bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spike sorting with Gaussian mixture models
Authors: Souza Bryan C. , Lopes-dos-Santos Vítor , Bacelo João , Tort Adriano B. L. 
Published: January 2018

AbstractThe shape of extracellularly recorded action potentials is a product of several variables, such as the biophysical and anatomical properties of the neuron and the relative position of the electrode. This allows for isolating spikes of different neurons recorded in the same channel into clusters based on waveform features. However, correctly classifying spike waveforms into their underlying neuronal sources remains a main challenge. This process, called spike sorting, typically consists of two steps: (1) extracting relevant waveform features (e.g., height, width), and (2) clustering them into non-overlapping groups believed to correspond to different neurons. In this study, we explored the performance of Gaussian mixture models (GMMs) in these two steps. We extracted relevant waveform features using a combination of common techniques (e.g., principal components and wavelets) and GMM fitting parameters (e.g., standard deviations and peak distances). Then, we developed an approach to perform unsupervised clustering using GMMs, which estimates cluster properties in a data-driven way. Our results show that the proposed GMM-based framework outperforms previously established methods when using realistic simulations of extracellular spikes and actual extracellular recordings to evaluate sorting performance. We also discuss potentially better techniques for feature extraction than the widely used principal components. Finally, we provide a friendly graphical user interface in MATLAB to run our algorithm, which allows for manual adjustment of the automatic results.
Conserved collateral susceptibility networks in diverse clinical strains of Escherichia coli
Authors: Podnecky Nicole L. , Fredheim Elizabeth G. A. , Kloos Julia , Sørum Vidar , Primicerio Raul , Roberts Adam P. , Rozen Daniel E. , Samuelsen Ørjan , Johnsen Pål J. 
Published: January 2018

AbstractThere is urgent need to develop novel treatment strategies to reduce antimicrobial resistance. Collateral sensitivity (CS), where resistance to one antimicrobial increases susceptibility to other drugs, is a uniquely promising strategy that enables selection against resistance during treatment. However, using CS-informed therapy depends on conserved CS networks across genetically diverse bacterial strains. We examined CS conservation in 10 clinical strains of E. coli resistant to four clinically relevant antibiotics. Collateral susceptibilities of these 40 resistant mutants were then determined against a panel of 16 antibiotics. Multivariate statistical analyses demonstrate that resistance mechanisms, in particular efflux-related mutations, as well as relative fitness were principal contributors to collateral changes. Moreover, collateral responses shifted the mutant selection window suggesting that CS-informed therapies could affect evolutionary trajectories of antimicrobial resistance. Our data allow optimism for CS-informed therapy and further suggest that early detection of resistance mechanisms is important to accurately predict collateral antimicrobial responses.
Trait and state patterns of basolateral amygdala connectivity at rest are related to endogenous testosterone and aggression in healthy young women
Authors: Buades-Rotger Macià , Engelke Christin , Krämer Ulrike M. 
Published: January 2018

AbstractThe steroid hormone testosterone (T) has been suggested to influence reactive aggression upon its action on the basolateral amygdala (BLA), a key brain region for threat detection. However, it is unclear whether T modulates resting-state functional connectivity (rsFC) of the BLA, and whether this predicts subsequent aggressive behavior. Aggressive interactions themselves, which often induce changes in T concentrations, could further alter BLA rsFC, but this too remains untested. Here we investigated the effect of endogenous T on rsFC of the BLA at baseline as well as after an aggressive encounter, and whether this related to behavioral aggression in healthy young women (n=39). Pre-scan T was negatively correlated with basal rsFC between BLA and left superior temporal gyrus (STG), which in turn predicted increased aggression. BLA-STG coupling at rest might thus underlie hostile readiness in low-T women. In addition, coupling between the BLA and the right superior parietal lobule (SPL), a brain region involved in higher-order perceptual processes, was reduced in aggressive participants. On the other hand, post-task increases in rsFC between BLA and medial orbitofrontal cortex (mOFC) were linked to reduced aggression, consistent with the established notion that the mOFC regulates amygdala activity in order to curb aggressive impulses. Finally, competition-induced changes in T were associated with increased coupling between the BLA and the right lateral OFC, but this effect was unrelated to aggression. We thus identified connectivity patterns that prospectively predict aggression in women, and showed how aggressive interactions in turn impact these neural systems.
Engineering Translational Resource Allocation Controllers: Mechanistic Models, Design Guidelines, and Potential Biological Implementations
Authors: Darlington Alexander P.S. , Kim Juhyun , Jiménez José I. , Bates Declan G. 
Published: January 2018

AbstractThe use of orthogonal ribosomes in combination with dynamic resource allocation controllers is a promising approach for relieving the negative effects of cellular resource limitations on the modularity of synthetic gene circuits. Here, we develop a detailed mechanistic model of gene expression and resource allocation, which when simplified to a tractable level of complexity, allows the rational design of translational resource allocation controllers. Analysis of this model reveals a fundamental design trade-off; that reducing coupling acts to decrease gene expression. Through a sensitivity analysis of the experimentally tuneable controller parameters, we identify how each controller design parameter affects the overall closed-loop behaviour of the system, leading to a detailed set of design guidelines for optimally managing this trade-off. Based on our designs, we evaluated a number of alternative potential experimental implementations of the proposed system using commonly available biological components. Finally, we show that the controller is capable of dynamically allocating ribosomes as needed to restore modularity in a number of more complex synthetic circuits, such as the repressilator, and activation cascades composed of multiple interacting modules.
A low-threshold potassium current enhances sparseness and reliability in a model of avian auditory cortex
Authors: Bjoring Margot C. , Meliza C. Daniel 
Published: January 2018

AbstractBirdsong is a complex vocal communication signal, and like humans, birds need to discriminate between similar sequences of sound with different meanings. The caudal mesopallium (CM) is a cortical-level auditory area implicated in song discrimination. CM neurons respond sparsely to conspecific song and are tolerant of production variability. Intracellular recordings in CM have identified a diversity of intrinsic membrane dynamics, which could contribute to the emergence of these higher-order functional properties. We investigated this hypothesis using a novel linear-dynamical cascade model that incorporated detailed biophysical dynamics to simulate auditory responses to birdsong. Neuron models that included a low-threshold potassium current present in a subset of CM neurons showed increased selectivity and coding efficiency relative to models without this current. These results demonstrate the impact of intrinsic dynamics on sensory coding and the importance of including the biophysical characteristics of neural populations in simulation studies.
Homologous recombination and transposon propagation shapes the population structure of an organism from the deep subsurface with minimal metabolism
Authors: Probst Alexander J , Banfield Jillian F. 
Published: January 2018

ABSTRACTDPANN archaea are primarily known based on genomes from metagenomes and single cells. We reconstructed a complete population genome for Candidatus “Forterrea”, a Diapherotrite with a predicted symbiotic lifestyle probably centered around nucleotide metabolism and RuBisCO. Genome-wide analysis of sequence variation provided insights into the processes that shape its population structure in the deep subsurface. The genome contains many transposons, yet reconstruction of a complete genome from a short-read insert dataset was possible because most occurred only in some individuals. Accuracy of the final reconstruction could be verified because the genome displays the pattern of cumulative GC skew known for some archaea but more typically associated with bacteria. Sequence variation is highly localized, and most pronounced around transposons and relatively close to the origin of replication. Patterns of variation are best explained by homologous recombination, a process previously not described for DPANN archaea.
Nuclear and mitochondrial genomes of the hybrid fungal plant pathogen Verticillium longisporum display a mosaic structure
Authors: Depotter Jasper R.L. , Beveren Fabian van , C.M. van den Berg Grardy , Wood Thomas A. , Thomma Bart P.H.J. , Seidl Michael F. 
Published: January 2018

ABSTRACTAllopolyploidization, genome duplication through interspecific hybridization, is an important evolutionary mechanism that can enable organisms to adapt to environmental changes or stresses. This increased adaptive potential of allopolyploids can be particularly relevant for plant pathogens in their quest for host immune response evasion. Allodiploidization likely caused the shift in host range of the fungal pathogen plant Verticillium longisporum, as V. longisporum mainly infects Brassicaceae plants in contrast to haploid Verticillium spp. In this study, we investigated the allodiploid genome structure of V. longisporum and its evolution in the hybridization aftermath. The nuclear genome of V. longisporum displays a mosaic structure, as numerous contigs consists of sections of both parental origins. V. longisporum encountered extensive genome rearrangements, whereas the contribution of gene conversion is negligible. Thus, the mosaic genome structure mainly resulted from genomic rearrangements between parental chromosome sets. Furthermore, a mosaic structure was also found in the mitochondrial genome, demonstrating its bi-parental inheritance. In conclusion, the nuclear and mitochondrial genomes of V. longisporum parents interacted dynamically in the hybridization aftermath. Conceivably, novel combinations of DNA sequence of different parental origin facilitated genome stability after hybridization and consecutive niche adaptation of V. longisporum.
The Innate Immune Response to Ischemic Injury: a Multiscale Modeling Perspective
Authors: Dimitrova Elena , Caromile Leslie A. , Laubenbacher Reinhard , Shapiro Linda H. 
Published: January 2018

ABSTRACTBackgroundCell death as a result of ischemic injury triggers powerful mechanisms regulated by germline-encoded Pattern Recognition Receptors (PRRs) with shared specificity that recognize invading pathogens and endogenous ligands released from dying cells, and as such are essential to human health. Alternatively, dysregulation of these mechanisms contributes to extreme inflammation, deleterious tissue damage and impaired healing in various diseases. The Toll-like receptors (TLRs) are a prototypical family of PRRs that may be powerful anti-inflammatory targets if agents can be designed that antagonize their harmful effects while preserving host defense functions. This requires an understanding of the complex interactions and consequences of targeting the TLR-mediated pathways as well as technologies to analyze and interpret these, which will then allow the simulation of perturbations targeting specific pathway components, predict potential outcomes and identify safe and effective therapeutic targets.ResultsWe constructed a multiscale mathematical model that spans the tissue and intracellular scales, and captures the consequences of targeting various regulatory components of injury-induced TLR4 signal transduction on potential pro-inflammatory or pro-healing outcomes. We applied known interactions to simulate how inactivation of specific regulatory nodes affects dynamics in the context of injury and to predict phenotypes of potential therapeutic interventions. We propose rules to link model behavior to qualitative estimates of pro-inflammatory signal activation, macrophage infiltration, production of reactive oxygen species and resolution. We tested the validity of the model by assessing its ability to reproduce published data not used in its construction.ConclusionsThese studies will enable us to form a conceptual framework focusing on TLR4-mediated ischemic repair to assess potential molecular targets that can be utilized therapeutically to improve efficacy and safety in treating ischemic/inflammatory injury.
Identification of human vaccinees that possess antibodies targeting the egg-adapted hemagglutinin receptor binding site of an H1N1 influenza vaccine strain
Authors: Garretson Tyler A. , Petrie Joshua G. , Martin Emily T. , Monto Arnold S. , Hensley Scott E. 
Published: January 2018

AbstractHuman influenza viruses passaged in eggs often acquire mutations in the hemagglutinin (HA) receptor binding site (RBS). To determine if egg-adapted H1N1 vaccines commonly elicit antibodies targeting the egg-adapted RBS of HA, we completed hemagglutinin-inhibition assays with A/California/7/2009 HA and egg-adapted A/California/7/2009-X-179A HA using sera collected from 159 humans vaccinated with seasonal influenza vaccines during the 2015-16 season. We found that ~5% of participants had ≥4-fold higher antibody titers to the egg-adapted viral strain compared to wild type viral strain. We used reverse-genetics to demonstrate that a single egg-adapted HA RBS mutation (Q226R) was responsible for this phenotype.
Environmental activity management: its use and impact on environmental performance
Authors: Phan Thanh Nguyet , Baird Kevin , Su Sophia 
Published: January 2018

PurposeThe study provides an insight into the application and usefulness of activity management (AM) principles in an environmental context. Specifically, the purpose of this paper is to examine the extent of use of environmental activity management (EAM) utilising Gosselin’s (1997) three levels of AM (namely, environmental activity analysis (EAA), environmental activity cost analysis (EACA), and environmental activity-based costing (EABC)). The study also examines the association between EAM and environmental performance, and the role of decision quality as a mediator in this relationship.Design/methodology/approachData were collected from 208 Australian organisations across different industries using a mail survey questionnaire.FindingsThe results indicate a relatively high extent of EAA use but a low extent of use of EACA and EABC. In addition, organisations using each level of EAM to a greater extent were found to experience higher levels of environmental performance. Furthermore, the relationship between EAA and EABC with environmental performance was found to be mediated by decision quality.Practical implicationsThe findings suggest that organisations should endeavour to increase their use of EAM, and modify their existing costing systems to consider the drivers and costs of environmental activities.Originality/valueThis is the first study to empirically examine the extent of use of EAM and its association with environmental performance.
The role of accounting in transforming public tertiary institutions in New Zealand
Authors: Narayan Anil , Stittle John 
Published: January 2018

Purpose
The purpose of this paper is to identify and evaluate the role and influence played by the discipline of accounting through its association with the multiple logics of government reforms to transform the public tertiary education sector in New Zealand.

Design/methodology/approach
The study adopts a case study approach utilising multiple data collection methods. Neo-institutional theory provides an insightful complement to neo-liberalism and enhances the understanding of institutional logics driving government reforms and the transformation of public tertiary institutions.

Findings
The findings reveal that accounting has become a powerful conduit for the exercise of the neo-liberalism reforms by government and implemented by managerial control over public tertiary education institutions.

Research limitations/implications
By addressing a gap in the literature, the paper shows how political and economic neo-liberal policies have been implemented in tertiary education with the discipline of accounting being adopted as a prime driver of these reforms. The paper has significant implications for educational management, academics and learners in understanding how and why the inherent nature, objectives and processes of the overall educational experience have undergone a radical reformation.

Originality/value
New Zealand is one of the first countries to implement these educational reforms and adopted “accounting technologies” to reduce costs and improve performance. But the reality has often been very different. Most of the government’s original objectives have not been fulfilled and the reforms have been costly for the academic profession. This paper provides a valuable source of learning for academics, managers and politicians.
Preliminary framework to manage tenant satisfaction in facilities management service encounters
Authors: Karunasena Gayani , Vijerathne Dimuthu , Muthmala Harsha 
Published: January 2018

PurposeHomogeneity in the main business of renting office spaces among commercial facilities has led to fierce competition. To retain tenant attractiveness, many are now concerned about the quality of facilities management (FM) services in addition to the rent, office space and location. The quality of FM service can be attained with successful service encounters. Thus, this paper aims to establish an initial platform on which tenant satisfaction in FM service encounters can be achieved.Design/methodology/approachThe preliminary survey focused on gaining insights into FM encounters in commercial sector and applicability of service attributes under SERVQUAL model. The detailed survey concentrated on determining tenant perceptions on satisfactory levels of service attributes developed in the preliminary study and relationships between FM encounters and different service attributes. The collection of descriptive and inferential statistics was used to analyze the results.FindingsThis study’s findings reveal assurance and empathy to be highly correlated to tenant satisfaction, while other attributes are less correlated. However, perceptions of satisfaction levels of tenants on tangibility and reliability provides contradictory results to its correlation values. Satisfaction level in remote service encounters is lower compared to phone and face-to-face encounters. Complexity and management concerns toward physical facilities are imperative to uplift satisfaction in remote encounters.Research limitations/implicationsThe scope of study was limited to FM encounters in Sri Lankan Grade “A” commercial office properties with high quality standard finishes, state-of-the-art systems, exceptional accessibility and a definite market presence in Colombo.Originality/valueThe study developed a preliminary framework that guides users to identify the best combinations of service attributes with respective FM encounters, where tenant satisfaction needs to be achieved.
Does lending to women lower sustainability of microfinance institutions? Moderating role of national cultures
Authors: Kittilaksanawong Wiboon , Zhao Hongyu 
Published: January 2018

PurposeThis study aims to investigate whether lending to women decreases sustainability of microfinance institutions (MFIs) and how regional characteristics where MFIs are located moderate this effect.Design/methodology/approachFinancial and operating data of MFIs and national cultures are available from the MIX Market database and the Hofstede’s publications. These data are analyzed by using multiple regression models with the financial self-sustainability, proportion of women borrowers in the MFI’s lending portfolio, and dimensions of national culture as dependent, explanatory and moderating variables.FindingsLending to women tends to reduce sustainability of MFIs. This negative effect is more pronounced in countries ranking higher on power distance and individualism, but the effect is less serious in countries ranking higher on masculinity and uncertainty avoidance.Originality/valueMany studies demonstrate that MFIs improve their repayment rates by targeting women borrowers. The increase in repayment rates, however, may not always improve their sustainability. Further, as microfinance industry increasingly diversifies geographically, regional characteristics where MFIs are located play a vital contingent role in their sustainability.
Rural-to-urban migration in Vietnam: conceptualized youth’s vulnerabilities in the city
Authors: Pham Nhu Ngoc K. , Do Mai , Bui Van H. , Nguyen Giang T. 
Published: January 2018

Purpose
Vietnam is experiencing high rates of young adult migration from rural hometowns to urban cities in search of new economic and social opportunities. However, limited internal migration research has examined the well-being of this population once they are in the urban destinations, as well as their interactions with the new lifestyles in the cities. Thus, the purpose of this paper is to explore the social transition of young Vietnamese migrants into city life.

Design/methodology/approach
In-depth interviews were conducted among ten female and six male temporary unmarried migrants, between ages of 18 and 25 years, currently living in Ha Noi through purposive sampling.

Findings
Despite a higher income in the city, young migrants often suffer from physical and mental health strains that decrease their overall well-being, caused by the factors such as barriers to assimilation to new lifestyles, continued attachment to origin hometowns, financial pressures, and poor living conditions. Important aspects in pre-migration expectations and actual experiences influenced the psychosocial well-being of these young migrants as they transitioned into adulthood during their migration process. Migration to the city and assimilation into city life also changed young migrants’ views on lifestyles and behaviors often considered misconducts in their rural hometowns, such as premarital sex. Female migrants faced higher stigmatization compared to male migrants, often described by fellow migrants as becoming “loose” in the new city.

Originality/value
The study findings highlight the important gender-specific implications for health services and programs to improve young migrants’ well-being in the city.