bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic changes in rhythmic and arrhythmic neural signatures in the subthalamic nucleus induced by anaesthesia and intubation
Authors: Huang Yongzhi , Hu Kejia , Green Alexander L. , Ma Xin , Gillies Martin J. , Wang Shouyan , Fitzgerald James J. , Pan Yixin , Martin Sean , Huang Peng , Zhan Shikun , Li Dianyou , Tan Huiling , Aziz Tipu Z. , Sun Bomin 
Published: September 2019

AbstractBackgroundSubcortical structures including the basal ganglia have been proposed to be crucial for arousal, consciousness, and behavioural responsiveness. However, how basal ganglia contributes to the loss and recovery of consciousness during anaesthesia has not been well characterized.MethodsIn this study, using local field potentials (LFPs) from subthalamic nucleus (STN) and scalp electroencephalogram in 12 Parkinson’s disease patients, we investigate STN neural signatures during propofol general anaesthesia and during intubation as an arousal intervention in anaesthesia.ResultsPropofol-induced anaesthesia resulted in changes in multiple frequency bands in STN LFPs, including increased low-frequency activities (slow-wave oscillation, delta, theta, and alpha bands) and decreased higher-frequency activities. This was also accompanied by increased STN-frontal cortical coherence in alpha frequency band. Beta and high-gamma activities in the STN temporally increased during intubation compared to the status of loss of consciousness. We also show that the dynamic changes in the high frequency activities (80-180 Hz) in STN LFPs induced by propofol and intubation correlated with power-law exponent in the power spectra between 2 and 80 Hz.ConclusionsOur findings suggest that anaesthesia and intubation induced changes in the STN LFPs in multiple frequency bands. They are also consistent with the hypothesis that the power-law exponent in the power spectra between 2 and 80 Hz reflect the excitation/inhibition balance in the STN, which is modulated by anaesthesia and intubation, and further modulate the high frequency activity.
Distributions of hypothalamic neuron populations co-expressing tyrosine hydroxylase and the vesicular GABA transporter in the mouse
Authors: Negishi Kenichiro , Payant Mikayla A. , Schumacker Kayla S. , Wittmann Gabor , Butler Rebecca M. , Lechan Ronald M. , Steinbusch Harry W. M. , Khan Arshad M. , Chee Melissa J. 
Published: September 2019

AbstractThe hypothalamus contains catecholaminergic neurons marked by the expression of tyrosine hydroxylase (TH). As multiple chemical messengers coexist in each neuron, we determined if hypothalamic TH-immunoreactive (ir) neurons express glutamate or GABA. We used Cre/loxP recombination to express enhanced GFP fluorescence (EGFP) in neurons that express the vesicular glutamate (vGLUT2) or GABA transporter (vGAT), then determined TH immunoreactivity in glutamatergic or GABAergic neurons, respectively. EGFP-positive vGLUT2 neurons were not TH-ir. However, discrete TH-ir signals colocalized with EGFP-positive vGAT neurons, which we validated by in situ hybridization for Vgat mRNA. In order to contextualize the observed pattern of TH+EGFP colocalization in vGAT neurons, we first performed Nissl-based parcellation and plane-of-section analysis, and then mapped the distribution of TH-ir vGAT neurons onto atlas templates from the Allen Reference Atlas (ARA) of the mouse brain. TH-ir vGAT neurons were distributed throughout the rostrocaudal extent of the hypothalamus. Within the ARA ontology of gray matter regions, TH-ir neurons localized primarily to the periventricular hypothalamic zone, periventricular hypothalamic region, and lateral hypothalamic zone. There was a very strong presence of EGFP fluorescence in TH-ir neurons across all brain regions, but the most striking colocalization was found in the zona incerta (ZI) – a region assigned to the hypothalamus in the ARA – where every TH-ir neuron was EGFP-positive. Neurochemical characterization of these ZI neurons revealed that they display immunoreactivity for dopamine but not dopamine β-hydroxylase. In aggregate, these findings indicate the existence of a novel hypothalamic population in the mouse that may signal through the release of GABA and/or dopamine.
Mean growth rate when rare is not a reliable metric for persistence of species
Authors: Pande Jayant , Fung Tak , Chisholm Ryan , Shnerb Nadav M. 
Published: September 2019

AbstractThe coexistence of many species within ecological communities poses a long-standing theoretical puzzle. Modern coexistence theory (MCT) and related techniques explore this phenomenon by examining the chance of a species population growing from rarity in the presence of all other species. The mean growth rate when rare, 𝔼[r], is used in MCT as a metric that measures persistence properties (like invasibility or time to extinction) of a population. Here we critique this reliance on 𝔼[r] and show that it fails to capture the effect of random abundance variations on persistence properties. The problem becomes particularly severe when an increase in the amplitude of stochastic temporal environmental variations leads to an increase in 𝔼[r], since at the same time it enhances random abundance fluctuations and the two effects are inherently intertwined. In this case, the chance of invasion and the mean extinction time of a population may even go down as 𝔼[r] increases.
Serotonergic development of active sensing
Authors: Azarfar Alireza , Zhang Yiping , Alishbayli Artoghrul , Schubert Dirk , Homberg Judith R. , Celikel Tansu 
Published: September 2019

AbstractActive sensing requires adaptive motor (positional) control of sensory organs based on contextual, sensory and task requirements, and develops postnatally after the maturation of intracortical circuits. Alterations in sensorimotor network connectivity during this period are likely to impact sensorimotor computation also in adulthood. Serotonin is among the cardinal developmental regulators of network formation, thus changing the serotonergic drive might have consequences for the emergence and maturation of sensorimotor control. Here we tested this hypothesis on an object localization task by quantifying the motor control dynamics of whiskers during tactile navigation. The results showed that sustained alterations in serotonergic signaling in serotonin transporter knockout rats, or the transient pharmacological inactivation of the transporter during early postnatal development, impairs the emergence of adaptive motor control of whisker position based on recent sensory information. A direct outcome of this altered motor control is that the mechanical force transmitted to whisker follicles upon contact is reduced, suggesting that increased excitability observed upon altered serotonergic signaling is not due to increased synaptic drive originating from the periphery upon whisker contact. These results argue that postnatal development of adaptive motor control requires intact serotonergic signaling and that even its transient dysregulation during early postnatal development causes lasting sensorimotor impairments in adulthood.
The theory and practice of measuring broad-range recombination rate from marker selected pools
Authors: Wei Kevin H.-C. , Mantha Aditya , Bachtrog Doris 
Published: September 2019

ABSTRACTRecombination is the exchange of genetic material between homologous chromosomes via physical crossovers. Pioneered by T. H. Morgan and A. Sturtevant over a century ago, methods to estimate recombination rate and genetic distance require scoring large number of recombinant individuals between molecular or visible markers. While high throughput sequencing methods have allowed for genome wide crossover detection producing high resolution maps, such methods rely on large number of recombinants individually sequenced and are therefore difficult to scale. Here, we present a simple and scalable method to infer near chromosome-wide recombination rate from marker selected pools and the corresponding analytical software MarSuPial. Rather than genotyping individuals from recombinant backcrosses, we bulk sequence marker selected pools to infer the allele frequency decay around the selected locus; since the number of recombinant individuals increases proportionally to the genetic distance from the selected locus, the allele frequency across the chromosome can be used to estimate the genetic distance and recombination rate. We mathematically demonstrate the relationship between allele frequency attenuation, recombinant fraction, genetic distance, and recombination rate in marker selected pools. Based on available chromosome-wide recombination rate models ofDrosophila, we simulated read counts and determined that nonlinear local regressions (LOESS) produce robust estimates despite the high noise inherent to sequencing data. To empirically validate this approach, we show that (single) marker selected pools closely recapitulate genetic distances inferred from scoring recombinants between double markers. We theoretically determine how secondary loci with viability impacts can modulate the allele frequency decay and how to account for such effects directly from the data. We generated the recombinant map of three wild derived strains which strongly correlates with previous genome-wide measurements. Interestingly, amidst extensive recombination rate variation, multiple regions of the genomes show elevated rates across all strains. Lastly, we apply this method to estimate chromosome-wide crossover interference. Altogether, we find that marker selected pools is a simple and cost effective method for broad recombination rate estimates. Although it does not identify instances of crossovers, it can generate near chromosome-wide recombination maps in as little as one or two libraries.
Phytochrome light receptors control metabolic flux, and their action during seedling development sets the trajectory for biomass production
Authors: Krahmer Johanna , Abbas Ammad , Mengin Virginie , Ishihara Hirofumi , Moraes Thiago A , Krohn Nicole , Annunziata Maria-Grazia , Feil Regina , Alseekh Saleh , Obata Toshihiro , Fernie Alisdair R , Stitt Mark , Halliday Karen J. 
Published: September 2019

AbstractThe phytochromes (phys) photoreceptors are known to be major regulators of plastic growth responses to vegetation shade. Recent reports have begun to uncover an important role for phys in carbon resource management. Our earlier work showed that phy mutants had a distinct metabolic profile with elevated levels of metabolites including TCA intermediates, amino acids and sugars. Here we show that in seedlings phy regulates the balance between glucose and starch. Multi-allele phy mutants have excess glucose and low starch levels, which is conducive to hypocotyl elongation. 13C-CO2 labelling demonstrates that metabolic flux balance in adult plants is markedly altered in phy mutants. Phytochrome reduces synthesis rates of stress metabolites, including raffinose and proline and several typical stress-induced biosynthetic genes related to these metabolites show higher expression in phy mutants.Since growth and metabolism are typically inter-connected, we investigated why phy mutants have severely reduced biomass. Quantification of carbon fixation, biomass accumulation, and 13C labelling of cell wall polysaccharides established that relative growth rate is impaired in multi allele phy mutants for the first 2.5 weeks after germination but equivalent to the WT thereafter. Mathematical modelling predicts that the altered growth dynamics and final biomass deficit can be explained by the smaller cotyledon size of the multiple phy mutants. This indicates that the established role of phy in promoting seedling establishment has enduring effects that govern adult plant biomass.
CloneRetriever: retrieval of rare clones from heterogeneous cell populations
Authors: Feldman David , Tsai FuNien , Garrity Anthony J. , O’Rourke Ryan , Brenan Lisa , Ho Patricia , Gonzalez Elizabeth , Konermann Silvana , Johannessen Cory M. , Beroukhim Rameen , Bandopadhayay Pratiti , Blainey Paul C. 
Published: September 2019

AbstractBackgroundMany biological processes, such as cancer metastasis, organismal development, and development of resistance to cytotoxic therapy, rely on the emergence of rare sub-clones from a larger population. Understanding how the genetic and epigenetic features of diverse clones affect clonal fitness provides insight into molecular mechanisms underlying selective processes. However, identifying causal drivers of clonal fitness remains challenging. Population-level analysis has limited resolution to characterize clones prior to selection, while high-resolution single-cell methods are destructive and challenging to scale across large populations, limiting further functional analysis of relevant clones.ResultsHere, we develop CloneRetriever, a methodology for tracking and retrieving rare clones throughout their response to selection. CloneRetriever utilizes a CRISPR sgRNA-barcode library that allows isolation of viable cells from specific clones within the barcoded population using a sequence-specific retrieval reporter. We demonstrated that CloneRetriever can measure clonal fitness of cancer cell modelsin vitroand retrieve targeted clones at abundance as low as 1 in 1,883 in a heterogeneous cell population.ConclusionsCloneRetriever provides a means to track and access specific and rare clones of interest across dynamic changes in population structure to comprehensively explore the basis of these changes.
Transfer ethnography: the recording of a heritage building
Authors: Sharif Ahlam Ammar 
Published: September 2019

Purpose
The purpose of this paper is to detail an actor-network theory inspired ethnography of recording heritage buildings. The case study focusses on Irbid School in Al Tal area, which is one of the oldest schools in Jordan and an important heritage building.

Design/methodology/approach
The recording process was undertaken by third-year architectural design studio students from Philadelphia University. The paper documents the interaction between the heritage building and the students in a two-phased ethnography, including fieldwork conducted between September and December 2017.

Findings
The paper proposes the concept of “transfer ethnography”, which considers the continuous changes in design across different locations. This extends beyond traditional ethnography, which focusses on a single location. Here, in contrast to the classical viewpoint, following the recording process shows that building design is ongoing and extends beyond implementation through the years as the building ages.

Research limitations/implications
Due to the chosen research approach, the research investigated the most relevant events from the author’s perspective, which might extend in various ways. Future research is encouraged to investigate more events that support the empirical findings.

Practical implications
The paper provides a new angle from which building design networks can be followed through the transfer ethnography, which has implications for the recording and similar processes that necessitate the continuous following of actors.

Originality/value
The research suggests the transfer ethnography, which entails close and in-depth engagement with actors but changes with the transformation of a design while following the actors and networks’ shifts between the different locations. It is more delicate, attentive and indispensable considering the dynamics of design.
Reflections of gender on the urban green space
Authors: Topcu Umran 
Published: September 2019

Purpose
Urban green spaces including parks and gardens are an essential part of a network of physical and social well-being. They provide spaces to socialize and opportunities to connect with nature. They are restorative enclaves. When it comes to scaling down spaces in general, they form important constituent parts of what we call the setting in which we behave. Barker elaborated the notion of behavior setting by describing how our behavior is influenced and constrained by settings. A setting consists of the space, its contents, its surroundings, the people and their activities. As Norberg-Schulz puts it, this is a microcosmos that wraps people and the space. The paper aims to discuss this issue.

Design/methodology/approach
In this study a behavior setting with different spatial attributes in an urban green space, namely, Kriton Curi Park on the Asian side of Istanbul is observed. Landscapes used by both men and women may be gendered even if men and women use them at the same time. Women’s and men’s experiences of the same setting can be different. The difference is likely to be the outcome of both the physical attributes of the setting and/or the social construction of the society. However, a general attribute of genders’ experience of space is that women are more sensitive to spatial contents and more selective about the use of space. According to previous research, men and women do not have equal control over behavior settings in urban green spaces, in Turkey.

Findings
The findings of this study address a social fact that appropriate physical features of urban green spaces like Criton Curi Park and its immediate environment reveal a higher degree of equality in gender roles.

Originality/value
As the literature indicates parks being among urban green spaces are not yet studied enough in the Turkish context. This study is an attempt to study the status of women in open public space. For the sustainability of social relations parks become even more important.
A time discontinuous Galerkin isogeometric analysis method for non-Fourier thermal wave propagation problem
Authors: Xia Yang , Guo Pan 
Published: September 2019

Purpose
Numerical instability such as spurious oscillation is an important problem in the simulation of heat wave propagation. The purpose of this study is to propose a time discontinuous Galerkin isogeometric analysis method to reduce numerical instability of heat wave propagation in the medium subjected to heat sources, particularly heat impulse.

Design/methodology/approach
The essential vectors of temperature and the temporal gradients are assumed to be discontinuous and interpolated individually in the discretized time domain. The isogeometric analysis method is applied to use its property of smooth description of the geometry and to eliminate the mesh-dependency. An artificial damping scheme with proportional stiffness matrix is brought into the final discretized form to reduce the numerical spurious oscillations.

Findings
The numerical spurious oscillations in the simulation of heat wave propagation are effectively eliminated. The smooth description of geometry with spline functions solves the mesh-dependency problem and improves the numerical precision.

Originality/value
The time discontinuous Galerkin method is applied within the isogeometric analysis framework. The proposed method is effective in the simulation of the wave propagation problems subjecting to impulse load with numerical stability and accuracy.
Different and diverse anaerobic microbiota were seen in women living with HIV with unsuppressed HIV viral load and in women with recurrent bacterial vaginosis: a cohort study
Authors: Elwood C , Albert AYK , McClymont E , Wagner E , Mahal D , Devakandan K , Quiqley BL , Pakzad Z , Yudin MH , Hill JE , Money D ,   the VOGUE Research Group
Published: September 2019

ObjectiveTo compare the vaginal microbiota of women living with HIV (WLWH) with the vaginal microbiota of women with recurrent bacterial vaginosis (BV) and healthy women without HIV to determine if there are differences in the vaginal microbiome, what factors influence these differences, and to characterise HIV clinical parameters including viral load and CD4 count in relation to the vaginal microbiome.DesignObservational cohort study.SettingCanada.PopulationWomen aged 18–49 years who were premenopausal and not pregnant were recruited into three cohorts: healthy women, WLWH and women with recurrent BV.MethodsDemographic and clinical data were collected via interviews and medical chart reviews. Vaginal swabs were collected for Gram‐stain assessment and microbiome profiling using the cpn60 barcode sequence.Main outcome measuresTo compare overall community composition differences, we used compositional data analysis methods, hierarchical clustering and Kruskal–Wallis tests where appropriate.ResultsClinical markers such as odour and abnormal discharge, but not irritation, were associated with higher microbial diversity. WLWH with unsuppressed HIV viral loads were more likely than other groups to have non‐Gardnerella‐dominated microbiomes. HIV was associated with higher vaginal microbial diversity and this was related to HIV viral load, with unsuppressed women demonstrating significantly higher relative abundance of Megasphaera genomosp. 1, Atopobium vaginae and Clostridiales sp. (all P < 0.05) compared with all other groups.ConclusionsIn WLWH, unsuppressed HIV viral loads were associated with a distinct dysbiotic profile consisting of very low levels of Lactobacillus and high levels of anaerobes.Tweetable abstractVaginal microbiomes in WLWH with viral load >50 copies/ml have distinct dysbiotic profiles with high levels of anaerobes.
How Aggressive Tax Planning Facilitates the Diversion of Corporate Resources: Evidence from Path Analysis
Authors: Bauer Andrew M. , Fang Junxiong , Pittman Jeffrey , Zhang Yinqi , Zhao Yuping 
Published: September 2019

ABSTRACTIn measuring tunneling with intercorporate loans disclosed by Chinese listed companies, we analyze the underlying channels through which aggressive tax planning facilitates the diversion of corporate resources by firm insiders. Using path analysis, we document that the path from tax aggressiveness to related loans is mediated by both the additional cash flows from tax savings and the increased financial opacity from tax planning, and that additional cash flows plays a much more important role than opacity in helping controlling shareholders to divert corporate resources under the guise of tax aggressiveness. Beyond the two mediated paths, we also detect a residual, direct path from tax aggressiveness to related loans. After an exogenous shock from the government crackdown on diversionary related loans, we find the direct path is fully mediated by the two indirect paths, suggesting that tunneling via related loans only occurs at firms where insiders can mask tunneling under the cover of opacity or can justify related loans on grounds of abnormal cash flows from tax savings. Our evidence supports the notion that greater outside scrutiny increases the hurdle for, but does not entirely eradicate, diversion facilitated by tax aggressiveness. Collectively, our research lends some support to recent theory on the importance of taxes to corporate governance by demonstrating how the agency costs of tax planning allow certain shareholders to benefit from firm activities at the expense of others.
How provider organisations interpret regulation in the context of residential dementia aged care
Authors: Biggs Simon , Carr Ashley 
Published: September 2019

ObjectiveTo explore how Australian residential dementia aged care providers respond to regulation via organisational culture, level, processes and interpretation.MethodsObservation took place in three provider organisations. Qualitative, semi‐structured in‐depth interviews were conducted with aged care staff (n = 60) at three different levels of each organisation: senior management from three head offices (n = 17), facility management (n = 13) and personal care workers (n = 30) from eight residential care facilities.ResultsOrientations towards regulation included the following: “above and beyond;” “pushing back;” and “engineering out.” Regulation was interpreted differently depending on the level of authority within an organisation where boundaries were managed according to strategic, operational and interactional priorities.DiscussionExamining regulation within an organisational context and at different staff levels suggests ways to balance dementia care with regulatory control. Both generate stress, mitigated by culture and interdependent role differentiation.