bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mandrake: visualising microbial population structure by embedding millions of genomes into a low-dimensional representation
Authors: Lees John A. , Tonkin-Hill Gerry , Yang Zhirong , Corander Jukka 
Published: October 2021

AbstractIn less than a decade, population genomics of microbes has progressed from the effort of sequencing dozens of strains to thousands, or even tens of thousands of strains in a single study. There are now hundreds of thousands of genomes available even for a single bacterial species and the number of genomes is expected to continue to increase at an accelerated pace given the advances in sequencing technology and widespread genomic surveillance initiatives. This explosion of data calls for innovative methods to enable rapid exploration of the structure of a population based on different data modalities, such as multiple sequence alignments, assemblies and estimates of gene content across different genomes. Here we present Mandrake, an efficient implementation of a dimensional reduction method tailored for the needs of large-scale population genomics. Mandrake is capable of visualising population structure from millions of whole genomes and we illustrate its usefulness with several data sets representing major pathogens. Our method is freely available both as an analysis pipeline (https://github.com/johnlees/mandrake) and as a browser-based interactive application (https://gtonkinhill.github.io/mandrake-web/).
DNA methylation patterns differ between free-living Rhizobium leguminosarum RCAM1026 and bacteroids formed in symbiosis with pea (Pisum sativum L.)
Authors: Afonin Alexey , Emma Gribchenko , Zorin Evgeny , Sulima Anton , Zhukov Vladimir 
Published: October 2021

AbstractRhizobium leguminosarum (Rl) is a common name for several genospecies of rhizobia able to form nitrogen-fixing nodules on the roots of pea (Pisum sativum L.) and undergo terminal differentiation into a symbiotic form called bacteroids. In this work, we compared the genomes of the free-living and differentiated forms of the Rl strain RCAM1026 using Oxford Nanopore long reads. No significant genome rearrangements were observed, but the relative abundances of replicons were different between the cell states. GANTC, GGCGCC and GATC methylated motifs have been found in the genome, along with genes for methyltransferases with matching predicted targets. Methylation patterns for the GANTC and GATC motives differed significantly depending on the cell state, which indicates their possible connection to the regulation of symbiotic differentiation. The GGCGCC motif was completely methylated in both bacteria states, and, apparently, is a target for the modification-restriction system. Currently, the methylation patterns in symbiotic bacteria are not extensively studied, so a further investigation of the topic coupled with gene expression data is needed to elucidate the function of differential methylation in terminal differentiation of R. leguminosarum and other rhizobia.
Cortical adaptation to sound reverberation
Authors: Ivanov Aleksandar Z , King Andrew J , Willmore Ben DB , Walker Kerry MM , Harper Nicol S 
Published: October 2021

AbstractIn almost every natural environment, sounds are reflected by nearby objects, producing many delayed and distorted copies of the original sound, known as reverberation. Our brains usually cope well with reverberation, allowing us to recognize sound sources regardless of their environments. In contrast, reverberation can cause severe difficulties for speech recognition algorithms and hearing-impaired people. The present study examines how the auditory system copes with reverberation. We trained a linear model to recover a rich set of natural, anechoic sounds from their simulated reverberant counterparts. The model neurons achieved this by extending the inhibitory component of their receptive filters for more reverberant spaces, and did so in a frequency-dependent manner. These predicted effects were observed in the responses of auditory cortical neurons of ferrets in the same simulated reverberant environments. Together, these results suggest that auditory cortical neurons adapt to reverberation by adjusting their filtering properties in a manner consistent with dereverberation.
Computational Fontan Analysis: Preserving accuracy while expediting workflow
Authors: Liu Xiaolong , Aslan Seda , Kim Byeol , Warburton Linnea , Jackson Derrick , Muhuri Abir , Subramanian Akshay , Mass Paige , Cleveland Vincent , Loke Yue-Hin , Hibino Narutoshi , Olivieri Laura , Krieger Axel 
Published: October 2021

AbstractBackgroundPost-operative outcomes of the Fontan operation have been linked to graft shape after implantation. Computational fluid dynamics (CFD) simulations are used to explore different surgical options. The objective of this study is to perform a systematic in vitro validation for investigating the accuracy and efficiency of CFD simulation to predict Fontan hemodynamics.MethodsCFD simulations were performed to measure indexed power loss (iPL) and hepatic flow distribution (HFD) in 10 patient-specific Fontan models, with varying mesh and numerical solvers. The results were compared with a novel in vitro flow loop setup with 3D printed Fontan models. A high-resolution differential pressure sensor was used to measure the pressure drop for validating iPL predictions. Microparticles with particle filtering system were used to measure HFD. The computational time was measured for a representative Fontan model with different mesh sizes and numerical solvers.ResultsWhen compared to in vitro setup, variations in CFD mesh sizes had significant effect on HFD (p = 0.0002) but no significant impact on iPL (p = 0.069). Numerical solvers had no significant impact in both iPL (p = 0.50) and HFD (P = 0.55). A transient solver with 0.5 mm mesh size requires computational time 100 times more than a steady solver with 2.5 mm mesh size to generate similar results.ConclusionsThe predictive value of CFD for Fontan planning can be validated against an in vitro flow loop. The prediction accuracy can be affected by the mesh size, model shape complexity and flow competition.
Glycosylated proteins identified for the first time in the alga Euglena gracilis
Authors: O’Neill Ellis 
Published: October 2021

AbstractProtein glycosylation, and in particular N-linked glycans, is a hall mark of Eukaryotic cells and has been well studied in mammalian cells and parasites. However, little research has been conducted to investigate the conservation and variation of protein glycosylation pathways in other eukaryotic organisms. Euglena gracilis is an industrially important microalga, used in the production of biofuels and nutritional supplements. It is evolutionarily highly divergent from green algae and more related to Kinetoplastid pathogens. It was recently shown that E. gracilis possesses the machinery for producing a range of protein glycosylations and make simple N-glycans, but the modified proteins were not identified. This study identifies the glycosylated proteins, including transporters, extra cellular proteases and those involved in cell surface signalling. Notably, many of the most highly expressed and glycosylated proteins are not related to any known sequences and are therefore likely to be involved in important novel functions in Euglena.
Single-nuclei RNA sequencing uncovers non-cell autonomous changes in cerebellar astrocytes and oligodendrocytes that may contribute to Spinocerebellar Ataxia Type 1 (SCA1) pathogenesis
Authors: Borgenheimer Ella , Zhang Ying , Cvetanovic Marija 
Published: October 2021

AbstractGlial cells, including astrocytes and oligodendrocytes are important for normal brain function. In many neurodegenerative diseases glial cells undergo significant morphological, functional and gene expression changes termed reactive gliosis. The cause, identity and neuroprotective or neurotoxic nature of these changes remains incompletely understood. This knowledge in needed to develop a framework of how individual pathological changes in glial cells contribute to progressive dysfunction and selective neuronal vulnerability in neurodegenerative diseases. This is particularly relevant during the early disease stages that allow for the effective therapies and reversal or slowing of disease phenotypes. Spinocerebellar ataxia type 1 (SCA1) is a progressive neurodegenerative disease caused by an abnormal expansion of CAG repeats in the gene Ataxin1 (ATXN1). While mutant ATXN1 is expressed broadly throughout the brain, SCA1 is characterized by severe degeneration of cerebellar Purkinje cells (PCs). Despite major advances in dissecting the effects of mutant ATXN1 on Purkinje cells, much less is understood how cerebellar astrocytes and oligodendrocytes respond to and contribute to Purkinje cell dysfunction in SCA1. To address this question we performed cerebellar single nuclei RNA sequencing (snRNA seq) of early disease stage Pcp2-ATXN1[82Q] mice, a transgenic SCA1 mouse model expressing mutant ATXN1 only in Purkinje cells. We found no changes in cell numbers in the SCA1 cerebellum. We validated previously indicated pathway and gene expression changes in the Purkinje cells, and identified novel DEG and pathways in Purkinje cells, including Ralyl that may provide compensatory roles and maintain PC function. Importantly we identified profound non-cell autonomous and potentially neuroprotective gene expression and pathway alterations in Bergman glia, velate astrocytes and oligodendrocytes that may contribute to disease pathogenesis.
The plastoglobule-localized AtABC1K6 is a Mn2+-dependent protein kinase necessary for timely transition to reproductive growth
Authors: Espinoza-Corral Roberto , Lundquist Peter K. 
Published: October 2021

ABSTRACTTheAbsence ofbc1Complex (ABC1) is an ancient, atypical protein kinase family that emerged prior to the archaeal-eubacterial divergence. Loss-of-function mutants in ABC1 genes are linked to respiratory defects in microbes and humans, and to compromised photosynthetic performance and stress tolerance in plants. However, demonstration of protein kinase activity remains elusive, hampering their study. Here, we investigate a homolog fromArabidopsis thaliana, AtABC1K6, and demonstratein vitroprotein kinase activity as autophosphorylation, which we replicate with a human ABC1 ortholog. We show that AtABC1K6 protein kinase activity requires an atypical buffer composition, including Mn2+as divalent cation co-factor and a low salt concentration. AtABC1K6 associates with plastoglobule lipid droplets ofA. thalianachloroplasts, along with five paralogs. Protein kinase activity associated with isolatedA. thalianaplastoglobules was inhibited at higher salt concentrations, but could accommodate Mg2+as well as Mn2+, indicating salt sensitivity, but not the requirement for Mn2+, may be a general characteristic of ABC1s. Loss of functional AtABC1K6 impairs the developmental transition from vegetative to reproductive growth. This phenotype is complemented by the wild-type sequence of AtABC1K6 but not by a kinase-dead point mutant in the unique Ala-triad of the ATP-binding pocket, demonstrating the physiological relevance of the protein’s kinase activity. We suggest that ABC1s are bona fide protein kinases with a unique regulatory mechanism. Our results open the door to detailed functional and mechanistic studies of ABC1s and plastoglobules.SIGNIFICANCE STATEMENTTheAbsence ofbc1Complex (ABC1) is an ancient, atypical protein kinase family with enigmatic physiological roles in a wide range of species including plants, humans and microbes. While mutants demonstrate their critical role for organismal survival, their study has been severely hampered by the previous inability to determine catalytic function. Here, we demonstratein vitroprotein kinase activity with anA. thalianahomolog, AtABC1K6. Loss of functional AtABC1K6 impairs the developmental transition from vegetative to reproductive growth. The lack of phenotypic complementation with a kinase-dead point mutant demonstrates the physiological relevance of the protein’s kinase activity. Our results present the experimental means to investigate the targets, functions, and regulation of ABC1s.
Efficient, selectable marker free gene targeting in soybean using novel Ochrobactrum haywardense-mediated delivery
Authors: Kumar Sandeep , Liu Zhan-Bin , Sanyour-Doyel Nathalie , Lenderts Brian , Worden Andrew , Anand Ajith , Cho Hyeon-Je , Bolar Joy , Harris Charlotte , Huang Lingxia , Xing Aiqiu , Richardson Alexandra 
Published: October 2021

AbstractWe report robust selectable marker-free gene targeting (GT) system in soybean, one of the most economically important crops. A novel efficient Ochrobactrum haywardense-mediated embryonic axis transformation method was used for the delivery of CRISPR-Cas9 components and donor template to regenerate T0 plants in 6-8 weeks after transformation. This approach generated up to 3.4% targeted insertion of the donor sequence into the target locus in T0 plants, with ∼ 90% mutation rate observed at the genomic target site. The GT was demonstrated in two genomic sites using two different donor DNA templates without a need of a selectable marker within the template. High-resolution Southern by Sequencing (SbS) analysis identified T1 plants with precise targeted insertion and without unintended plasmid DNA. Unlike previous low-frequency GT reports in soybean that involved particle bombardment-mediated delivery and extensive selection, the method described here is fast, efficient, reproducible, does not require selectable marker within the donor DNA, and generates non-chimeric plants with heritable GT.
Organizational citizenship behavior and job flexibility in Family-Responsible Companies: a study from the perspective of employee family situation
Authors: Arredondo-Trapero Florina Guadalupe , Vázquez-Parra José Carlos , González-Arredondo Ana Sofía 
Published: October 2021

PurposeThe aim of this article is to analyze the relationship between the personal life situation and marital status of the worker and how this relates to organizational citizenship behavior (OCB) and job flexibility. The study has been carried out with a group of Mexican employees from a commercial company located in the northeast of the México.Design/methodology/approachThe research is a nonexperimental empirical study using t-test, Levene’s test and Cohen’s test to analyze the significant relationship between the variables under study for 419 employees. The questionnaire was applied only once without a control group against which to compare. The study was carried out in a commercial company located in a city in northeastern Mexico, covering four municipalities in the conurbation area.FindingsThe research reveals that those workers who participated in the study and who have direct family responsibilities show greater OCB and value job flexibility more highly. The tests also found that a flexible working policy is valued by all those with direct family responsibilities, regardless of their marital status. It is also shown that there is a positive relationship between job flexibility and OCB, although not a strong one.Practical implicationsDecent work implies labor policies that support women and men to have an adequate work–life balance. Companies seeking work–family balance through the implementation of policies such as flexible working arrangements should consider the domestic background of their employees, as this has a direct impact on competitive advantage and is of importance when recruiting and retaining human talent. These findings may also be useful for companies interested in implementing flexible working policies to retain employees with family responsibilities who value the ability to reconcile work and family life.Originality/valueThis research demonstrates the relevance of OCB and job flexibility for employees. If the company wants to enhance OCB, they must consider that personal situation as well as the employee's marital status influences OCB. They should also consider that work flexibility is highly valued by those employees who have children or family dependents.
What does well-being mean to mental health peer workers?
Authors: Edge Jenny , Wheatley Susan 
Published: October 2021

Purpose
This paper aims to gain a detailed understanding of their experience of well-being from the perspective of mental health peer workers.

Design/methodology/approach
An interpretative phenomenological analysis design using semi-structured interviews was conducted with four peer workers. Interviews were transcribed verbatim and then analysed using thematic analysis.

Findings
Participants described their experience of well-being in terms of a journey over time that followed an unpredictable course. They understood their well-being in terms of their engagement in occupations. An occupational science framework was used to understand the participants’ experience of their well-being in terms of doing, being and becoming.

Originality/value
This paper is among the first to approach the exploration of the experience of well-being for peer workers using an Interpretative Phenomenological Analysis design.
A student-focused checklist for creating infographics
Authors: Kapel Scottie , Schmidt Krista 
Published: October 2021

PurposeThis paper discusses efforts to produce instructional support objects for undergraduate students engaged in creating infographics, an alternative assignment growing in popularity at the authors' university.Design/methodology/approachThe authors examined scholarly, professional, trade and open-web sources to identify best practices for design and data visualization for this type of assignment. They categorized their findings and used a preponderance-of-evidence method for final selection of relevant practices. The authors detail the creation of their support products (instructional checklists and example infographics) and offer recommendations for librarians engaged in similar efforts.FindingsDespite the growing popularity of alternative assignments, guidance for best practices in data and design as they relate to student-created infographics is nascent, and best practices for design and data visualization in this context have yet to be concretely identified. Without extant guidance for student-created infographics, the authors developed a checklist of potential best practices for design and data visualization.Practical implicationsThe use of alternative projects assigned in lieu of traditional research papers is growing. Additional guidance may be required for students creating non-traditional works as standards and best practices for these projects are under-developed in the academic setting. Librarians will want to consider their role in supporting students assigned to create an alternative project.Originality/valueA consideration of best practices for data and design visualization for students designing research infographics has not yet been written.
Status quo of tet regulation in bacteria
Authors: Bertram Ralph , Neumann Bernd , Schuster Christopher F. 
Published: October 2021

SummaryThe tetracycline repressor (TetR) belongs to the most popular, versatile and efficient transcriptional regulators used in bacterial genetics. In the tetracycline (Tc) resistance determinant tet(B) of transposon Tn10, tetR regulates the expression of a divergently oriented tetA gene that encodes a Tc antiporter. These components of Tn10 and of other natural or synthetic origins have been used for tetracycline‐dependent gene regulation (tet regulation) in at least 40 bacterial genera. Tet regulation serves several purposes such as conditional complementation, depletion of essential genes, modulation of artificial genetic networks, protein overexpression or the control of gene expression within cell culture or animal infection models. Adaptations of the promoters employed have increased tet regulation efficiency and have made this system accessible to taxonomically distant bacteria. Variations of TetR, different effector molecules and mutated DNA binding sites have enabled new modes of gene expression control. This article provides a current overview of tet regulation in bacteria.
Modulation of dopamine release by ethanol is mediated by atypical GABAA receptors on cholinergic interneurons in the nucleus accumbens
Authors: Yorgason Jordan T. , Wadsworth Hillary A. , Anderson Elizabeth J. , Williams Benjamin M. , Brundage James N. , Hedges David M. , Stockard Alyssa L. , Jones Stephen T. , Arthur Summer B. , Hansen David Micah , Schilaty Nathan D. , Jang Eun Young , Lee Anna M. , Wallner Martin , Steffensen Scott C. 
Published: October 2021

AbstractPrevious studies indicate that moderate‐to‐high ethanol (EtOH) concentrations enhance dopamine (DA) neurotransmission in the mesolimbic DA system from the ventral tegmental area (VTA) and projecting to the nucleus accumbens core (NAc). However, voltammetry studies demonstrate that moderate‐to‐high EtOH concentrations decrease evoked DA release at NAc terminals. The involvement of γ‐aminobutyric acid (GABA) receptors (GABAARs), glycine (GLY) receptors (GLYRs) and cholinergic interneurons (CINs) in mediating EtOH inhibition of evoked NAc DA release were examined. Fast scan cyclic voltammetry, electrophysiology, optogenetics and immunohistochemistry techniques were used to evaluate the effects of acute and chronic EtOH exposure on DA release and CIN activity in C57/BL6, CD‐1, transgenic mice and δ‐subunit knockout (KO) mice (δ−/−). Ethanol decreased DA release in mice with an IC50 of 80 mM ex vivo and 2.0 g/kg in vivo. GABA and GLY decreased evoked DA release at 1–10 mM. Typical GABAAR agonists inhibited DA release at high concentrations. Typical GABAAR antagonists had minimal effects on EtOH inhibition of evoked DA release. However, EtOH inhibition of DA release was blocked by the α4β3δ GABAAR antagonist Ro15‐4513, the GLYR antagonist strychnine and by the GABA ρ1 (Rho‐1) antagonist TPMPA (10 μM) and reduced significantly in GABAAR δ−/− mice. Rho‐1 expression was observed in CINs. Ethanol inhibited GABAergic synaptic input to CINs from the VTA and enhanced firing rate, both of which were blocked by TPMPA. Results herein suggest that EtOH inhibition of DA release in the NAc is modulated by GLYRs and atypical GABAARs on CINs containing δ‐ and Rho‐subunits.
Post‐traumatic stress disorder and major depression among frontline healthcare staff working during the COVID‐19 pandemic
Authors: Wild Jennifer , McKinnon Aimee , Wilkins Abbie , Browne Haddi 
Published: October 2021

ObjectivesHigh rates of probable post‐traumatic stress disorder (PTSD) and major depressive disorder (MDD) have been reported for frontline healthcare staff during the COVID‐19 pandemic. However, rates determined by diagnostic assessment are unknown, as are the onset of symptoms and associated index events.MethodsWe assessed frontline healthcare staff with the Structured Clinical Interview for DSM‐5.ResultsForty‐four percent met criteria for PTSD and 39% met criteria for MDD. Twenty‐four percent reported COVID‐19 trauma as their index event, with the majority of staff reporting trauma that pre‐dated the pandemic. While PTSD was likely to be pre‐existing, MDD was more likely to develop during pandemic working.ConclusionThese findings indicate the propensity of healthcare staff to experience a range of occupational and personal trauma associated with PTSD and the need to assess index trauma when diagnosing psychopathology in order to best understand the needs of this workforce.Practitioner points

We found high diagnostic rates of PTSD (44%) and major depression (39%) among frontline healthcare staff working during the COVID‐19 pandemic.

Although major depression developed during the pandemic, PTSD was more likely to be pre‐existing.

When assessing pandemic‐related psychopathology, it is important to assess the onset and index event related to symptoms.

Healthcare workers appear to have high rates of PTSD related to occupational and personal trauma, which warrants specific focus in service planning.