bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative study between two antifungal agents, Luliconazole and Efinaconazole, of their preventive effects in a Trichophyton-infected guinea pig onychomycosis model
Authors: Nakamura Akihiro , Hirakawa Satoko , Nagai Hiroaki , Inagaki Katsuhiro 
Published: December 2020

Abstract
An efficacious period of two topical antifungal drugs was compared in a Trichophyton mentagrophytes-infected onychomycosis model in guinea pigs treated with antifungal drugs prior to infection. Luliconazole 5% (LLCZ) and efinaconazole 10% (EFCZ) test solutions were applied to the animals’ nails once daily for 2 weeks followed by a nontreatment period of 2, 4, and 8 weeks. After each nontreatment period, the nails were artificially infected by the fungus. Drug efficacy was quantitatively evaluated by qPCR and histopathological examination of the nails collected following a 4-week post-infection period. The fungal infection was confirmed in the untreated group. Both LLCZ and EFCZ prevented fungal infection in the treated groups with the nontreatment period of 2 weeks. After the nontreatment period of 4 weeks, no infection was observed in the LLCZ-treated group; however, infection into the nail surface and fungal invasion into the nail bed were observed in the EFCZ-treated group. After the nontreatment period of 8 weeks, fungi were found in the nail surface and nail bed in some nails treated with EFCZ; however, no infection was observed in the nail bed of the LLCZ-treated group. The results suggest that LLCZ possesses longer-lasting antifungal effect in nails of the guinea pigs than EFCZ, and that this animal model could be useful for translational research between preclinical and clinical studies to evaluate the pharmacological efficacy of antifungal drugs to treat onychomycosis. This experimentally shown longer-lasting preventive effects of LLCZ could also decrease the likelihoods of onychomycosis recurrence clinically.
The hierarchical structure of galactic haloes: classification and characterization with halo-optics
Authors: Oliver William H , Elahi Pascal J , Lewis Geraint F , Power Chris 
Published: December 2020

ABSTRACT
We build upon Ordering Points To Identify the Clustering Structure (optics ), a hierarchical clustering algorithm well known to be a robust data miner, in order to produce halo-optics , an algorithm designed for the automatic detection and extraction of all meaningful clusters between any two arbitrary sizes. We then apply halo-optics to the 3D spatial positions of halo particles within four separate synthetic Milky Way-type galaxies, classifying the stellar and dark matter structural hierarchies. Through visualization of the halo-optics output, we compare its structure identification to the state-of-the-art galaxy/(sub)halo finder VELOCIraptor , finding excellent agreement even though halo-optics does not consider kinematic information in this current implementation. We conclude that halo-optics is a robust hierarchical halo finder, although its determination of lower spatial-density features such as the tails of streams could be improved with the inclusion of extra localized information such as particle kinematics and stellar metallicity into its distance metric.
Correlations between supermassive black holes and hot gas atmospheres in IllustrisTNG and X-ray observations
Authors: Truong Nhut , Pillepich Annalisa , Werner Norbert 
Published: December 2020

ABSTRACT
Recent X-ray observations have revealed remarkable correlations between the masses of central supermassive black holes (SMBHs) and the X-ray properties of the hot atmospheres permeating their host galaxies, thereby indicating the crucial role of the atmospheric gas in tracing SMBH growth in the high-mass regime. We examine this topic theoretically using the IllustrisTNG cosmological simulations and provide insights to the nature of this SMBH – gaseous halo connection. By carrying out a mock X-ray analysis for a mass-selected sample of TNG100 simulated galaxies at $z$ = 0, we inspect the relationship between the masses of SMBHs and the hot gas temperatures and luminosities at various spatial and halo scales – from galactic (∼Re) to group/cluster scales (∼R500c). We find strong SMBH-X-ray correlations mostly in quenched galaxies and find that the correlations become stronger and tighter at larger radii. Critically, the X-ray temperature (kBTX) at large radii (r ≳ 5Re) traces the SMBH mass with a remarkably small scatter (∼0.2 dex). The relations emerging from IllustrisTNG are broadly consistent with those obtained from recent X-ray observations. Overall, our analysis suggests that, within the framework of IllustrisTNG, the present-time MBH–kBTX correlations at the high-mass end (MBH ≳ 108M⊙) are fundamentally a reflection of the SMBH mass–halo mass relation, which at such high masses is set by the hierarchical assembly of structures. The exact form, locus, and scatter of those scaling relations are, however, sensitive to feedback processes such as those driven by star formation and SMBH activity.
A physico-chemical model to study the ion density distribution in the inner coma of comet C/2016 R2 (Pan-STARRS)
Authors: Raghuram Susarla , Bhardwaj Anil , Hutsemékers Damien , Opitom Cyrielle , Manfroid Jean , Jehin Emmanuel 
Published: December 2020

ABSTRACT
The recent observations show that comet C/2016 R2 (Pan-Starrs) has a unique and peculiar composition when compared with several other comets observed at 2.8 au heliocentric distance. Assuming solar resonance fluorescence is the only excitation source, the observed ionic emission intensity ratios are used to constrain the corresponding neutral abundances in this comet. We developed a physico-chemical model to study the ion density distribution in the inner coma of this comet by accounting for photon and electron impact ionization of neutrals, charge exchange and proton transfer reactions between ions and neutrals, and electron–ion thermal recombination reactions. Our calculations show that CO2+ and CO+ are the major ions in the inner coma, and close to the surface of nucleus CH3OH+, CH3OH2+, and O2+ are also important ions. By considering various excitation sources, we also studied the emission mechanisms of different excited states of CO+, CO2+, N2+, and H2O+. We found that the photon and electron impact ionization and excitation of corresponding neutrals significantly contribute to the observed ionic emissions for radial distances smaller than 300 km and at larger distances, solar resonance fluorescence is the major excitation source. Our modelled ion emission intensity ratios are consistent with the ground-based observations. Based on the modelled emission processes, we suggest that the observed ion emission intensity ratios can be used to derive the neutral composition in the cometary coma only when the ion densities are significantly controlled by photon and photoelectron impact ionization of neutrals rather than by the ion–neutral chemistry.
A Scoping Review of Implementation Science in Adult Critical Care Settings
Authors: McNett Molly , O’Mathúna Dónal , Tucker Sharon , Roberts Haley , Mion Lorraine C. , Balas Michele C. 
Published: December 2020

Objectives:
The purpose of this scoping review is to provide a synthesis of the available literature on implementation science in critical care settings. Specifically, we aimed to identify the evidence-based practices selected for implementation, the frequency and type of implementation strategies used to foster change, and the process and clinical outcomes associated with implementation.

Data Sources:
A librarian-assisted search was performed using three electronic databases.

Study Selection:
Articles that reported outcomes aimed at disseminating, implementing, or sustaining an evidence-based intervention or practice, used established implementation strategies, and were conducted in a critical care unit were included.

Data Extraction:
Two reviewers independently screened titles, abstracts, and full text of articles to determine eligibility. Data extraction was performed using customized fields established a priori within a systematic review software system.

Data Synthesis:
Of 1,707 citations, 82 met eligibility criteria. Studies included prospective research investigations, quality improvement projects, and implementation science trials. The most common practices investigated were use of a ventilator-associated pneumonia bundle, nutritional support protocols, and the Awakening and Breathing Coordination, Delirium Monitoring/Management, and Early Exercise/Mobility bundle. A variety of implementation strategies were used to facilitate evidence adoption, most commonly educational meetings, auditing and feedback, developing tools, and use of local opinion leaders. The majority of studies (76/82, 93%) reported using more than one implementation strategy. Few studies specifically used implementation science designs and frameworks to systematically evaluate both implementation and clinical outcomes.

Conclusions:
The field of critical care has experienced slow but steady gains in the number of investigations specifically guided by implementation science. However, given the exponential growth of evidence-based practices and guidelines in this same period, much work remains to critically evaluate the most effective mechanisms to integrate and sustain these practices across diverse critical care settings and teams.
Multiscale and integrative single-cell Hi-C analysis with Higashi
Authors: Zhang Ruochi , Zhou Tianming , Ma Jian 
Published: December 2020

AbstractThe advent of single-cell Hi-C (scHi-C) technologies offers an unprecedented opportunity to unveil cell-to-cell variability of 3D genome organization. However, the development of computational methods that can effectively enhance scHi-C data quality and extract 3D genome features in single cells remains a major challenge. Here, we report Higashi, a new algorithm that achieves state-of-the-art analysis of scHi-C data based on hypergraph representation learning. Extensive evaluations demonstrate that Higashi significantly outperforms existing methods for embedding and imputation of scHi-C data. Higashi is uniquely able to identify multiscale 3D genome features (such as compartmentalization and TAD-like domain boundaries) in single cells, allowing markedly refined delineation of cell-to-cell variability of 3D genome features. By applying to a scHi-C dataset from human prefrontal cortex, Higashi reveals complex cell types as well as new connections between 3D genome features and cell type-specific gene regulation. Higashi provides an end-to-end solution to scHi-C data analysis and is applicable to studying single-cell 3D genomes in a wide range of biological contexts.
How inhibitory neurons increase information transmission under threshold modulation
Authors: Hsu Wei-Mien M. , Kastner David B. , Baccus Stephen A. , Sharpee Tatyana O. 
Published: December 2020

AbstractModulation of neuronal thresholds is ubiquitous in the brain. Phenomena such as figure-ground segmentation, motion detection, stimulus anticipation and shifts in attention all involve changes in a neuron’s threshold based on signals from larger scales than its primary inputs. However, this modulation reduces the accuracy with which neurons can represent their primary inputs, creating a mystery as to why threshold modulation is so widespread in the brain. We find that modulation is less detrimental than other forms of neuronal variability and that its negative effects can be nearly completely eliminated if modulation is applied selectively to sparsely responding neurons in a circuit by inhibitory neurons. We verify these predictions in the retina where we find that inhibitory amacrine cells selectively deliver modulation signals to sparsely responding ganglion cell types. Our findings elucidate the central role that inhibitory neurons play in maximizing information transmission under modulation.
STUB1 is an intracellular checkpoint for interferon gamma sensing
Authors: Ng Simon , Lim Shuhui , Sim Adrian Chong Nyi , Mangadu Ruban , Lau Ally , Zhang Chunsheng , Martinez Sarah Bollinger , Chandramohan Arun , Lim U-Ming , Ho Samantha Shu Wen , Chang Shih Chieh , Gopal Pooja , Hong Lewis Z. , Schwaid Adam , Fernandis Aaron Zefrin , Loboda Andrey , Li Cai , Phan Uyen , Henry Brian , Partridge Anthony W. 
Published: December 2020

AbstractImmune checkpoint blockade (ICB) leads to durable and complete tumour regression in some patients but in others gives temporary, partial or no response. Accordingly, significant efforts are underway to identify tumour-intrinsic mechanisms underlying ICB resistance.Results from a published CRISPR screen in a mouse model suggested that targeting STUB1, an E3 ligase involved in protein homeostasis, may overcome ICB resistance but the molecular basis of this effect remains unclear. Herein, we report an under-appreciated role of STUB1 to dampen the interferon gamma (IFNγ) response. Genetic deletion of STUB1 increased IFNGR1 abundance on the cell surface and thus enhanced the downstream IFNγ response as showed by multiple approaches including Western blotting, flow cytometry, qPCR, phospho-STAT1 assay, immunopeptidomics, proteomics, and gene expression profiling. Human prostate and breast cancer cells with STUB1 deletion were also susceptible to cytokine-induced growth inhibition.Furthermore, blockade of STUB1 protein function recapitulated theSTUB1-null phenotypes. Despite these encouragingin vitrodata and positive implications from clinical datasets, we did not observein vivobenefits of inactivatingStub1in mouse syngeneic tumour models – with or without combination with anti-PD-1 therapy. However, our findings elucidate STUB1 as a barrier to IFNγ sensing, prompting further investigations to assess if broader inactivation of human STUB1 in both tumors and immune cells could overcome ICB resistance.
Towards robust, unobtrusive sensing of respiration using ultra-wideband impulse radar for the care of people living with dementia
Authors: Chen Ziwei , Bannon Alan , Rapeaux Adrien , Constandinou Timothy G. 
Published: December 2020

AbstractThe unobtrusive monitoring of vital signals and behaviour can be used to gather intelligence to support the care of people living with dementia. This can provide insights into the persons wellbeing and the neurogenerative process, as well as enable them to continue to live safely at home, thereby improving their quality of life. Within this context, this study investigated the deployability of non-contact respiration rate (RR) measurement based on an Ultra-Wideband (UWB) radar System-on-Chip (SoC). An algorithm was developed to simultaneously and continuously extract the respiration signal, together with the confidence level of the respiration signal and the target position, without needing any prior calibration. The radar-measured RR results were compared to the RR results obtained from a ground truth measure based on the breathing sound, and the error rates were within 8% with a mean value of 2.4%. The target localisation results match to the radar-to-chest distances with a mean error rate of 5.4%. The tested measurement range was up to 5m. The results suggest that the algorithm could perform sufficiently well in non-contact stationary respiration rate detection.
Functional single-cell profiling identifies that exosomes are associated with increased immune cell infiltration in non-metastatic breast cancer
Authors: Fathi Mohsen , Joseph Robiya , Adolacion Jay R T. , Martinez-Paniagua Melisa , An Xingyue , Gabrusiewicz Konrad , Mani Sendurai A. , Varadarajan Navin 
Published: December 2020

AbstractExosomes mediate intercellular communication in health and disease. Conventional assays are limited in profiling exosomes secreted from large populations of cells and are unsuitable for studying the functional consequences of individual cells exhibiting varying propensity for exosome secretion. In cancer, since exosomes can support the development of the pre-metastatic niche, cells with varying abilities to secrete exosomes can directly impact tumorigenesis. Here, we developed a high throughput single-cell technique that enabled the mapping of exosome secretion dynamics. By utilizing clinically relevant models of breast cancer, we established that non-metastatic cancer cells secrete more exosomes than metastatic cancer cells. Single-cell RNA-sequencing confirmed that pathways related to exosome secretion were enriched in the non-metastatic cells compared to the metastatic cells. We established isogenic clonal cell lines from non-metastatic cells with differing propensities for exosome secretion and showed that exosome secretion is an inheritable property preserved during cell division. Combined in vitro and in vivo studies with these cell lines suggested that exosome secretion can impede tumor formation. In human non-metastatic breast tumors, tumors with higher secretion of exosomes have a better prognosis, higher immune cytolytic activity, and enrichment of pro-inflammatory macrophages compared to tumors with lower secretion of exosomes. Our single-cell methodology can become an essential tool that enables the direct integration of exosome secretion with multiple cellular functions.
Predicting recombination frequency from map distance
Authors: Kivikoski Mikko , Rastas Pasi , Löytynoja Ari , Merilä Juha 
Published: December 2020

AbstractMap distance is one of the key measures in genetics and indicates the expected number of crossovers between two loci. Map distance is estimated from the observed recombination frequency using mapping functions, the most widely used of those, Haldane and Kosambi, being developed at the time when the number of markers was low and unobserved crossovers had a substantial effect on the recombination fractions. In contemporary high-density marker data, the probability of multiple crossovers between adjacent loci is negligible and different mapping functions yield the same result, that is, the recombination frequency between adjacent loci is equal to the map distance in Morgans. However, high-density linkage maps contain an interpretation problem: the map distance over a long interval is additive and its association with recombination frequency is not defined. Here, we demonstrate with high-density linkage maps from humans and stickleback fishes that the inverse of Haldane or Kosambi mapping functions fail to predict the recombination frequency from map distance, and show that this is because the expected number of crossovers is not sufficient to predict recombination frequency. We formulate a piecewise function to calculate the probability of no crossovers between the markers that yields more accurate predictions of recombination frequency from map distance. Our results demonstrate that the association between map distance and recombination frequency is context-dependent and no universal solution exists. We anticipate that our study will motivate further research on this subject to yield a more accurate mathematical description of map distance in the context of modern data.
Development of additional microsatellite primers for the mangrove tree speciesAvicennia germinans
Authors: Craig Hayley , Feller Ilka C. , Rowntree Jennifer K. 
Published: December 2020

AbstractObjectiveThe objective of this study was to develop additional microsatellite primers for the mangrove tree speciesAvicennia germinansthat work in multiplex PCR panels to enable cost effective population analyses of this species at a finer scale.ResultsPrimer sets were identified from whole genome sequencing data and combined into multiplex PCR panels. Five multiplex reactions containing 20 novel primer sets with trinucleotide repeats were successfully developed. Fifteen of the microsatellite loci were polymorphic in the samples tested, with 1-4 alleles per locus.
Effects of Ca2+on encystment and growth inScrippsiella trochoidea
Authors: Wang Zhifu , Feng Weihua , Cao Jing , Zhang Haifeng , Zhang Dongrong , Qian Jian , Xu Heng Tao , Hao Zhe 
Published: December 2020

AbstractCysts serve as a seed source for the initiation and recurrence of a harmful algal bloom (HAB) caused by dinoflagellates. And the influence of calcium on cyst formation has been relatively understudied. In the present study, we investigated the effects of calcium (Ca2+) on the growth and encystment ofScrippsiella trochoidea.We incubatedS. trochoideain modified f/2 media in flasks which were divided into five groups and treated with different Ca2+concentrations (0, 0.2, 0.4, 0.6, and 0.8 g·L−1). We revealed that cell density increased with increasing Ca2+concentrations; however, cell density was reduced when Ca2+concentrations exceeded 0.2 g·mL−1. Additionally, the number of cysts and the cyst formation rate similarly increased as Ca2+concentrations increased, but these were reduced when Ca2+concentrations exceeded 0.4 g·mL−1. Lastly,S. trochoideaabsorbed Ca2+from the water when cysts were formed and under high Ca2+concentrations, more calcareous thorn cysts formed.
Juvenile exposure to acute traumatic stress leads to long-lasting alterations in grey matter myelination in adult female but not male rats
Authors: Breton Jocelyn M. , Barraza Matthew , Hu Kelsey Y. , Frias Samantha Joy , Long Kimberly L.P. , Kaufer Daniela 
Published: December 2020

AbstractStress early in life can have a major impact on brain development, and there is increasing evidence that childhood stress confers vulnerability for later developing psychiatric disorders. In particular, during peri-adolescence, brain regions crucial for emotional regulation, such as the prefrontal cortex (PFC), amygdala (AMY) and hippocampus (HPC), are still developing and are highly sensitive to stress. Changes in myelin levels have been implicated in mental illnesses and stress effects on myelin and oligodendrocytes (OLs) are beginning to be explored as a novel and underappreciated mechanism underlying psychopathologies. Yet there is little research on the effects of acute stress on myelin during peri-adolescence, and even less work exploring sex-differences. Here, we used a rodent model to test the hypothesis that exposure to acute traumatic stress as a juvenile would induce changes in OLs and myelin content across limbic brain regions. Male and female juvenile rats underwent three hours of restraint stress with exposure to a predator odor on postnatal day (p) 28. Acute stress induced a physiological response, increasing corticosterone release and reducing weight gain in stress-exposed animals. Brain sections containing the PFC, AMY and HPC were taken either in adolescence (p40), or in adulthood (p95) and stained for markers of OLs and myelin. We found that acute stress induced sex-specific changes in grey matter (GM) myelination and OLs in both the short- and long-term. Exposure to a single stressor as a juvenile increased GM myelin content in the AMY and HPC in p40 males, compared to the respective control group. At p40, corticosterone release during stress exposure was also positively correlated with GM myelin content in the AMY of male rats. Single exposure to juvenile stress also led to long-term effects exclusively in female rats. Compared to controls, stress-exposed females showed reduced GM myelin content in all three brain regions. Acute stress exposure decreased PFC and HPC OL density in p40 females, perhaps contributing towards this observed long-term decrease in myelin content. Overall, our findings suggest that the juvenile brain is vulnerable to exposure to a brief severe stressor. Exposure to a single short traumatic event during peri-adolescence produces long-lasting changes in GM myelin content in the adult brain of female, but not male, rats. These findings highlight myelin plasticity as a potential contributor to sex-specific sensitivity to perturbation during a critical window of development.