bluuebunny/crossref_metadata_2025_split huggingface dataset:
The zebrafish mutantdreammistimplicates sodium homeostasis in sleep regulation
Authors: Barlow Ida L. , Mackay Eirinn , Wheater Emily , Goel Aimee , Lim Sumi , Zimmerman Steve , Woods Ian , Prober David A. , Rihel Jason 
Published: November 2020

AbstractSleep is a nearly universal feature of animal behaviour, yet many of the molecular, genetic, and neuronal substrates that orchestrate sleep/wake transitions lie undiscovered. Employing a viral insertion sleep screen in larval zebrafish, we identified a novel gene,dreammist(dmist), whose loss results in behavioural hyperactivity and reduced sleep at night. The neuronally expresseddmistgene is conserved across vertebrates and encodes a small single-pass transmembrane protein that is structurally similar to the Na+,K+-ATPase regulator, FXYD1/Phospholemman. Disruption of eitherfxyd1oratp1a3a, a Na+,K+-ATPase alpha-3 subunit associated with several heritable movement disorders in humans, led to decreased night-time sleep. Sinceatpa1a3aanddmistmutants have elevated intracellular Na+levels and non-additive effects on sleep amount at night, we propose that Dmist-dependent enhancement of Na+pump function modulates neuronal excitability to maintain normal sleep behaviour.Significance statementSleep is an essential behavioral state, but the genes that regulate sleep and wake states are still being uncovered. A viral insertion screen in zebrafish identified a novel sleep mutant calleddreammist, in which a small, highly-conserved transmembrane protein is disrupted. The discovery ofdreammisthighlights the importance of a class of small transmembrane-protein modulators of the sodium pump in setting appropriate sleep duration.
Improved production of SARS-CoV-2 spike receptor-binding domain (RBD) for serology assays
Authors: Mehalko Jennifer , Drew Matthew , Snead Kelly , Denson John-Paul , Wall Vanessa , Taylor Troy , Sadtler Kaitlyn , Messing Simon , Gillette William , Esposito Dominic 
Published: November 2020

AbstractThe receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a commonly used antigen for serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Different versions of the RBD protein have been developed and utilized in assays, with higher sensitivity attributed to particular forms of the protein. To improve the yield of these high-sensitivity forms of RBD and support the increased demand for this antigen in serology assays, we investigated several protein expression variables including DNA elements such as promoters and signal peptides, cell culture expression parameters, and purification processes. Through this investigation, we developed a simplified and robust purification strategy that consistently resulted in high levels of the high-sensitivity form of RBD and demonstrated that a carboxyterminal tag is responsible for the increased sensitivity in the ELISA. These improved reagents and processes produce high-quality proteins which are functional in serology assays and can be used to investigate seropositivity to SARS-CoV-2 infection.Highlights:Improved yields of SARS-CoV-2 spike RBD through modification of DNA constructs and purification parametersTwo versions of RBD show different sensitivity in serology assaysYields of greater than 50 mg/l obtained under optimal conditionsMagnetic bead purification technology improves throughput of protein production
Heme is crucial for medium-dependent metronidazole resistance in clinical isolates ofC. difficile
Authors: Boekhoud Ilse M. , Sidorov Igor , Nooij Sam , Harmanus Céline , Bos-Sanders Ingrid M.J.G. , Viprey Virginie , Spittal Bill , Clark Emma , Davies Kerrie , Freeman Jane , Kuijper Ed J. , Smits Wiep Klaas 
Published: November 2020

AbstractUntil recently, metronidazole was the first-line treatment forClostridioides difficileinfection and it is still commonly used. Though resistance has been reported due to the plasmid pCD-METRO, this does not explain all cases. Here, we investigate resistance to metronidazole in a collection of clinical isolates ofC. difficile. We find that nearly all isolates demonstrate a heme-dependent increase in the minimal inhibitory concentration for metronidazole, which in some cases leads to isolates being qualified as resistant (MIC > 2 mg/L). Moreover, whole genome sequence analysis reveals a single nucleotide polymorphism in the heme responsive genehsmA, which defines a metronidazole resistant lineage of PCR ribotype 010 / multilocus sequence type 15 isolates that also includes pCD-METRO containing strains. Together our data demonstrate that heme is crucial for medium-dependent metronidazole resistance inC. difficile.
The multi-scale architecture of mammalian sperm flagella and implications for ciliary motility
Authors: Leung Miguel Ricardo , Roelofs Marc C. , Ravi Ravi Teja , Maitan Paula , Zhang Min , Henning Heiko , Bromfield Elizabeth G. , Howes Stuart C. , Gadella Bart M. , Bloomfield-Gadêlha Hermes , Zeev-Ben-Mordehai Tzviya 
Published: November 2020

SummaryMotile cilia are molecular machines used by a myriad of eukaryotic cells to swim through fluid environments. However, available molecular structures represent only a handful of cell types, limiting our understanding of how cilia are modified to support motility in diverse media. Here, we use cryo-focused ion beam milling-enabled cryo-electron tomography to image sperm flagella from three mammalian species. We resolve in-cell structures of centrioles, axonemal doublets, central pair apparatus, and endpiece singlets, revealing novel protofilament-bridging microtubule inner proteins throughout the flagellum. We present native structures of the flagellar base, which is crucial for shaping the flagellar beat. We show that outer dense fibers are directly coupled to microtubule doublets in the principal piece but not in the midpiece. Thus, mammalian sperm flagella are ornamented across scales, from protofilament-bracing structures rein-forcing microtubules at the nano-scale to accessory structures that impose micron-scale asymmetries on the entire assembly. Our structures provide vital foundations for linking molecular structure to ciliary motility and evolution.
Production of anti-SARS-CoV-2 hyperimmune globulin from convalescent plasma
Authors: Vandeberg Peter , Cruz Maria , María Diez José , Merritt W. Keither , Santos Benjamin , Trukawinski Susan , Wellhouse Andrea , José Marta , Willis Todd 
Published: November 2020

AbstractBACKGROUNDIn late 2019, the SARS-CoV-2 virus emerged in China and quickly spread into a world-wide pandemic. Prior to the development of specific drug therapies or a vaccine, more immediately available treatments were sought including convalescent plasma. A potential improvement from convalescent plasma could be the preparation of anti-SARS-CoV-2 hyperimmune globulin (hIVIG).STUDY DESIGN AND METHODSConvalescent plasma was collected from an existing network of plasma donation centers. A caprylate/chromatography purification process was used to manufacture hIVIG. Initial batches of hIVIG were manufactured in a versatile, small-scale facility designed and built to rapidly address emerging infectious diseases.RESULTSProcessing convalescent plasma into hIVIG resulted in a highly purified IgG product with more concentrated neutralizing antibody activity. hIVIG will allow for the administration of greater antibody activity per unit of volume with decreased potential for several adverse events associated with plasma administration. IgG concentration and IgG antibody specific to SARS-CoV-2 were increased over 10-fold from convalescent plasma to the final product. Normalized ELISA activity (per mg/mL IgG) was maintained throughout the process. Protein content in these final product batches was 100% IgG, consisting of 98% monomer and dimer forms. Potentially hazardous proteins (IgM, IgA, and anti-A, anti-B and anti-D antibodies) were reduced to minimal levels.CONCLUSIONSMultiple batches of anti-SARS-CoV-2 hyperimmune globulin (hIVIG) that met regulatory requirements were manufactured from human convalescent plasma. The first clinical study in which the hIVIG will be evaluated will be Inpatient Treatment with Anti-Coronavirus Immunoglobulin (ITAC) [NCT04546581].
Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse neocortex
Authors: Liang Lindsay , Darbandi Siavash Fazel , Pochareddy Sirisha , Gulden Forrest O. , Gilson Michael C. , Sheppard Brooke K. , Sahagun Atehsa , An Joon-Yong , Werling Donna M. , Rubenstein John L.R. , Šestan Nenad , Bender Kevin J. , Sanders Stephan J. 
Published: November 2020

AbstractObjectiveGenetic variants in the voltage-gated sodium channelsSCN1A, SCN2A, SCN3A,andSCN8Aare leading causes of epilepsy, developmental delay, and autism spectrum disorder. The mRNA splicing patterns of all four genes vary across development in the rodent brain, including mutually exclusive copies of the fifth protein-coding exon detected in the neonate (5N) and adult (5A). A second pair of mutually exclusive exons is reported inSCN8Aonly (18N and 18A). We aimed to quantify the expression of individual exons in the developing human neocortex.MethodsRNA-seq data from 176 human dorsolateral prefrontal cortex samples across development were analyzed to estimate exon-level expression. Developmental changes in exon utilization were validated by assessing intron splicing. Exon expression was also estimated in RNA-seq data from 58 developing mouse neocortical samples.ResultsIn the mature human neocortex, exon 5A is consistently expressed at least 4-fold higher than exon 5N in all four genes. ForSCN2A, SCN3A,andSCN8Aa synchronized 5N/5A transition occurs between 24 post-conceptual weeks (2ndtrimester) and six years of age. In mice, the equivalent 5N/5A transition begins at or before embryonic day 15.5. InSCN8A,over 90% of transcripts in the mature human cortex include exon 18A. Early in fetal development, most transcripts include 18N or skip both 18N and 18A, with a transition to 18A inclusion occurring from 13 post-conceptual weeks to 6 months of age. No other protein-coding exons showed comparably dynamic developmental trajectories.SignificanceSplice isoforms, which alter the biophysical properties of the encoded channels, may account for some of the observed phenotypic differences across development and between specific variants. Manipulation of the proportion of splicing isoforms at appropriate stages of development may act as a therapeutic strategy for specific mutations or even epilepsy in general.
Dorsal Periaqueductal gray ensembles represent approach and avoidance states
Authors: Reis Fernando MCV , Lee Johannes Y , Maesta-Pereira Sandra , Schuette Peter J , Chakerian Meghmik , Liu Jinhan , La-Vu Mimi Q , Tobias Brooke C , Canteras Newton S , Kao Jonathan C , Adhikari Avishek 
Published: November 2020

AbstractAnimals must balance needs to approach threats for risk-assessment and to avoid danger. The dorsal periaqueductal gray (dPAG) controls defensive behaviors, but it is unknown how it represents states associated with threat approach and avoidance. We identified a dPAG threat-avoidance ensemble in mice that showed higher activity far from threats such as the open arms of the elevated plus maze and a live predator. These cells were also more active during threat-avoidance behaviors such as escape and freezing, even though these behaviors have antagonistic motor output. Conversely, the threat-approach ensemble was more active during risk-assessment behaviors and near threats. Furthermore, unsupervised methods showed approach/avoidance states were encoded with shared activity patterns across threats. Lastly, the relative number of cells in each ensemble predicted threat-avoidance across mice. Thus, dPAG ensembles dynamically encode threat approach and avoidance states, providing a flexible mechanism to balance risk-assessment and danger avoidance.
Real-space quantum-based refinement for cryo-EM: Q|R#3
Authors: Wang Lum , Kruse Holger , Sobolev Oleg V. , Moriarty Nigel W. , Waller Mark P. , Afonine Pavel V. , Biczysko Malgorzata 
Published: November 2020

Electron cryo-microscopy (cryo-EM) is rapidly becoming a major competitor to X-ray crystallography, especially for large structures that are difficult or impossible to crystallize. While recent spectacular technological improvements have led to significantly higher resolution three-dimensional reconstructions, the average quality of cryo-EM maps is still at the low-resolution end of the range compared with crystallography. A long-standing challenge for atomic model refinement has been the production of stereochemically meaningful models for this resolution regime. Here, it is demonstrated that including accurate model geometry restraints derived from ab initio quantum-chemical calculations (HF-D3/6-31G) can improve the refinement of an example structure (chain A of PDB entry 3j63). The robustness of the procedure is tested for additional structures with up to 7000 atoms (PDB entry 3a5x and chain C of PDB entry 5fn5) using the less expensive semi-empirical (GFN1-xTB) model. The necessary algorithms enabling real-space quantum refinement have been implemented in the latest version of qr.refine and are described here.
The crystal structure of AjiA1 reveals a novel structural motion mechanism in the adenylate-forming enzyme family
Authors: de Paiva Fernanda C. R. , Chan Karen , Samborskyy Markiyan , Silber Ariel M. , Leadlay Peter F. , Dias Marcio V. B. 
Published: November 2020

Adenylate-forming enzymes (AFEs) are a mechanistic superfamily of proteins that are involved in many cellular roles. In the biosynthesis of benzoxazole antibiotics, an AFE has been reported to play a key role in the condensation of cyclic molecules. In the biosynthetic gene cluster for the benzoxazole AJI9561, AjiA1 catalyzes the condensation of two 3-hydroxyanthranilic acid (3-HAA) molecules using ATP as a co-substrate. Here, the enzymatic activity of AjiA1 is reported together with a structural analysis of its apo form. The structure of AjiA1 was solved at 2.0 Å resolution and shows a conserved fold with other AFE family members. AjiA1 exhibits activity in the presence of 3-HAA (K
m = 77.86 ± 28.36, k
cat = 0.04 ± 0.004) and also with the alternative substrate 3-hydroxybenzoic acid (3-HBA; K
m = 22.12 ± 31.35, k
cat = 0.08 ± 0.005). The structure of AjiA1 in the apo form also reveals crucial conformational changes that occur during the catalytic cycle of this enzyme which have not been described for any other AFE member. Consequently, the results shown here provide insights into this protein family and a new subgroup is proposed for enzymes that are involved in benzoxazole-ring formation.
The influence of the shoulder depth on the properties of the thin sheet joint made by FSW technology
Authors: Burek Rafał , Wydrzyński Dawid , Kubit Andrzej , Łogin Waldemar 
Published: November 2020

Purpose
This paper aims to experimentally determine the influence of the tool shoulder depth value on the structural and strength properties of the single lap joints made of 7075-T6 aluminium alloy made with friction stir welding (FSW) technology. The aim of the preliminary tests is to optimize the parameters of joining process of thin-walled structures such as the skin-stringer joint or skin-frame joint of the aircraft fuselage. The tests were carried out for materials commonly used in such structures, i.e. 1.6 mm thick sheet 7075–T6 aluminium alloy with cladding on both sides (cladding thickness 4% per each side). The layer of clad protects plates from corrosion.

Design/methodology/approach
This study shows the results of the investigation for the joining of 7075–T6 ALCLAD aluminium alloy sheets. The welding process was carried out on a computer numerical control milling machine SOLARUCE TA–20A. Linear FSW welding was performed using a commercial tool from RSS SCHILLING with the symbol 10–K–4–Z–M–O, which is fabricated of hot work tool steel. Constant parameters of the technological process were applied. The welding process was executed for different values of the shoulder depth ZS.

Findings
This paper investigated the dependence between the thinning of the welded material and the depth value of the tool shoulder during the FSW process. The influence of the depth value of tool shoulder on joint strength in the static tensile/shear test was also performed. With the increase of the depth of the tool, the size of flash and structures of the face of the joint changes as well (its annular surface resulting from the tool’s work and the accompanying process of material flow on the run-off side). Such conditions in the process require a proper tool depression to reduce the occurrence of flash and minimize material thinning to achieve high joint strength and maintain the conditions for plasticizing the material.

Practical implications
Based on the experimental tests carried out, a number of guidelines for the correct conduct of the welding process can be outlined.

Originality/value
Taking into account the various aspects of the process, the optimal range of the tool depth into the material is a value of approximately 0.06 mm. At this value, the face of the weld is not porous; the flash is easily removed; and the strength of the joint and the deformation of contact line are at an acceptable quality level.
Mobile money system and market risk mitigation: an econometric case study of Kenya's farm business
Authors: Gopane Thabo J. 
Published: November 2020

PurposeThe study presents and evaluates a proposition that there is market information bundled with the mobile money (m-money) system. Also, that such information is disseminated to farmers in the process of their normal financial transactions and business interactions. This market information is important to mitigate the price uncertainty of farm products.Design/methodology/approachThe empirical analysis is conducted with a two-stage econometric procedure. First, a probit model is used to estimate the likelihood of m-money take-up by farm entrepreneurs. Second, the ordinary least squares model is used to regress the farming price uncertainty index on the m-money take-up, which is quantified with a set of predicted values from the probit model in the first stage. The data used in econometric estimation come from Kenya's FinAccess Household Survey published in 2016.FindingsThe results of this paper show a negative effect of m-money service take-up on the price uncertainty index. A one unit increase in the m-money system is associated with a 12% reduction in the price uncertainty index. The authors interpret this as saying that access to the m-money system by farm business has a beneficial spillover effect on product risk mitigation, ceteris paribus.Research limitations/implicationsThe implication of this research is that policy initiatives which support farm entrepreneurs to access the m-money system should be encouraged not only for their financial inclusion advantage but also for their positive externality on product risk amelioration for rural farm businesses.Originality/valueThe paper introduces an idea that the m-money system is bundled with relevant information for mitigating price risk to the benefit of rural farm businesses.
Attitude and labelling preferences towards gene-edited food: a consumer study amongst millennials and Generation Z
Authors: Ferrari Linda , Baum Chad M. , Banterle Alessandro , De Steur Hans 
Published: November 2020

PurposeThis study jointly examines consumer attitudes towards gene-edited (GE) food and their preferences for labelling such products. Thus, it contributes to understanding the role of educational background, objective/subjective knowledge, environmental concern and socio-demographics in the context of GE food.Design/methodology/approachAn online survey was administered to two generations of young individuals (millennials and Generation Z; n = 234) from two neighbouring European Union (EU) regions (Belgium and The Netherlands), which have a stringent policy on (labelling) genetically modified (GM) food. Ordinary least squares (OLS) and ordered logit models (OLMs) were employed to identify key determinants of attitudes towards GE food and GE labelling preferences, respectively.FindingsAttitudes towards GE food were determined by environmental concern (negative) and objective knowledge (positive). Key factors influencing preferences for GE labelling were a non-hard-scientific background, knowledge about relevant policies and a negative attitude towards GE food. Preference for applying a similar labelling policy to both GM and GE was itself linked to having low, objective EU policy-related GM food knowledge and one's nationality.Originality/valueThis is one of the first studies to examine consumer attitudes towards GE food products, while also addressing a lack of research on GE food labelling preferences. By highlighting the preferences of young generations for a revised policy approach, this study sheds new light on the current GE debate, notably, by promoting a deeper understanding of a group which has so far received limited attention in the discourse on the acceptance of novel plant-breeding technologies.
Assessing the objectives of dry ports: main issues, challenges and opportunities in Brazil
Authors: Rodrigues Thiago de Almeida , Mota Caroline Maria de Miranda , Ojiako Udechukwu , Dweiri Fikri 
Published: November 2020

PurposeThe purpose is to identify the main characteristics of dry ports (DPs) in Brazil, discussing the role of this logistic player, challenges and opportunities. Furthermore, this study provides a structured framework to drive DP decision-makers, identifying and assessing a network of means–end objectives, which could be replicable to other contexts.Design/methodology/approachThis article approached initially a literature review and exploratory research to discuss the main characteristics of DPs in Brazil. The second step was to conduct a qualitative analysis following the value-focused thinking (VFT) approach in two case studies in Pernambuco state to assess the achievement of the main objectives.FindingsThis article identified that the main characteristics of DPs in Brazil are offering additional services with a cheaper storage cost, handling mainly import cargo and being connected to seaports through highways. Moreover, this study resulted in a framework to assess the objectives of DPs, which could be replicable in other contexts, improving the current operations of DPs.Practical implicationsThe framework to assess DPs' objectives bridged the gap between the literature and the practice working as a tool to drive decision-makers to improve the current performance of DPs in Brazil. Additionally, the main issues, challenges and opportunities discussed provide managers, policymakers and DPs operators with valuable insights into this theme.Originality/valueThis paper is the first study to present a framework to assess the objectives of DPs as a valuable tool to drive decision-makers to improve DPs operations. From this study, lessons could be learned and the process described could be replicable in other countries.