bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental asymmetries in learning to adjust to cooperative and uncooperative environments
Authors: Westhoff Bianca , Molleman Lucas , Viding Essi , van den Bos Wouter , van Duijvenvoorde Anna C. K. 
Published: July 2020

AbstractLearning to successfully navigate social environments is a critical developmental goal, predictive of long-term wellbeing. However, little is known about how people learn to adjust to different social environments, and how this behaviour emerges across development. Here, we use a series of economic games to assess how children, adolescents, and young adults learn to adjust to social environments that differ in their level of cooperation (i.e., trust and coordination). Our results show an asymmetric developmental pattern: adjustment requiring uncooperative behaviour remains constant across adolescence, but adjustment requiring cooperative behaviour improves markedly across adolescence. Behavioural and computational analyses reveal that age-related differences in this social learning are shaped by age-related differences in the degree of inequality aversion and in the updating of beliefs about others. Our findings point to early adolescence as a phase of rapid change in cooperative behaviours, and highlight this as a key developmental window for interventions promoting well-adjusted social behaviour.
Recombinational repair of nuclease-generated mitotic double-strand breaks with different end structures in yeast
Authors: Gamble Dionna , Shaltz Samantha , Jinks-Robertson Sue 
Published: July 2020

ABSTRACTMitotic recombination is the predominant mechanism for repairing double-strand breaks inSaccharomyces cerevisiae. Current recombination models are largely based on studies utilizing the enzyme I-SceI or HO to create a site-specific break, each of which generates broken ends with 3’ overhangs. In this study sequence-diverged ectopic substrates were used to assess whether the frequent Pol δ-mediated removal of a mismatch 8 nucleotides from a 3’ end affects recombination outcomes and whether the presence of a 3’versus5’ overhang at the break site alters outcomes. Recombination outcomes monitored were the distributions of recombination products into crossoversversusnoncrossovers, and the position/length of transferred sequence (heteroduplex DNA) in noncrossover products. A terminal mismatch that was 22 nucleotides from the 3’ end was rarely removed and the greater distance from the end did not affect recombination outcomes. To determine whether the recombinational repair of breaks with 3’versus5’ overhangs differs, we compared the well-studied 3’ overhang created by I-SceI to a 5’ overhang created by a ZFN (Zinc Finger Nuclease). Initiation with the ZFN yielded more recombinants, consistent with more efficient cleavage and potentially faster repair rate relative to I-SceI. While there were proportionally more COs among ZFN-than I-SceI-initiated events, NCOs in the two systems were indistinguishable in terms of the extent of strand transfer. These data demonstrate that the method of DSB induction and the resulting differences in end polarity have little effect on mitotic recombination outcomes despite potential differences in repair rate.
Nuclear and cytoplasmic huntingtin inclusions exhibit distinct biochemical composition, interactome and ultrastructural properties
Authors: Riguet Nathan , Mahul-Mellier Anne-Laure , Maharjan Niran , Burtscher Johannes , Croisier Marie , Knott Graham , Hastings Janna , Patin Alice , Reiterer Veronika , Farhan Hesso , Nasarov Sergey , Lashuel Hilal A. 
Published: July 2020

AbstractDespite the strong evidence linking the aggregation of the Huntingtin protein (Htt) to the pathogenesis of Huntington’s disease (HD), the mechanisms underlying Htt aggregation and neurodegeneration remain poorly understood. Herein, we investigated the ultrastructural properties and protein composition of Htt cytoplasmic and nuclear inclusions in mammalian cells and primary neurons overexpressing mutant exon1 of the Htt protein. Our findings provide novel insight into the ultrastructural properties of cytoplasmic and nuclear Htt inclusions and their mechanisms of formation. We show that Htt inclusion formation and maturation are complex processes that, although initially driven by polyQ-dependent Htt aggregation, also involve 1) polyQ and PRD domain-dependent sequestration of lipids and cytoplasmic and cytoskeletal proteins related to HD dysregulated pathways; 2) recruitment and accumulation of remodeled or dysfunctional membranous organelles, and 3) impairment of the protein quality control and degradation machinery. We also show that nuclear and cytoplasmic Htt inclusions exhibit distinct biochemical compositions and ultrastructural properties, suggesting different mechanisms of aggregation and toxicity.Graphical AbstractSchematic depictions and original electron micrographs of cytoplasmic inclusions formed by native (tag-free) mutant Huntingtin exon1 proteins (Httex1 72Q, left) and the corresponding GFP fusion protein (Httex1 72Q-GFP, right).
Validating gene-phenotype associations using relationships in the UMLS
Authors: Blumenfeld Andrew L , Gonzaga-Jauregui Claudia , Sharma Deepika ,   Geisinger-Regeneron DiscovEHR Collaboration,   Regeneron Genetics Center, Yadav Ashish , Khalid Shareef , Balasubramanian Suganthi , Reid Jeffrey G , Habegger Lukas , Cantor Michael N , Staples Jeffrey 
Published: July 2020

AbstractObjectiveLarge scale next-generation sequencing of population cohorts paired with patients’ electronic health records (EHR) provides an excellent resource for the study of gene-disease associations. To validate those associations, researchers often consult databases that identify relationships between genes of interest and relevant disease phenotypes, which we refer to as simply “phenotypes”. However, most of these databases contain phenotypes that are not suited for automated analysis of EHR data, which often captured these phenotypes in the form of International Classification of Diseases (ICD) codes. There is a need for a resource that comprehensively provides gene-phenotype mappings in a format that can be used to evaluate phenotypes from EHR.MethodsWe built a directed graph database of genes, medical concepts and ICD codes based on a subset of the National Library of Medicine’s Unified Medical Language System (UMLS) and other resources. To obtain associations between genes and ICD codes, we traversed the defined relationships from gene, variant and disease concepts to ICD codes, resulting in a set of mappings that link specific genes and variants to these ICD codes.ResultsOur method created 249,764 mappings between genes and ICD codes, including 27,226 “disease” phenotypes and 222,538 “symptom” phenotypes, and provided mappings for 4,456 unique genes. Paths were validated by manual review of a diverse sample of paths. In a cohort of 92,455 samples, we used these mappings to validate gene-phenotype associations in 32,786 samples where a person had a potentially disease-causing genetic mutation and at least one corresponding diagnosis in their EHR.ConclusionThe concepts and relationships in the UMLS can be used to generate gene-ICD phenotype mappings that are not explicit in the source vocabularies. We were able use these mappings to validate gene-disease associations in a large cohort of sequenced exomes paired with EHR.
Plankton food webs of the Gulf of Mexico spawning grounds of Atlantic Bluefin tuna
Authors: Stukel Michael R. , Gerard Trika , Kelly Thomas , Knapp Angela N. , Laiz-Carrión Raúl , Lamkin John , Landry Michael R. , Malca Estrella , Selph Karen E. , Shiroza Akihiro , Shropshire Taylor A. , Swalethorp Rasmus 
Published: July 2020

ABSTRACTWe used linear inverse ecosystem modeling techniques to assimilate data from extensive Lagrangian field experiments into a mass-balance constrained food web for the Gulf of Mexico open-ocean ecosystem. This region is highly oligotrophic, yet Atlantic Bluefin Tuna (ABT) travel long distances from feeding grounds in the North Atlantic to spawn there. Our results show that the food web is dominated by the microbial loop (>80% of net primary productivity is respired by heterotrophic bacteria and protists that feed on them). In contrast, herbivorous food web pathways from phytoplankton to metazoan zooplankton process <4% of net primary production in the mixed layer. Nevertheless, ABT larvae feed preferentially on calanoid copepods and other suspension-feeding zooplankton that in turn derive much of their nutrition from diatoms and mixotrophic flagellates. This allows ABT larvae to maintain a comparatively low trophic level (∼4.0 for pre-flexion larvae; ∼4.2 for post-flexion larvae) that increases trophic transfer from phytoplankton to larval fish.
Global relationships between crop diversity and nutritional stability
Authors: Nicholson Charlie C. , Emery Benjamin F. , Niles Meredith T. 
Published: July 2020

AbstractNutritional stability – a food system’s capacity to provide sufficient nutrients despite disturbance – is a critical feature of sustainable agriculture, especially in light of ongoing climate change. Yet, measuring nutritional stability has proven challenging. Addressing this challenge will help identify resilient food systems, detect shortcomings in nutrient availability, and evaluate if stability-focused interventions actually work. We develop a novel approach that uses 55 years of crop data across 184 countries to assemble over 22,000 bipartite crop-nutrient networks. We then quantify the tolerance of these networks to disturbance simulated via sequential crop loss (Fig. 1) and evaluate patterns of crop diversity and nutritional stability across countries, over time and between crop supply scenarios (imports versus in country production). We observe a positive, saturating relationship between crop diversity and nutritional stability across countries; however there is substantial variability between countries over time. Next, despite crop diversity gains since 1961, nutritional stability has remained stagnant or decreased in all regions except Asia. A decline in the average number of nutritional links per network (range: -3 to -18% across regions) and the aforementioned saturating relationship explain this counter-intuitive finding. Finally, we find that imports increase crop diversity and improve or sustain stability, indicating that nutrient availability is market exposed in many countries, particularly developing states. Although applied globally, our approach is applicable across levels of organization, from household intake to sub-national production, and provides a way forward for understanding the contributions of crop diversity to the stability of nutrients available for human consumption.
3D single cell scale anatomical map of sex-dependent variability of the rat intrinsic cardiac nervous system
Authors: Leung Clara , Robbins Shaina , Moss Alison , Heal Maci , Osanlouy Mahyar , Christie Richard , Farahani Navid , Monteith Corey , Chen Jin , Hunter Peter , Tappan Susan , Vadigepalli Rajanikanth , Cheng Zixi (Jack) , Schwaber James S. 
Published: July 2020

SummaryWe developed and analyzed a single cell scale anatomical map of the rat intrinsic cardiac nervous system (ICNS) across 4 male and 3 female hearts. We find the ICNS has a reliable structural organizational plan across individuals that may provide the foundation for further analyses of the ICNS in cardiac function and disease. The distribution of the ICNS was evaluated by 3D visualization and using data-driven clustering. The pattern, distribution and clustering of ICNS neurons across all male and female rat hearts is highly conserved, demonstrating a coherent organizational plan in which distinct clusters of neurons are consistently localized. Female hearts had fewer neurons, lower packing density and slightly reduced distribution, but with the same localization. We registered the anatomical data from each heart to a geometric scaffold, normalizing their 3D coordinates for the standardization of common anatomical planes and providing the path where multiple experimental results and data types can be integrated and compared.
Multiple stages of evolutionary change in anthrax toxin receptor expression in humans
Authors: Choate Lauren A. , Barshad Gilad , McMahon Pierce W. , Said Iskander , Rice Edward J. , Munn Paul R. , Lewis James J. , Danko Charles G. 
Published: July 2020

AbstractThe advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease influenced human evolution, we studied changes in human expression of anthrax toxin receptor 2 (ANTXR2), which encodes a cell surface protein necessary forBacillus anthracisvirulence toxins to cause anthrax disease. In immune cells,ANTXR2was 8-fold down-regulated in all available human samples compared to non-human primates, indicating regulatory changes early in the evolution of modern humans. We also observed multiple genetic signatures consistent with recent positive selection driving a European-specific decrease inANTXR2expression in several non-immune tissues affected by anthrax toxins. Our observations fit a model in which humans adapted to anthrax disease following early ecological changes associated with hunting and scavenging, as well as a second period of adaptation after the rise of modern agriculture.
Motifs of the C-terminal Domain of MCM9 Direct Localization to Sites of Mitomycin-C Damage for RAD51 Recruitment
Authors: McKinzey David R. , Gomathinayagam Shivasankari , Griffin Wezley C. , Klinzing Kathleen N. , Jeffries Elizabeth P. , Rajkovic Aleksandar , Trakselis Michael A. 
Published: July 2020

AbstractThe MCM8/9 complex is implicated in aiding fork progression and facilitating homologous recombination (HR) in response to several DNA damage agents. MCM9 itself is an outlier within the MCM family containing a long C-terminal extension (CTE) comprising 42% of the total length, but with no known functional components and high predicted disorder. In this report, we identify and characterize two unique motifs within the primarily unstructured CTE that are required for localization of MCM8/9 to sites of mitomycin C (MMC) induced DNA damage. First, an unconventional ‘bipartite-like’ nuclear localization (NLS) motif consisting of two positively charged amino acid stretches separated by a long intervening sequence is required for the nuclear import of both MCM8 and MCM9. Second, a variant of the BRC motif (BRCv), similar to that found in other HR helicases, is necessary for localization to sites of MMC damage. The MCM9-BRCv directly interacts with and recruits RAD51 downstream to MMC-induced damage to aid in DNA repair. Patient lymphocytes devoid of functional MCM9 and discrete MCM9 knockout cells have a significantly impaired ability to form RAD51 foci after MMC treatment. Therefore, the disordered CTE in MCM9 is functionally important in promoting MCM8/9 activity and in recruiting downstream interactors; thus, requiring full length MCM9 for proper DNA repair.
Dopamine release and its control over early Pavlovian learning differs between the NAc core and medial NAc shell
Authors: Stelly Claire E. , Girven Kasey S. , Lefner Merridee J. , Fonzi Kaitlyn M. , Wanat Matthew J. 
Published: July 2020

AbstractDopamine neurons respond to cues to reflect the value of associated outcomes. These cue-evoked dopamine responses can encode the relative rate of reward in rats with extensive Pavlovian training. Specifically, a cue that always follows the previous reward by a short delay (high reward rate) evokes a larger dopamine response in the nucleus accumbens (NAc) core relative to a distinct cue that always follows the prior reward by a long delay (low reward rate). However, it was unclear if these reward rate dopamine signals are evident during early Pavlovian training sessions and across NAc subregions. To address this, we performed fast-scan cyclic voltammetry recordings of dopamine levels to track the pattern of cue- and reward-evoked dopamine signals in the NAc core and medial NAc shell. We identified regional differences in the progression of cue-evoked dopamine signals across training. However, the dopamine response to cues did not reflect the reward rate in either the NAc core or the medial NAc shell during early training sessions. Pharmacological experiments found that dopamine-sensitive conditioned responding emerged in the NAc core before the medial NAc shell. Together, these findings illustrate regional differences in NAc dopamine release and its control over behavior during early Pavlovian learning.
SCFCdc4ubiquitin ligase regulates synaptonemal complex formation during meiosis
Authors: Zhu Zhihui , Ismail Mohammad Bani , Shinohara Miki , Shinohara Akira 
Published: July 2020

AbstractHomologous chromosomes pair with each other during meiosis, culminating in the formation of the synaptonemal complex (SC), which is coupled with meiotic recombination. In this study, we showed that a meiosis-specific depletion mutant of a cullin (Cdc53) of the SCF (Skp-Cullin-F-box) ubiquitin ligase, which plays a critical role in cell cycle regulation during mitosis, is deficient in SC formation, but is proficient in the formation of crossovers, indicating uncoupling of meiotic recombination with SC formation in the mutant. Furthermore, the deletion of thePCH2gene encoding a meiosis-specific AAA+ ATPase suppresses SC-assembly defect induced byCDC53depletion. On the other hand, thepch2 cdc53double mutant is defective in meiotic crossover formation, suggesting the SC assembly with unrepaired DSBs. A temperature-sensitive mutant of theCDC4, which encodes a F-box protein of the SCF, shows similar meiotic defects to theCDC53depletion mutant. These suggest that SCFCdc4, probably SCFCdc4-dependnet protein ubiquitylation, regulates and collaborates with Pch2 in SC assembly and meiotic recombination.SummaryDuring meiosis, homologous chromosomes pair with each other and form the synaptonemal complex (SC). In this study, components of the SCF (Skp-Cullin-F-box) ubiquitin ligase, Cdc53 and Cdc4, are required for SC formation. A meiosis-specific AAA+ ATPase Pch2 antagonize the functions of Cdc53 and Cdc4 for proper SC assembly.
A novel approach for improving information security management and awareness for home environments
Authors: Alotaibi Fayez Ghazai , Clarke Nathan , Furnell Steven M. 
Published: July 2020

Purpose
The human factor is a major consideration in securing systems. A wide and increasing range of different technologies, devices, platforms, applications and services are being used every day by home users. In parallel, home users are also experiencing a range of different online threats and attacks and are increasingly being targeted as they lack the knowledge and awareness about potential threats and how to protect themselves. The increase in technologies and platforms also increases the burden upon a user to understand how to apply security across differing technologies, operating systems and applications. This results in managing the security across their technology portfolio increasingly more troublesome and time consuming. This paper aims to propose an approach that attempts to propose a system for improving security management and awareness for home users.

Design/methodology/approach
The proposed system is capable of creating and assigning different security policies for different digital devices in a user-friendly fashion. These assigned policies are monitored, checked and managed to review the user’s compliance with the assigned policies to provide bespoke awareness content based on the user’s current needs.

Findings
A novel framework was proposed for improving information security management and awareness for home users. In addition, a mock-up design was developed to simulate the proposed approach to visualise the main concept and the functions which might be performed when it is deployed in a real environment. A number of different scenarios have been simulated to show how the system can manage and deal with different types of users, devices and threats. In addition, the proposed approach has been evaluated by experts in the research domain. The overall feedback is positive, constructive and encouraging. The experts agreed that the identified research problem is a real problem. In addition, they agreed that the proposed approach is usable, feasible and effective in improving security management and awareness for home users.

Research limitations/implications
The proposed design of the system is a mock-up design without real data. Therefore, implementing the proposed approach in a real environment can provide the researcher with a better understanding of the effectiveness and the functionality of the proposed approach.

Practical implications
This study offers a framework and usable mock-up design which can help in improving information security management for home users.

Originality/value
Improving the security management and awareness for home users by monitoring, checking and managing different security controls and configurations effectively are the key to strengthen information security. Therefore, when home users have a good level of security management and awareness, this could protect and secure the home network and subsequently business infrastructure and services as well.
An intelligent robot for indoor substation inspection
Authors: Wang Chenjie , Yin Lu , Zhao Qing , Wang Wei , Li Chengyuan , Luo Bin 
Published: July 2020

PurposeTo ensure the safety of electric power supply, it is necessary to inspect substation equipment. With the dramatic increase in the number of substations, especially indoor substations, intelligent robot inspection has become an important development direction. This paper aims to describe the design of a trackless robot with a robotic arm, which is capable of navigating autonomously and inspecting the equipment in a narrow and complex indoor substation.Design/methodology/approachA robust four-wheel platform powered by electric motors is used to carry the robot. By fusing multiple-sensor data and visual markers, the robot achieves autonomous movement based on simultaneous localization and mapping. In addition, to accurately obtain the reading of meters located at height or in a narrow space, the robot is equipped with a newly designed visual servo robotic arm.FindingsIn practical application, the robot satisfies the requirements of substation inspection, improves work efficiency, saves costs and achieves good results. The robot is also approved by the relevant departments of the State Grid Corporation of China.Practical implicationsAfter stable operation in a substation for a period of one year, the robot shows high efficiency and stability, meeting the requirements of indoor substation inspection. Meanwhile, the robot greatly promoted the realization of indoor and outdoor integrated substation automatic inspection, and is expected to be further applied in other industrial inspection sites, including mine, tunnel and nuclear power plant.Originality/valueDue to the complex indoor environment, most of the existing inspection robots are only used outdoors, and there are no good trackless inspection robots for use indoors. The proposed robot is a trackless intelligent inspection robot for use in indoor substations. The robot features a number of important modules, including an autonomous localization and navigation module and a visual servo manipulator module, which can be used in narrow spaces or at height.