bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome sequencing ofAcinetobacter baumanniiAC1633 andAcinetobacter nosocomialisAC1530 unveils a large multidrug resistant plasmid encoding the NDM-1 and OXA-58 carbapenemases
Authors: Alattraqchi Ahmed Ghazi , Rani Farahiyah Mohd. , Rahman Nor Iza A. , Ismail Salwani , Cleary David W. , Clarke Stuart C. , Yeo Chew Chieng 
Published: October 2020

ABSTRACTCarbapenem-resistantAcinetobacterspp. are considered priority drug-resistant human pathogenic bacteria. The genomes of two carbapenem-resistantAcinetobacterspp. clinical isolates obtained from the same tertiary hospital in Terengganu, Malaysia, namelyA. baumanniiAC1633 andA. nosocomialisAC1530, were sequenced. Both isolates were found to harbor the carbapenemase genesblaNDM-1andblaOXA-58in a large (ca. 170 kb) plasmid designated pAC1633-1 and pAC1530, respectively, that also encodes genes that confer resistance to aminoglycosides, sulfonamides, and macrolides. The two plasmids were almost identical except for the insertion of ISAba11and an IS4family element in pAC1633-1, and ISAba11along withrelBEtoxin-antitoxin genes flanked by inversely orientated pdif(XerC/XerD) recombination sites in pAC1530. TheblaNDM-1gene was encoded in aTn125composite transposon structure flanked by ISAba125whereasblaOXA-58was flanked by ISAba11and ISAba3downstream and a partial ISAba3element upstream within a pdifmodule. The presence of conjugative genes in plasmids pAC1633-1/pAC1530 and their discovery in two distinct species ofAcinetobacterfrom the same hospital are suggestive of conjugative transfer but mating experiments failed to demonstrate transmissibility under standard laboratory conditions. Comparative sequence analysis strongly inferred that pAC1633-1/pAC1530 was derived from two separate plasmids in an IS1006-mediated recombination or transposition event.A. baumanniiAC1633 also harbored three other plasmids designated pAC1633-2, pAC1633-3 and pAC1633-4. Both pAC1633-3 and pAC1633-4 are cryptic plasmids whereas pAC1633-2 is a 12,651 bp plasmid of the GR8/GR23 Rep3-superfamily group that encodes thetetA(39)tetracycline resistance determinant in a pdifmodule.
Cellular birthdate predicts laminar and regional cholinergic projection topography in the forebrain
Authors: Allaway Kathryn C. , Muñoz William , Tremblay Robin , Sherer Mia , Herron Jacob , Rudy Bernardo , Machold Robert , Fishell Gord 
Published: October 2020

AbstractThe basal forebrain cholinergic system projects broadly throughout the cortex and constitutes a critical source of neuromodulation for arousal and attention. Traditionally, this system was thought to function diffusely. However, recent studies have revealed a high degree of spatiotemporal specificity in cholinergic signaling. How the organization of cholinergic afferents confers this level of precision remains unknown. Here, using intersectional genetic fate mapping, we demonstrate that cholinergic fibers within the cortex exhibit remarkable laminar and regional specificity and that this is organized in accordance with cellular birthdate. Strikingly, birthdated cholinergic projections within the cortex follow an inside-out pattern of innervation. While early born cholinergic populations target deep layers, late born ones innervate superficial laminae. We also find that birthdate predicts cholinergic innervation patterns within the amygdala, hippocampus, and prefrontal cortex. Our work reveals previously unappreciated specificity within the cholinergic system and the developmental logic by which these circuits are assembled.
Use of immunoglobulin-binding bacterial proteins in immunodetection
Authors: Justiz-Vaillant Angel , Ferrer-Cosme Belkis , Vera Albert 
Published: October 2020

AbstractOne of the aim of this study was to make universal chimeric conjugates to react with both avian and mammalian immunoglobulins in enzyme-linked immunosorbent assays (ELISAs). The periodate method was used in the conjugation process of cross-linking horseradish peroxidase to immunoglobulin-binding proteins (IBP) including staphylococcal protein A (SpA), streptococcal protein G (SpG) and peptostreptococcal protein L (SpL). By mixing up these three conjugates another four hybrid protein conjugates were created including protein LA (SpLA), protein LG (SpLG), protein AG (SpAG) and protein LAG (PLAG). Thirty-five ELISAs were standardized by a probabilistic combination of these immunoreagents. By using a panel of mainly mammalian immunoglobulins their reproducibility was checked by the determination of coefficient of variations (CV) for each one of the IgG-IBP binding. The source of immunoglobulins was their purification by affinity chromatography using a commercially available kit (PURE-1A). The other aim was to immunize chicken with the peptide fragment 254-274 of gp120 to produce anti-HIV peptide hyper-immune egg. Cats and rats were fed these eggs for a determined period until they produced the anti-HIV peptide antibody, which was tested by an indirect SpLA-ELISA and dot blot analysis that corroborated the production of anti-HIV antibodies by the mammalian species including positive humans samples for HIV. We conclude that the single and hybrid immunoglobulin-binding protein were effective in their binding capacity to immunoglobulins from a variety of mammalian species. The potential use of this proteins is in the arena of immunodiagnosis and immunoglobulin detection. Dot blot analysis proves effective in the detection of HIV anti-gp120 antibodies in several animal species. These antibodies can be used as reagents in the development of immunodiagnostic tests or experimental vaccines.
Loss of clustered protocadherin diversity alters the spatial distribution of cortical interneurons
Authors: Gallerani Nicholas , Au Edmund 
Published: October 2020

AbstractCortical interneurons (cINs) are locally-projecting inhibitory neurons that are distributed throughout the cortex. Due to their relatively limited range of influence, their arrangement in the cortex is critical to their function. cINs achieve this arrangement through a process of tangential and radial migration, and apoptosis during development. In this study, we investigated the role of clustered protocadherins (cPcdhs) in establishing the spatial patterning of cINs. cPcdhs are expressed in cINs, and are known to play key functions in cell spacing and cell survival, but their role in cINs is poorly understood. Using spatial statistical analysis, we found that the two main subclasses of cINs, parvalbumin-expressing (PV) and somatostatin-expressing (SST) cINs, are non-randomly spaced within subclass, but randomly with respect to each other. We also found that the relative laminar distribution of each subclass was distinctly altered in whole α- or β-cluster mutants. Examination of perinatal timepoints revealed that the mutant phenotypes emerged relatively late, suggesting that cPcdhs may be acting during cIN morphological elaboration and synaptogenesis. We then analyzed an isoform-specific knockout for pcdh-αc2 and found that it recapitulated the α-cluster knockout, but only in SST cells, suggesting that subtype-specific expression of cPcdh isoforms may help govern subtype-specific spatial distribution.
Data-driven yield projections suggest large opportunities to improve Europe’s soybean self-sufficiency under climate change
Authors: Guilpart Nicolas , Iizumi Toshichika , Makowski David 
Published: October 2020

AbstractCurrently, demand for soybean in Europe is mostly fulfilled by imports. However, soybean-growing areas across Europe have been rapidly increasing in response to a rising demand for locally-produced, non-GM soybean in recent years. This raises questions about the suitability of European agro-climatic conditions for soybean production. We used data-driven relationships between climate and soybean yield derived from machine-learning techniques to make yield projections under current and future climate with moderate (RCP 4.5) to intense (RCP 8.5) warming, up to the 2050s and 2090s time horizons. Results suggest that a self-sufficiency level of 50% (100%) would be achievable in Europe under historical and future climate if 4-5% (9-12%) of the current European cropland is dedicated to soybean production. The associated increase in soybean area in Europe would bring environmental benefits, with a potential decrease of nitrogen fertilizer use in Europe by 5-8% (13-18%) and a possible reduction of deforestation in biodiversity hotspots in South America. However, it would also lead to an important reduction in the production of other cultivated species in Europe (e.g. cereals) and a potential increase in the use of irrigation water.
Environmental DNA Metabarcoding Reveals Winners and Losers of Global Change in Coastal Waters
Authors: Gallego Ramón , Jacobs-Palmer Emily , Cribari Kelly , Kelly Ryan P. 
Published: October 2020

2AbstractStudies of the ecological effects of global change often focus on one or few species at a time. Consequently, we know relatively little about the changes underway at real-world scales of biological communities, which typically have hundreds or thousands of interacting species. Here, we use monthly samples of environmental DNA to survey 222 planktonic taxa along a gradient of temperature, salinity, dissolved oxygen, and carbonate chemistry in nearshore marine habitat. The result is a high-resolution picture of changes in ecological communities using a technique replicable across a wide variety of ecosystems. We estimate community-level differences associated with time, space and environmental variables, and use these results to forecast near-term community changes due to warming and ocean acidification. We find distinct communities in warmer and more acidified conditions, with overall reduced richness in diatom assemblages and increased richness in dinoflagellates. Individual taxa finding greater suitable habitat in near-future waters are more taxonomically varied and include the ubiquitous coccolithophoreEmiliania huxleyiand the harmful dinoflagellateAlexandrium sp. These results suggest foundational changes for nearshore food webs under near-future conditions.
Identification, Characterization, and Targeting of a Rare and Temporal Dendritic Cell State that Facilitates Adaptive Immune Responses
Authors: Deak Peter , Studnitzer Bradley , Steinhardt Rachel , Esser-Kahn Aaron 
Published: October 2020

SummaryThe heterogeneity of innate immune cells facilitates efficient antigen presentation and immune activation in the presence of pathogens via cooperativity of various cell subsets and cell states but also obscures the contribution of individual antigen presenting cells (APCs) to overall immune response.1It has been hypothesized that a small number of APCs, which are more sensitive to the initial pathogen stimulus, are responsible for coordinating neighboring APCs in an effort to share the metabolic strain associated with heightened pathogen sensitivity.2In this study, we have identified a temporally-controlled state of dendritic cells (DCs) that demonstrate greater sensitivity to toll-like-receptor (TLR) agonists and secrete the majority of paracrine activating cytokines (TNFα, IL-6…ect). We were able to isolate this distinct population of DCs preferentially phagocytosed the majority of fluorescently labeled, TLR agonist conjugated microparticles (MPs).3We call this population First Responder cells (FRs) due to their ability to first uptake the MPs and activate neighboring APCs via paracrine signaling. We show that FRs exist in this state for <3 hours, cycle through this state on a <24-hour timescale and show a distinct mRNA profile. Furthermore, FRs are necessary for generation of adaptive responses both in vitro and in vivo. We also show that we can improve both IgG titers and CD8 responses in vivo by targeting two highly upregulated receptors on FR cells, DAP12 and PRG2. Given the significance of FR involvement in APC activation, this study has broad immunological value because it offers a critical first evaluation of a new APC cell state but also has important translational value for improving vaccine efficacy via FR targeting.
First report of Infectious Spleen and Kidney Necrosis Virus in Nile tilapia in Brazil
Authors: Pereira Figueiredo Henrique César , Tavares Guilherme Campos , Dorella Fernanda Alves , Câmara Rosa Júlio César , Correia Marcelino Sóstenes Apolo , Pierezan Felipe 
Published: October 2020

SummaryIn June 2020, an atypical fatal outbreak in the Nile tilapia farm was investigated. Twenty-three animals were collected and different tissues were used for bacterial isolation, histopathological and electron microscopic examination, and viral detection using molecular methods. A large number of megalocytes were observed in the histopathological analysis of several tissues. Icosahedral virions, with a diameter of approximately 160 nm, were visualized inside the megalocytes through transmission electron microscopy of the spleen tissue. The virions were confirmed to beinfectious spleen and kidney necrosis virus(ISKNV) through PCR and sequencing analyses of the fish samples. This viral pathogen is fatal in the early stages of Nile tilapia farms in the USA, Thailand, and Ghana; however, until now, there have been no reports from Brazil. In 14 of the sampled fish,Streptococcus agalactiae, Edwardsiella tarda, orAeromonas hydrophila infectionswere also detected. This is the first report of fatal ISKNV infections in the Brazilian Nile tilapia fish farms.
Structure and mechanism of TRAPPIII-mediated Rab1 activation
Authors: Joiner Aaron M.N. , Phillips Ben P. , Yugandhar Kumar , Sanford Ethan J. , Smolka Marcus B. , Yu Haiyuan , Miller Elizabeth A. , Fromme J. Christopher 
Published: October 2020

ABSTRACTThe GTPase Rab1 is a master regulator of both the early secretory pathway and autophagy. Rab1 activation is controlled by its GEF (guanine nucleotide exchange factor), the multi-subunit TRAPPIII complex. The Trs85 regulatory subunit is critical for robust activation of Rab1 but its mechanistic role within the complex has remained unclear. Here we report the cryo-EM structure of the intact yeast TRAPPIII complex bound to its substrate Rab1/Ypt1. The orientation of the Rab1/Ypt1 hypervariable domain when bound to the complex leads to a model for how TRAPPIII associates with and activates Rab1/Ypt1 at the membrane surface. We identify a conserved amphipathic α-helix motif within Trs85 and demonstrate that this helix is required for stable membrane binding and Rab1/Ypt1 activation by TRAPPIII. Taken together, our results provide a comprehensive analysis of the structure and function of the yeast TRAPPIII complex and reveal that the key function of Trs85 is to serve as a membrane anchor, via its amphipathic helix, for the entire TRAPPIII complex.
Catechol-Containing Compounds are a Broad Class of Amyloid Inhibitors: Redox State is a Key Determinant of the Inhibitory Activities
Authors: Velander Paul , Wu Ling , Hildreth Sherry B. , Vogelaar Nancy J. , Mukhopadhyay Biswarup , Zhang Shijun , Helm Richard F. , Xu Bin 
Published: October 2020

ABSTRACTMechanisms of amyloid inhibition remains poorly understood, in part because most protein targets of amyloid assembly are partially unfolded or intrinsically disordered, which hinders detailed structural characterization of protein-inhibitor complexes and structural-based mechanistic elucidation. Herein we employed a small molecule screening approach to identify inhibitors against three prototype amyloidogenic proteins: amylin, Aβ and tau. One remarkable class of inhibitors identified was catechol-containing compounds and redox-related quinones/anthraquinones. Further mechanistic studies determined that the redox state of the broad class of catechol-containing compounds is a key determinant of the amyloid inhibitor activities.
Alternative conformation of the C-domain of the P140 protein from Mycoplasma genitalium
Authors: Vizarraga David , Pérez-Luque Rosa , Martín Jesús , Fita Ignacio , Aparicio David 
Published: October 2020

The human pathogen Mycoplasma genitalium is responsible for urethritis in men, and for cervicitis and pelvic inflammatory disease in women. The adherence of M. genitalium to host target epithelial cells is mediated through an adhesion complex called Nap, which is essential for infectivity. Nap is a transmembrane dimer of heterodimers of the immunodominant proteins P110 and P140. The M. genitalium genome contains multiple copies of portions that share homology with the extracellular regions of P140 and P110 encoded by the genes mg191 and mg192, respectively. Homologous recombination between the genes and the copies allows the generation of a large diversity of P140 and P110 variants to overcome surveillance by the host immune system. Interestingly, the C-terminal domain (C-domain) of the extracellular region of P140, which is essential for the function of Nap by acting as a flexible stalk anchoring the protein to the mycoplasma membrane, presents a low degree of sequence variability. In the present work, the X-ray crystal structures of two crystal forms of a construct of the P140 C-domain are reported. In both crystal forms, the construct forms a compact octamer with D4 point-group symmetry. The structure of the C-domain determined in this work presents significant differences with respect to the structure of the C-domain found recently in intact P140. The structural plasticity of the C-domain appears to be a possible mechanism that may help in the functioning of the mycoplasma adhesion complex.
An evaluation of the library connectivity project through the lens of the digital inclusion model
Authors: Ayoung Daniel Azerikatoa , Bugre Charles , Baada Frederic Naazi-Ale 
Published: October 2020

Purpose
It has been a decade, as the collaboration between the Ghana Investment Fund for Electronic Communications (GIFEC) and the Ghana Library Authority (GhLA) to extend information and communication technology (ICT) and library services to rural deprived, unserved and underserved communities in Ghana dubbed the library connectivity project. This paper aims to evaluate this initiative from the perspective of relevant key stakeholders and through the lens of the digital inclusion model.

Design/methodology/approach
The study adopted a qualitative approach to evaluate the library connectivity project offered to deprived communities in the Upper East Region of Ghana. Interviews were conducted with the head librarians, ICT teachers and school librarians. Focus group discussions were held with pupils from four beneficiary schools of the project. The researchers also witnessed four of the outreach programmes and training sessions and observed the mode of instruction.

Findings
The study brought to fore the enormous benefits of the library connectivity project as it aided school pupils to acquire practical ICT skills, which were found to be useful towards their final exam. Despite the enormous benefit of the project, it was bereft with a lot of challenges such as inadequate logistics and personnel thereby restricting the project to very few schools. Low staff motivation and unmotorable roads were also found to be a challenge, which could all be as a result of lack of funds.

Research limitations/implications
The paper underscores the importance of computer and information literacy and reveals how the GhLA is using innovative mobile library services to bridge the digital divide through the library connectivity project.

Originality/value
This paper makes a further contribution to the paucity of literature on the role of mobile libraries in the promotion of computer and information literacy.
Investigating the suitability and cost-benefit of copper tailings as partial replacement of sand in concrete in Zambia: an exploratory study
Authors: Muleya Franco , Mulenga Bodwin , Zulu Sambo Lyson , Nwaubani Sunday , Tembo Chipozya Kosta , Mushota Henry 
Published: October 2020

Purpose
This study aimed to investigate the suitability and cost-benefit of using copper tailings as partial replacement of sand in concrete production. The study was motivated by the accumulation and non-use of copper tailings in dams among them tailing dam 25 also known as TD 25 in Kitwe city of the Copperbelt province in Zambia that take up approximately 111 hectares of unused land.

Design/methodology/approach
Laboratory experimental approach of concrete production based on water/cement ratios of 0.3 and 0.5 was used because this was an exploratory study designed to establish the primary performance of concrete. In total, 30 concrete cubes were cast based on the two water-cement ratios. In total, 0% to 30% partial sand replacement with copper tailings was used in both mixes with the 0% copper tailings replacement being the control mix and reference point. Other concrete tests included workability, density, compressive strength and element composition analysis.

Findings
Results revealed that copper tailings from TD 25 were suitable for partial replacement of sand in concrete. Thirty per cent of sand replacement with copper tailings was established as the maximum replacement amount to produce optimum compressive strength values from both mixes. The drier mix of 0.3 water-cement ratios produced higher compressive strength results of 23 MPa at 28 days of concrete curing with 2.34% as optimum concrete cost reduction.

Practical implications
The research results provide the cost-benefit analysis and savings that can be attained from using cheaper copper tailings based concrete. The study further provided the quantity of land available for development arising from absorption of copper tailings as a sustainable construction material. The local authority now has statistics and numerical values that it can use to absorb copper tailings as a concrete raw material.

Originality/value
The study provides guidance on optimum concrete grade produced and cost reduction details of copper tailing-based concrete to support for local authorities in suitable land wand waste management using real data.
Intrapreneurship in teams/groups: self-determination theory and compensation
Authors: Chakrabarty Subrata 
Published: October 2020

PurposeThe literature on intrapreneurship recognizes the notion that regular employees can be expected to be entrepreneurial. Using self-determination theory as a basis, the purpose of this conceptual paper is to focus on the role of compensation systems in incentivizing entrepreneurial action by regular employees who constitute the bulk of the organizational workforce.Design/methodology/approachThis conceptual paper suggests that greater clarity on the role of compensation systems in entrepreneurial action by regular employees would require an understanding of how entrepreneurial action happens through relationships among employees. An exploration of both compensation systems and the relationships among employees undertaking entrepreneurial action as part of team/group settings can deepen our understanding of intrapreneurship. Self-determination theory and relationship-focused theory allow for such an exploration.FindingsThe literature on self-determination theory, has identified the needs of autonomy and relatedness among employees. This conceptual paper will propose that the interaction between compensation systems and the needs for autonomy versus relatedness among employees determines the type of relationships chosen for entrepreneurial action. After the chosen type of relationships are formed and entrepreneurial action begins, challenges in the implementation of compensation systems are likely to emerge – distributive justice issues under individual based compensation and free-riding issues under team-based compensation. The entrepreneurial performance of the team/group will likely be influenced by the interaction between the challenges in the implementation of compensation systems and the type of relationships chosen for entrepreneurial action.Originality/valueThis conceptual paper gives a new direction to how collective entrepreneurial processes and outcomes can be understood. Self-determination theory and relationship-focused theory, in unison, can be useful in analyzing the role of intrinsic motivators, extrinsic motivators, and relationships during entrepreneurial action.