bluuebunny/crossref_metadata_2025_split huggingface dataset:
FishNET: An automated relational database for zebrafish colony management
Authors: Gutierrez Abiud Cantu , Gutierrez Manuel Cantu , Rhyner Alexander M. , Ruiz Oscar E. , Eisenhoffer George T. , Wythe Joshua D. 
Published: December 2018

ABSTRACTThe zebrafishDanio reriois a powerful model system to study the genetics of development and disease. However, maintenance of zebrafish husbandry records is both time intensive and laborious, and a standardized way to manage and track the large amount of unique lines in a given laboratory or centralized facility has not been embraced by the field. Here we present FishNet, an intuitive, open source, relational database for managing data and information related to zebrafish husbandry and maintenance. By creating a “virtual facility”, FishNET enables users to remotely inspect the rooms, racks, tanks and lines within a given facility. Importantly, FishNET scales from one laboratory, to an entire facility with several laboratories, to multiple facilities, generating a cohesive laboratory and community-based platform. Automated data entry eliminates confusion regarding line nomenclature and streamlines maintenance of individual lines, while flexible query forms allow researchers to retrieve database records based on user-defined criteria. FishNet also links associated embryonic and adult biological samples with data, such as genotyping results or confocal images, to enable robust and efficient colony management and storage of laboratory information. A shared calendar function with email notifications and automated reminders for line turnover, automated tank counts and census reports promote communication with both end-users and administrators. The expected benefits of FishNET are improved vivaria efficiency, increased quality control for experimental numbers, and flexible data reporting and retrieval. FishNet’s easy, intuitive record management and open source, end user-modifiable architecture provides an efficient solution to real-time zebrafish colony management for users throughout a facility and institution, and in some cases across entire research hubs.
Apigenin as a Candidate Prenatal Treatment for Trisomy 21: Effects in Human Amniocytes and the Ts1Cje Mouse Model
Authors: Guedj Faycal , Pennings Jeroen LA , Siegel Ashley E , Alsebaa Fatimah , Massingham Lauren J , Tantravahi Umadevi , Bianchi Diana W 
Published: December 2018

ABSTRACTHuman fetuses with trisomy 21 (T21) have atypical brain development that is apparent sonographically in the second trimester. Prenatal diagnosis provides a potential opportunity to begin treatmentin utero. We hypothesize that by analyzing and integrating dysregulated gene expression and pathways common to humans with DS and mouse models we can discover novel targets for therapy. Here, we tested the safety and efficacy of apigenin (4’, 5, 7-trihydroxyflavone), identified using this approach, in both human amniocytes from fetuses with T21 and in the Ts1Cje mouse model. The experiments compared treated to untreated results in T21 and euploid cells, as well as in Ts1Cje mice and their wild-type littermate controls. T21 cells cultured with apigenin (2µM) had significantly reduced oxidative stress and improved antioxidant defense responsein vitro. Apigenin (333-400 mg/kg/day), mixed with chow, was initiated prenatally to the dams and fed to the pups over their lifetimes. There was no significant increase in birth defects or pup deaths resulting from prenatal apigenin treatment. Apigenin significantly improved several developmental milestones and spatial olfactory memory in Ts1Cje neonates. In addition, we noted sex-specific effects on exploratory behavior and long-term hippocampal memory in adult mice, with males showing significantly more improvement than females. Global gene expression analyses demonstrated that apigenin targets similar signaling pathways through common upstream regulators bothin vitroandin vivo. These studies provide proof-of-principle that apigenin has therapeutic effects in preclinical models of Down syndrome.ONE SENTENCE SUMMARYAs a candidate prenatal treatment for Down syndrome, apigenin improved oxidative stress/antioxidant capacity imbalance and reduced pathways associated with inflammation in human cells while improving aspects of behavior in the Ts1Cje mouse model.
The hippocampus encodes delay and value information during delay-discounting decision making
Authors: Masuda Akira , Sano Chie , Zhang Qi , Goto Hiromichi , McHugh Thomas J. , Fujisawa Shigeyoshi , Itohara Shigeyoshi 
Published: December 2018

SummaryThe hippocampus, a region critical for memory and spatial navigation, has been implicated in delay discounting, the decline in subjective reward value when a delay is imposed. However, how delay discounting is encoded in the hippocampus is poorly understood. Here we recorded from the hippocampal CA1 region of mice performing a delay-discounting decision-making task, where delay lengths and reward amounts were changed across sessions, and identified subpopulations of neurons in CA1 which increased or decreased their firing rate during long delays. The activity of both delay-active and -suppressive cells reflected delay length, reward amount, and arm position, however manipulating reward amount differentially impacted the two populations, suggesting distinct roles in the valuation process. Further, genetic deletion of NMDA receptor in hippocampal pyramidal cells impaired delay-discount behavior and diminished delay-dependent activity in CA1. Our results suggest that distinct subclasses of hippocampal neurons concertedly support delay-discounting decision in a manner dependent on NMDA receptor function.
Gene encoding a novel enzyme of LDH2/MDH2 family is lost in plant and animal genomes during transition to land
Authors: Puzakova L.V. , Puzakov M.V. , Soldatov A.A. 
Published: December 2018

AbstractL-lactate/malate dehydrogenases (LDH/MDH) and type 2 L-lactate/malate dehydrogenases (LDH2/MDH2) belong to NADH/NADPH-dependent oxidoreductases (anaerobic dehydrogenases). They form a large protein superfamily with multiple enzyme homologs found in all branches of life: from bacteria and archaea to eukaryotes, and play an essential role in metabolism. Here we describe the gene encoding a new enzyme of LDH2/MDH2 oxidoreductase family. This gene is found in genomes of all studied groups/classes of bacteria and fungi. In the plant kingdom this gene was observed only in algae, but not in bryophyta or spermatophyta. This gene is present in all taxonomic groups of animal kingdom beginning with protozoa, but is lost in lungfishes and other, higher taxa of vertebrates (amphibians, reptiles, avians and mammals). Since the gene encoding the new enzyme is found only in taxa associated with the aquatic environment, we named itAqE (aquatic enzyme). We demonstrated thatAqEgene is convergently lost in different independent lineages of animals and plants. Interestingly, the loss of the gene is consistently associated with transition from aquatic to terrestrial life forms, which suggests that this enzyme is essential in aquatic environment, but redundant or even detrimental in terrestrial organisms.
Qtlizer: comprehensive QTL annotation of GWAS results
Authors: Munz Matthias , Wohlers Inken , Simon Eric , Reinberger Tobias , Busch Hauke , Schaefer Arne S. , Erdmann Jeanette 
Published: December 2018

ABSTRACTExploration of genetic variant-to-gene relationships by quantitative trait loci such as expression QTLs is a frequently used tool in genome-wide association studies. However, the wide range of public QTL databases and the lack of batch annotation features complicate a comprehensive annotation of GWAS results. In this work, we introduce the tool “Qtlizer” for annotating lists of variants in human with associated changes in gene expression and protein abundance using an integrated database of published QTLs. Features include incorporation of variants in linkage disequilibrium and reverse search by gene names. Analyzing the database for base pair distances between best significant eQTLs and their affected genes suggests that the commonly used cis-distance limit of 1,000,000 base pairs might be too restrictive, implicating a substantial amount of wrongly and yet undetected eQTLs. We also ranked genes with respect to the maximum number of tissue-specific eQTL studies in which a most significant eQTL signal was consistent. For the top 100 genes we observed the strongest enrichment with housekeeping genes (P=2×10−6) and with the 10% highest expressed genes (P=0.005) after grouping eQTLs by r2>0.95, underlining the relevance of LD information in eQTL analyses. Qtlizer can be accessed via http://genehopper.de/qtlizer or by using the respective Bioconductor R-package (DOI: 10.18129/B9.bioc.Qtlizer).
Sequence learning recodes cortical representations instead of strengthening initial ones
Authors: Kalm Kristjan , Norris Dennis 
Published: December 2018

AbstractWe contrast two computational models of sequence learning. The associative learner posits that learning proceeds by strengthening existing association weights. Alternatively, recoding posits that learning creates new and more efficient representations of the learned sequences. Importantly, both models propose that humans act as optimal learners but capture different statistics of the stimuli in their internal model. Furthermore, these models make dissociable predictions as to how learning changes the neural representation of sequences. We tested these predictions by using fMRI to extract neural activity patters from the dorsal visual processing stream during a sequence recall task. We observed that only the recoding account can explain the similarity of neural activity patterns, suggesting that participants recode the learned sequences using chunks. We show that associative learning can theoretically store only very limited number of overlapping sequences, such as common in ecological working memory tasks, and hence an efficient learner should recode initial sequence representations.
Additive effect of contrast and velocity proves the role of strong excitatory drive in suppression of visual gamma response
Authors: Orekhova E.V. , Prokofyev A.O. , Nikolaeva A.Yu. , Schneiderman J.F. , Stroganova T.A. 
Published: December 2018

AbstractVisual gamma oscillations are generated through interactions of excitatory and inhibitory neurons and are strongly modulated by sensory input. A moderate increase in excitatory drive to the visual cortex via increasing contrast or motion velocity of drifting gratings results in strengthening of the gamma response (GR). However, increasing the velocity beyond some ‘transition point’ leads to the suppression of the GR. There are two theoretical models that can explain such suppression. The ‘excitatory drive’ model infers that, at high drifting rates, GR suppression is caused by excessive excitation of inhibitory neurons. Since contrast and velocity have an additive effect on excitatory drive, this model predicts that the GR ‘transition point’ for low-contrast gratings would be reached at a higher velocity, as compared to high-contrast gratings. The alternative ‘velocity tuning’ model implies that the GR is maximal when the drifting rate of the grating corresponds to the preferable velocity of the motion-sensitive V1 neurons. This model predicts that lowering contrast either will not affect the transition point or will shift it to a lower drifting rate. We tested these models with magnetoencephalography-based recordings of the GR during presentation of low (50%) and high (100%) contrast gratings drifting at four velocities. We found that lowering contrast led to a highly reliable shift of the GR suppression transition point to higher velocities, thus supporting the excitatory drive model. No effects of contrast or velocity were found for the alpha-beta response power. The results have important implications for the understanding of the neural mechanisms underlying gamma oscillations and the development of gamma-based biomarkers of brain disorders.
Deep Learning provides exceptional accuracy to ECoG-based Functional Language Mapping for epilepsy surgery
Authors: RaviPrakash Harish , Korostenskaja Milena , Castillo Eduardo M. , Lee Ki H. , Salinas Christine M. , Baumgartner James , Anwar Syed M. , Spampinato Concetto , Bagci Ulas 
Published: December 2018

AbstractThe success of surgical resection in epilepsy patients depends on preserving functionally critical brain regions, while removing pathological tissues. Being the gold standard, electro-cortical stimulation mapping (ESM) helps surgeons in localizing the function of eloquent cortex through electrical stimulation of electrodes placed directly on the cortical brain surface. Due to the potential hazards of ESM, including increased risk of provoked seizures, electrocorticography based functional mapping (ECOG-FM) was introduced as a safer alternative approach. However, ECoG-FM has a low success rate when compared to the ESM. In this study, we address this critical limitation by developing a new algorithm based on deep learning for ECoG-FM and thereby we achieve an accuracy comparable to ESM in identifying eloquent language cortex. In our experiments, with 11 epilepsy patients who underwent presurgical evaluation (through deep learning-based signal analysis on 637 electrodes), our proposed algorithm made an exceptional 23% improvement with respect to the conventional ECoG-FM analysis (∼60%). We obtained the state-of-the-art accuracy of 83.05% in identifying language regions, which has never been achieved before. Our findings have demonstrated, for the first time, that deep learning powered ECoG-FM can serve as a stand-alone modality and avoid likely hazards of the ESM in epilepsy surgery. Hence, reducing the potential for developing post-surgical morbidity in the language function.
Non-random sister chromatid segregation mediates rDNA copy number maintenance in Drosophila
Authors: Watase George J. , Yamashita Yukiko M. 
Published: December 2018

AbstractAlthough considered to be exact copies of each other, sister chromatids can segregate non-randomly in some cases. For example, sister chromatids of the X and Y chromosomes segregate non-randomly during asymmetric division of male germline stem cells (GSCs) in D. melanogaster. Here we identify that the ribosomal DNA (rDNA) loci, which are located on the X and Y chromosomes, and an rDNA-binding protein, Indra, are required for non-random sister chromatid segregation (NRSS). We provide the evidence that NRSS is a mechanism by which GSCs recover rDNA copy number, which occurs through unequal sister chromatid exchange, counteracting the spontaneous copy number loss that occurs during aging. Our study reveals an unexpected role for NRSS in maintaining germline immortality through maintenance of a vulnerable genomic element, rDNA.One Sentence SummaryrDNA copy number maintenance by non-random sister chromatid segregation contributes to germline immortality in Drosophila
Digital trade in Latin America: mapping issues and approaches
Authors: Aguerre Carolina 
Published: December 2018

Purpose
In Latin America, digital trade is still a marginal issue in the internet policy and governance debate, as well as in the trade regime. However, there are signs that this is beginning to change. This paper aims to discuss why this is changing and how, against the backdrop of the internet governance field.

Design/methodology/approach
The research has used a mixed methods approach based on interviews and participant observation in one regional process, as well as an extensive literature review and document analysis.

Findings
There is a current scenario for expanding the digital trade agenda in the regional commercial blocs with the aim of rapidly incorporating them to a process of digitization that will be challenging their economic foundations. The tangibility of the impact of the expanding digital economy is much more prevalent than other internet governance debates, and these initiatives seem to be adopting a pragmatic approach, rather than questioning the existing rules that govern the trade and the internet regimes. There are significant challenges emerging from a fragmented institutional background for trade-related policy in the region and the digital single market might be one of the solutions. Finally, domestic coordination among competing laws regarding data protection and their enforcement without conflicting with cross border data flows will be a challenge to be addressed.

Originality/value
There is a lack of evidence-based research on the subject in the region. Many of the accounts stem from normative perspectives (many from scholars with legal backgrounds). This paper explores the connections between the internet governance regime and the emerging digital trade based on existing policies and processes.
Towards a new web of rules
Authors: Wright Chris F. , Wood Alex J. , Trevor Jonathan , McLaughlin Colm , Huang Wei , Harney Brian , Geelan Torsten , Colfer Barry , Chang Cheng , Brown William 
Published: December 2018

PurposeThe purpose of this paper is to review “institutional experimentation” for protecting workers in response to the contraction of the standard employment relationship and the corresponding rise of “non-standard” forms of paid work.Design/methodology/approachThe paper draws on the existing research and knowledge base of the authors as well as a thorough review of the extant literature relating to: non-standard employment contracts; sources of labour supply engaging in non-standard work; exogenous pressures on the employment relationship; intermediaries that separate the management from the control of labour; and entities that subvert the employment relationship.FindingsPost-war industrial relations scholars characterised the traditional regulatory model of collective bargaining and the standard employment contract as a “web of rules”. As work relations have become more market mediated, new institutional arrangements have developed to govern these relations and regulate the terms of engagement. The paper argues that these are indicative of an emergent “patchwork of rules” which are instructive for scholars, policymakers, workers’ representatives and employers seeking solutions to the contraction of the traditional regulatory model.Research limitations/implicationsWhile the review of the institutional experimentation is potentially instructive for developing solutions to gaps in labour regulation, a drawback of this approach is that there are limits to the realisation of policy transfer. Some of the initiatives discussed in the paper may be more effective than others for protecting workers on non-standard contracts, but further research is necessary to test their effectiveness including in different contexts.Social implicationsThe findings indicate that a task ahead for the representatives of government, labour and business is to determine how to adapt the emergent patchwork of rules to protect workers from the new vulnerabilities created by, for example, employer extraction and exploitation of their individual bio data, social media data and, not far off, their personal genome sequence.Originality/valueThe paper addresses calls to examine the “institutional intersections” that have informed the changing ways that work is conducted and regulated. These intersections transcend international, national, sectoral and local units of analysis, as well as supply chains, fissured organisational dynamics, intermediaries and online platforms. The analysis also encompasses the broad range of stakeholders including businesses, labour and community groups, nongovernmental organisations and online communities that have influenced changing institutional approaches to employment protection.
Multi-energy combined peak dispatching system synthetic benefit evaluation based on variable weight theory and matter-element extension model
Authors: Song Zongyun , Zhang Jian , Xiao XInli , Niu Dongxiao 
Published: December 2018

Purpose
To improve power system peak dispatching ability, connecting energy-storage device such as electric vehicle (EV) and regenerative electric heater (REH) to power grid is a good choice.

Design/methodology/approach
This paper establishes a multi-energy combined peak dispatching system MCPDS which includes EV, REH and wind power. The matter-element extension model based on improved variable weight theory is applied to evaluate MCPDS synthetic benefit.

Findings
The research shows that the MCPDS established in this paper performs excellently in security benefit, economic benefit, social benefit and environmental benefit.

Originality/value
With the assistance of energy storage devices such as EV and REH, the electrical system peak dispatching ability and power system operation efficiency has improved. More devices with energy-storage ability should be introduced into electrical power system to improve its synthetic benefit.
Role of organizational career websites for employer brand development
Authors: Gunesh Priya , Maheshwari Vishwas 
Published: December 2018

PurposeThe paper aims to demonstrate the utilization of banks’ career website for publicizing the employer branding strategy to enable effective strategic talent relationship management through talent attraction, engagement and retention.Design/methodology/approachA qualitative approach using purposive sample comprising HR professionals involving HR directors, reward managers and talent relationship managers, participated in semi-structured interviews.FindingsThis paper provides empirical insights on the use of career websites to disseminate the employer brand. The findings reveal the presence of recruitment orientation career websites across the banking sector. It also conveys HR practitioners’ suggestions for revamping the banks’ career websites to a more screening orientation approach for greater interactivity by both the internal and external talent pools.Research limitations/implicationsThe paper depicts the importance attributed around the utilization of career websites in promoting the employer brand by the HR community across the banking sector. It provides clear insights about the specific contents of career websites to enable sustainable talent attraction, engagement and retention.Originality/valueThis paper provides a qualitative insight to the study of employer branding and career websites. Whereas most previous research on career websites have been of a quantitative nature relying predominantly on fictitious websites, having mostly undergraduate students as research participants. This study contributes enormously to the existing literature and practice by unveiling the perceptions of HR professionals on the dissemination of the employer brand through the career website.