermore, by using the protein sequences for particular metabolic functions and pathway sets, such as central carbon-, nitrogen-, and sulfur-metabolism, as basis for the organism comparisons, we generate highly specific phylogenetic trees. We believe the generation of phylogenetic trees based on metabolic reaction content, in particular when focused on specific functions and pathways, could aid the identification of functionally important metabolic enzymes and be of value for genome-scale metabolic modellers and enzyme-engineers.
Umbilical cord blood derived microglia-like cells to model COVID-19 exposure
Authors: Sheridan Steven D. , Thanos Jessica M. , De Guzman Rose M. , McCrea Liam T. , Horng Joy , Fu Ting , Sellgren Carl M. , Perlis Roy H. , Edlow Andrea G. 
Published: October 2020

AbstractMicroglia, the resident brain immune cells, play a critical role in normal brain development, and are impacted by the intrauterine environment, including maternal immune activation and inflammatory exposures. The COVID-19 pandemic presents a potential developmental immune challenge to the fetal brain, in the setting of maternal SARS-CoV-2 infection with its attendant potential for cytokine production and, in severe cases, cytokine storming. There is currently no biomarker or model forin uteromicroglial priming and function that might aid in identifying the neonates and children most vulnerable to neurodevelopmental morbidity, as microglia remain inaccessible in fetal life and after birth. This study aimed to generate patient-derived microglial-like cell models unique to each neonate from reprogrammed umbilical cord blood mononuclear cells, adapting and extending a novel methodology previously validated for adult peripheral blood mononuclear cells. We demonstrate that umbilical cord blood mononuclear cells can be used to create microglial-like cell models morphologically and functionally similar to microglia observedin vivo. We illustrate the application of this approach by generating microglia from cells exposed and unexposed to maternal SARS-CoV-2 infection. Our ability to create personalized neonatal models of fetal brain immune programming enables non-invasive insights into fetal brain development and potential childhood neurodevelopmental vulnerabilities for a range of maternal exposures, including COVID-19.
Conformational Dynamics of NSP11 Peptide of SARS-CoV-2 Under Membrane Mimetics and Different Solvent Conditions
Authors: Gadhave Kundlik , Kumar Prateek , Kumar Ankur , Bhardwaj Taniya , Garg Neha , Giri Rajanish 
Published: October 2020

AbstractThe intrinsically disordered proteins/regions (IDPs/IDPRs) are known to be responsible for multiple cellular processes and are associated with many chronic diseases. In viruses, the existence of a disordered proteome is also proven and is related to its conformational dynamics inside the host. The SARS-CoV-2 has a large proteome, in which, structure and functions of many proteins are not known yet, along with nsp11. In this study, we have performed extensive experimentation on nsp11. Our results based on the CD spectroscopy gives characteristic disordered spectrum for IDPs. Further, we investigated the conformational behavior of nsp11 in the presence of membrane mimetic environment, α-helix inducer, and natural osmolyte. In the presence of negatively charged and neutral liposomes, nsp11 remains disordered. However, with SDS micelle, it adopted an α-helical conformation, suggesting the helical propensity of nsp11. Finally, we again confirmed the IDP behavior of nsp11 using MD simulations. In future, this conformational dynamic study could help to clarify its functional importance in SARS-CoV-2 infection.
Abscission Checkpoint Bodies Reveal a New Facet of Abscission Checkpoint Control
Authors: Williams Lauren K. , Mackay Douglas R. , Whitney Madeline A. , Sundquist Wesley I. , Ullman Katharine S. 
Published: October 2020

AbstractThe abscission checkpoint regulates the ESCRT membrane fission machinery and thereby delays cytokinetic abscission to protect genomic integrity in response to residual mitotic errors. The checkpoint is maintained by Aurora B kinase, which phosphorylates multiple targets, including CHMP4C, a regulatory ESCRT-III subunit necessary for this checkpoint. We now report the discovery that cytoplasmic abscission checkpoint bodies (ACBs) containing phospho-Aurora B and tri-phospho-CHMP4C develop in telophase under an active checkpoint. ACBs are derived from Mitotic Interchromatin Granules (MIGs), transient mitotic structures whose components are housed in splicing-related nuclear speckles during interphase. ACB formation requires CHMP4C, and the ESCRT factor ALIX also contributes. ACB formation is conserved across cell types and under multiple circumstances that activate the checkpoint. Finally, ACBs retain a population of ALIX, and their presence correlates with delayed recruitment of ALIX to the midbody where it would normally promote abscission. Thus, a cytoplasmic mechanism helps regulate midbody machinery to delay abscission.
Fathers and substance misuse: a literature review
Authors: Bell Linda , Herring Rachel , Annand Fizz 
Published: October 2020

PurposeThe purpose of this paper is to review the following research questions from the available literature: What evidence is there to suggest that substance misuse specifically by fathers (including alcohol and other drugs) causes wider harms, including child welfare concerns? substance misuse, recovery, parents, fathers, fathering, drugs/ alcohol services. How do professionals respond specifically to substance misuse by fathers? Do interventions aimed at parental substance misuse (particularly in the UK) include both mothers and fathers and if so how?Design/methodology/approachA scoping literature review was conducted which identified 34 papers (including scoping reviews published in 2006 and 2008, covering the period 1990-2005) and 26 additional studies published between 2002 and 2020.FindingsThe review in this paper is organised into six themes: Negative impact of men’s substance misuse problems on their parenting behaviours; quality of the relationship between parents affected by substance misuse of the fathers, in turn affecting the parenting behaviour and outcomes for children; importance to fathers of their fathering role (for example, as a financial provider); difficulties fathers may face in developing their fathering role; sidelining of the fathering role in substance misuse services; and professionals tending to focus on the mother’s role in parenting inventions and services.Originality/valueThis paper focusses on fathers and substance misuse, which is an under-researched field within the wider contexts of fathering research and research into parental substance misuse.
A cognitive process model of trust repair
Authors: Tomlinson Edward C. , Nelson Christopher A. , Langlinais Luke A. 
Published: October 2020

Purpose
This paper aims to investigate how the reparative efforts of extensive apologies, compensation and structural change affect trust after a violation has occurred. Specifically, this paper presents a cognitive process model positing that voluntary reparative efforts will shape the victim’s stability attributions for the cause of the violation such that it will be deemed less stable (i.e. unlikely to recur); as a result, the victim is more likely to perceive the transgressor as being fair, and hence extend subsequent trust.

Design/methodology/approach
Two experiments were conducted to test the cognitive process model.

Findings
The results of both experiments supported this predicted sequence for extensive apologies. Support for the predicted sequence was also found when compensation and structural change are invoked as reparative efforts.

Originality/value
This research has theoretical and practical implications for a more nuanced understanding of how causal attribution theory and organizational justice theory can be integrated within the context of trust repair.
High-performance work practices and medical professionals' work outcomes: the mediating effect of perceived organizational support
Authors: Rubel Mohammad Rabiul Basher , Hung Kee Daisy Mui , Rimi Nadia Newaz 
Published: October 2020

PurposeIn this research, we investigate the effect of high-performance work practices (HPWPs) on medical professionals' work outcomes through the mediating effect of perceived organizational support (POS).Design/methodology/approachThe study analyzes the opinions of 218 medical doctors from private hospitals in Bangladesh, employing Partial Least Square-Structural Equation Modeling (PLS-SEM).FindingsWe find that HPWPs enhance employee performance and POS and minimize turnover intention. POS also has a substantial influence on both employee performance and turnover intention. Moreover, POS finds a significant mediating effect on HPWPs and performance as well as HPWPs and turnover intention relations.Research limitations/implicationsThe current research focuses on medical doctors who are presently working in private hospitals in Bangladesh.Practical implicationsFirst, the hospital would recognize the role of employee perceived HPWPs. Second, they might understand how HPWPs would utilize and maintain employees effectively via POS that might further improve the healthcare industry. Suggestions for future research indicate the models potential to provide optimal workplace environments that can benefit organizations as well as improve employee performance.Originality/valueThe study would provide a unique insight into the higher-order HPWPs system and its effects on the health care organizations in developing country contexts like Bangladesh. This study also extends the research on POS as a mediator between higher-order HPWPs and employee outcomes in the organization.