bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D bioprinting of co-cultured osteogenic spheroids for bone tissue fabrication
Authors: Heo Dong Nyoung , Ayan Bugra , Dey Madhuri , Banerjee Dishary , Wee Hwabok , Lewis Gregory S. , Ozbolat Ibrahim T. 
Published: June 2020

AbstractConventional top-down approaches in tissue engineering involving cell seeding on scaffolds have been widely used in bone engineering applications. However, scaffold-based bone tissue constructs have had limited clinical translation due to constrains in supporting scaffolds, minimal flexibility in tuning scaffold degradation, and low achievable cell seeding density as compared with native bone tissue. Here, we demonstrate a pragmatic and scalable bottom-up method, inspired from embryonic developmental biology, to build three-dimensional (3D) scaffold-free constructs using spheroids as building blocks. Human umbilical vein endothelial cells (HUVECs) were introduced to human mesenchymal stem cells (hMSCs) (hMSC/HUVEC) and spheroids were fabricated by an aggregate culture system. Bone tissue was generated by induction of osteogenic differentiation in hMSC/HUVEC spheroids for 10 days, with enhanced osteogenic differentiation and cell viability in the core of the spheroids compared to hMSC-only spheroids. Aspiration-assisted bioprinting (AAB) is a new bioprinting technique which allows precise positioning of spheroids (11% with respect to the spheroid diameter) by employing aspiration to lift individual spheroids and bioprint them onto a hydrogel. AAB facilitated bioprinting of scaffold-free bone tissue constructs using the pre-differentiated hMSC/HUVEC spheroids. These constructs demonstrated negligible changes in their shape for two days after bioprinting owing to the reduced proliferative potential of differentiated stem cells. Bioprinted bone tissues showed interconnectivity with actin-filament formation and high expression of osteogenic and endothelial-specific gene factors. This study thus presents a viable approach for 3D bioprinting of complex-shaped geometries using spheroids as building blocks, which can be used for various applications including but not limited to, tissue engineering, organ-on-a-chip and microfluidic devices, drug screening and, disease modeling.
Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection
Authors: de Almeida Rita M.C. , Thomas Gilberto L. , Glazier James A. 
Published: June 2020

AbstractTo understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1in vitroinfection of a human lung epithelial cell line. Transcriptograms, a Bioinformatics tool to analyze genome-wide gene expression data, allow us to define an appropriate context-dependent threshold for mechanistic relevance of gene differential expression. Without knowing in advance which genes are relevant, classical analyses detecteverygene with statistically-significant differential expression, leaving us with too many genes and hypotheses to be useful. Using a Transcriptogram-based top-down approach, we identified three major, differentially-expressed gene sets comprising 219 mainly immune-response-related genes. We identified timescales for alterations in mitochondrial activity, signaling and transcription regulation of the innate and adaptive immune systems and their relationship to viral titer. At the individual-gene level, EGR3 was significantly upregulated in infected cells. Similar activation in T-cells and fibroblasts in infected lung could explain the T-cell anergy and eventual fibrosis seen in SARS-CoV-1 infection. The methods can be applied to RNA data sets for SARS-CoV-2 to investigate the origin of differential responses in different tissue types, or due to immune or preexisting conditions or to compare cell culture, organoid culture, animal models, and human-derived samples.
Uncovering temporally sensitive targeting motifs for traumatic brain injury via phage display
Authors: Martinez Briana I. , Mousa Gergey Alzaem , Fleck Kiera , MacCulloch Tara , Diehnelt Chris W. , Stephanopoulos Nicholas , Stabenfeldt Sarah E. 
Published: June 2020

AbstractThe heterogeneous injury pathophysiology of traumatic brain injury (TBI) is a barrier to developing highly sensitive and specific diagnostic tools. Embracing neural injury complexity is critical for the development and advancement of diagnostics and therapeutics. The current study employs a unique discovery pipeline to identify targeting motifs that recognize specific phases of TBI pathology. This pipeline entailsin vivobiopanning with a domain antibody (dAb) phage display library, next generation sequencing (NGS) analysis, and peptide synthesis. Here, we identify targeting motifs based on the HCDR3 structure of dAbs for acute (1 day) and subacute (7 days) post-injury timepoints using a mouse controlled cortical impact model. Their bioreactivity was validated using immunohistochemistry and candidate target epitopes were identified via immunoprecipitation-mass spectrometry. The acute targeting motif recognizes targets associated with metabolic and mitochondrial dysfunction whereas the subacute motif was largely associated with neurodegenerative processes. This phage display biomarker discovery pipeline for TBI successfully achieved discovery of temporally specific TBI targeting motif/epitope pairs that will advance the TBI diagnostics and therapeutics.
Dissociation of task engagement and arousal effects in auditory cortex and midbrain
Authors: Saderi Daniela , Schwartz Zachary P. , Heller Charlie R. , Pennington Jacob R. , David Stephen V. 
Published: June 2020

AbstractBoth generalized arousal and engagement in a specific task influence sensory neural processing. To isolate effects of these state variables in the auditory system, we recorded single-unit activity from primary auditory cortex (A1) and inferior colliculus (IC) of ferrets during a tone detection task, while monitoring arousal via changes in pupil size. We used a generalized linear model to assess the influence of task engagement and pupil size on sound-evoked activity. In both areas, these two variables affected independent neural populations. Pupil size effects were more prominent in IC, while pupil and task engagement effects were equally likely in A1. Task engagement was correlated with larger pupil; thus, some apparent effects of task engagement should in fact be attributed to fluctuations in pupil size. These results indicate a hierarchy of auditory processing, where generalized arousal enhances activity in midbrain, and effects specific to task engagement become more prominent in cortex.
Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks
Authors: Fagny Maud , Kuijjer Marieke Lydia , Stam Maike , Joets Johann , Turc Olivier , Rozière Julien , Pateyron Stéphanie , Venon Anthony , Vitte Clémentine 
Published: June 2020

AbstractEnhancers are important regulators of gene expression during numerous crucial processes including tissue differentiation across development. In plants, their recent molecular characterization revealed their capacity to activate the expression of several target genes through the binding of transcription factors. Nevertheless, identifying these target genes at a genome-wide level remains a challenge, in particular in species with large genomes, where enhancers and target genes can be hundreds of kilobases away. Therefore, the contribution of enhancers to regulatory network is still poorly understood in plants. In this study, we investigate the enhancer-driven regulatory network of two maize tissues at different stages: leaves at seedling stage and husks (bracts) at flowering. Using a systems biology approach, we integrate genomic, epigenomic and transcriptomic data to model the regulatory relationship between transcription factors and their potential target genes. We identify regulatory modules specific to husk and V2-IST, and show that they are involved in distinct functions related to the biology of each tissue. We evidence enhancers exhibiting binding sites for two distinct transcription factor families (DOF and AP2/ERF) that drive the tissue-specificity of gene expression in seedling immature leaf and husk. Analysis of the corresponding enhancer sequences reveals that two different transposable element families (TIR transposonMutatorand MITEPif/Harbinger) have shaped the regulatory network in each tissue, and that MITEs have provided new transcription factor binding sites that are involved in husk tissue-specificity.SignificanceEnhancers play a major role in regulating tissue-specific gene expression in higher eukaryotes, including angiosperms. While molecular characterization of enhancers has improved over the past years, identifying their target genes at the genome-wide scale remains challenging. Here, we integrate genomic, epigenomic and transcriptomic data to decipher the tissue-specific gene regulatory network controlled by enhancers at two different stages of maize leaf development. Using a systems biology approach, we identify transcription factor families regulating gene tissue-specific expression in husk and seedling leaves, and characterize the enhancers likely to be involved. We show that a large part of maize enhancers is derived from transposable elements, which can provide novel transcription factor binding sites crucial to the regulation of tissue-specific biological functions.
Can fMRI reveal the representation of syntactic structure in the brain?
Authors: Reddy Aniketh Janardhan , Wehbe Leila 
Published: June 2020

AbstractWhile studying semantics in the brain, neuroscientists use two approaches. One is to identify areas that are correlated with semantic processing load. Another is to find areas that are predicted by the semantic representation of the stimulus words. However, in the domain of syntax, most studies have focused only on identifying areas correlated with syntactic processing load. One possible reason for this discrepancy is that representing syntactic structure in an embedding space such that it can be used to model brain activity is a non-trivial computational problem. Another possible reason is that it is unclear if the low signal-to-noise ratio of neuroimaging tools such as functional Magnetic Resonance Imaging (fMRI) can allow us to reveal correlates of complex (and perhaps subtle) syntactic representations. In this study, we propose novel multi-dimensional features that encode information about the syntactic structure of sentences. Using these features and fMRI recordings of participants reading a natural text, we model the brain representation of syntax. First, we find that our syntactic structure-based features explain additional variance in the brain activity of various parts of the language system, even after controlling for complexity metrics that capture processing load. At the same time, we see that regions well-predicted by syntactic features are distributed in the language system and are not distinguishable from those processing semantics.
Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs
Authors: Shiver Anthony L. , Osadnik Hendrik , Peters Jason M. , Mooney Rachel A. , Wu Peter I. , Hu James C. , Landick Robert , Huang Kerwyn Casey , Gross Carol A. 
Published: June 2020

AbstractThe multi-subunit bacterial RNA polymerase (RNAP) and its associated regulators carry out transcription and integrate myriad regulatory signals. Numerous studies have interrogated the inner workings of RNAP, and mutations in genes encoding RNAP drive adaptation ofEscherichia colito many health- and industry-relevant environments, yet a paucity of systematic analyses has hampered our understanding of the fitness benefits and trade-offs from altering RNAP function. Here, we conduct a chemical-genetic analysis of a library of RNAP mutants. We discover phenotypes for non-essential insertions, show that clustering mutant phenotypes increases their predictive power for drawing functional inferences, and illuminate a connection between transcription and cell division. Our findings demonstrate that RNAP chemical-genetic interactions provide a general platform for interrogating structure-function relationshipsin vivoand for identifying physiological trade-offs of mutations, including those relevant for disease and biotechnology. This strategy should have broad utility for illuminating the role of other important protein complexes.
Exploring how institutions shape managerialist employment relations and work-life balance (WLB) challenges in Nigeria
Authors: Nwagbara Uzoechi 
Published: June 2020

PurposeThis study explores the nexus between institutions and managerialist employment relations and subsequent work-life balance (WLB) challenges for Nigerian employees. Through an exploratory approach, the paper investigates how institutions shape employment relations, which is characterised by systematic and normalised managerialist practices and lack of employee participation.Design/methodology/approachRelying on a qualitative, interpretive approach, this study explores the relationship between institutional pressures, managerialism and employment relations. 31 semi-structured interviews and nine focus group interviews data was used.FindingsThis paper found that institutions shape organisational practice, specifically employment relations and human resource management (HRM) practice generally through its normative tendency. The study also found that although managerialist employment relations leads to WLB challenges, Nigeria's unique context aggravates this situation constituting serious WLB challenges for workers.Research limitations/implicationsResearches dealing with the relationship between managerialism, employment relations and WLB are largely underdeveloped and under-theorised. HRM phenomena such as unhappy workforce, stress, lack of flexibility, burnout, turnover and turnover intention, associated with management practice, have major implications for engagement procedures and HRM strategies. However, the sample size used potentially limits generalisation including its qualitative approach.Originality/valueThis study contributes to the dearth of researches focusing on employer–employee relationship quality as a precursor to WLB challenges and a mediator between managerialist employment relations and WLB challenges. Additionally, the study contributes to the burgeoning WLB discourse from developing countries perspective, which is understudied. It also sheds light on how Nigeria's unique context can bring new insights into the nascent WLB discourse and its associated HRM practices.
Judicial exclusivity in actions against public authorities: civil procedure rule, O’Reilly and human rights
Authors: Ng May Yee 
Published: June 2020

Purpose
This paper aims to provide an account of the legal development concerning civilian right to pursue legal action against public authorities. Review includes historical recap of the state of law practiced prior to 1977 and the decision in the case of O’Reilly that forcefully limit individual’s right to bring action. Despite its blatant disregard of the relevant statute, the O’Reilly decision remains a valid precedent. The essay then considers subsequent law reform and the effect of the Human Rights Act 1998 in limiting the applicability of the O’Reilly principle. The essay aims to benefit law students and non-legal lay person.

Design/methodology/approach
The paper adopts a hermeneutics positivism approach in considering relevant case laws that is precedent to the matter under discussion. Thereupon, an interpretivism approach is applied to examine subsequent reforms and its impact on civilian right to seek justice.

Findings
Judicial exclusivity restrains right to seek justice, but is it not totally discredited due to public policy. UK membership in the EU is an obstacle to judicial sovereignty, but it is also an avenue to dilute exclusivity.

Social implications
This paper is presented in a simple easy-to-understand form that enable lay-person to understand the current state of law in matters concerning public law violation by public authorities and avenues available to them.

Originality/value
The paper contributes to reinforce understanding on the conflict between common law and statute, and current state of law concerning individual’s right to access to the court of law in cases related to public laws and public authorities.
Empirical evidence on the profitability of momentum trading strategies using ETFs
Authors: Yu Susana , Webb Gwendolyn 
Published: June 2020

PurposeWe extend empirical evidence on the profitability of momentum trading to the realm of plain-equity ETFs.Design/methodology/approachWe employ several ranking measures used in prior research, and for each we apply a traditional ranking based on total return, and a variation based only on the capital gain/loss portion of return.FindingsWhile we find that past momentum is not a strong predictor of future performance in our overall sample period, 2007 to June 2018, we find that the percent off 52-week high price results in positive performance in the recovery years following the financial crisis of 2008–2009.Research limitations/implicationsOur study is limited by the availability of ETF experience and data, and our test period covers just 2007 through June 2018. This period includes the financial crisis of 2008–2009, which previous research finding is associated with the momentum strategy's loss of profitability. When we exclude that period, we find evidence of a profitable momentum strategy based on the measure of percent off 52-week high price, enabling us to reject the null hypothesis that the momentum trading strategy is no longer profitable.Practical implicationsIt is profitable based on both return measures used in the rankings. Our finding of a profitable momentum trading strategy suggests that the null hypothesis that the momentum strategy is no longer profitable can be rejected.Originality/valueWhile perhaps not so strong as to reject the efficient markets hypothesis fully, our empirical findings are more consistent with a behavioral explanation and a market inefficiency. In view of the relative ease and low transactional costs of trading in ETFs, the markets have yet another opportunity to recognize an apparent mispricing and employ arbitrage based on it. To the extent that the relative ease of trading in ETFs makes momentum strategies easier to employ, the momentum anomaly might still be expected to disappear in an efficient market.
Scalp microbiota in members of a Japanese high school judo team including Trichophyton tonsurans carriers
Authors: Futatsuya Taketoshi , Ushigami Tsuyoshi , Nomura Fumie , Anzawa Kazushi , Mochizuki Takashi , Cho Otomi , Sugita Takashi 
Published: June 2020

AbstractTrichophyton tonsurans is a major causative fungus of human dermatophytosis, which has been isolated from contact sport players in Japan. The microbiome in the scalp of judoists with or without T. tonsurans infection was analyzed to investigate the correlation between T. tonsurans infection and microbiome profile. Among 30 members of the same judo team in a high school, samples were collected by scrubbing their scalp with shampoo hairbrushes; then, DNA was extracted directly from the obtained scales. Twenty‐seven datasets were subjects for microbiome analysis and T. tonsurans was detected in six members (no T. tonsurans‐positive participants had scalp lesions). Regarding the fungal microbiome, Cyphellophora were more abundant in the T. tonsurans‐positive group (TP) than T. tonsurans‐negative group (TN) (P < 0.05). Regarding the Malassezia microbiome, Malassezia caprae were more abundant in TP than TN (P < 0.01). Regarding the bacterial microbiome, Lactococcus, Actinobacillus, Beijerinckiaceae and Xanthomonas were more abundant in TP than TN (P < 0.05). Also, the Shannon diversity index revealed no significant diversity between TP and TN, and 3‐D principal coordinate analysis revealed no clear separation between TP and TN. There was practically no difference in microbiome between TP and TN, indicating that T. tonsurans could colonize humans regardless of their original microbiome. T. tonsurans coexisted with other fungi and bacteria without affecting species diversity in asymptomatic carriers. To our knowledge, this is the first investigation of the correlation between T. tonsurans infection and microbiome profile.
Crossing extreme habitat boundaries: Jack‐of‐all‐trades facilitates invasion but is eroded by adaptation to a master‐of‐one
Authors: Ord Terry J. , Hundt Peter J. 
Published: June 2020

AbstractThe invasion of new environments can be a key instigator of adaptive diversification, but the likelihood of such invasions succeeding can depend on the attributes of would‐be invaders. Chief among these seems to be a generalist or ‘jack‐of‐all‐trades’ phenotype.Yet, despite the obvious link between habitat transitions and adaptation, we know surprisingly little about how phenotypes that might initially allow taxa to transition between habitats subsequently evolve or influence post‐invasion differentiation.We tested how a generalist phenotype of a broad diet and behavioural plasticity in marine blenny fish has facilitated the repeated invasion of extreme environments—particularly land—and how the conditions post‐invasion have impacted that generalist phenotype and associated trophic morphology.Our data show that a wide diet and plasticity in being able to shift between environments freely have been instrumental in the progressive invasion of land by amphibious blennies. Once established, however, terrestrial blennies have experienced strong stabilizing selection for a restricted diet, little to no plasticity and a highly specialized morphology. Instead of promoting diversification, the invasion of land appears to offer only a limited niche for survival, constraining descendent blennies to a specific adaptive phenotype.While our study supports the view that generalism facilitates invasion and that habitat transitions instigate adaptation, it also shows a generalist strategy is not optimal for successful establishment and new environments may offer fewer (not more) opportunities for diversification. This has broad implications for how taxa might be expected to respond or adapt to abrupt environmental change more generally.A freeplain language summarycan be found within the Supporting Information of this article.
Assessing the potential of passive seismic receiver functions for ore body exploration
Authors: Subašić Senad , Piana Agostinetti Nicola , Bean Christopher J. 
Published: June 2020

ABSTRACTWe use a passive seismic high‐frequency receiver function method to image the shallow structure around a mine site. This is a relatively new application of a standard method for mapping major discontinuities in the crust and upper mantle at a scale small enough to be relevant in an exploration context. Data collected in a 21‐instrument array is inverted for isotropic velocity structure. The retrieved velocities in the south‐eastern part of the array match very well with available sonic log measurements in the top 800 m. Based on the differences in receiver function behaviour for stations across the array, recovered velocity profiles and their similarity to sonic log measurements, the target area is split into two separate regions along a north‐northeast trending line that correlates well to the strike of the dominant structure in the area – the Navan Fault. Our results demonstrate the ability of receiver functions to provide both qualitative and quantitative information in an exploration environment.