bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anin vitroChondro-osteo-vascular Triphasic Model of the Osteochondral Complex
Authors: Pirosa Alessandro , Gottardi Riccardo , Alexander Peter G. , Puppi Dario , Chiellini Federica , Tuan Rocky S. 
Published: August 2020

AbstractThe generation of engineered models of the osteochondral complex to study its pathologies and develop possible treatments is hindered by the distinctly different properties of articular cartilage and subchondral bone, with the latter characterized by vascularization.In vitromodels of the osteochondral complex have been mainly engineered as biphasic constructs containing just cartilage and bone cells, a condition very dissimilar from thein vivoenvironment. The different cellular components of the osteochondral complex are governed by interacting biochemical signaling; hence, to study the crosstalk among chondrocytes, osteoblasts, and endothelial cells, we have developed a novel triphasic model of the osteochondral tissue interface. Wet-spun poly(ε-caprolactone) (PCL) and PCL/hydroxyapatite (HA) scaffolds in combination with a methacrylated gelatin (gelMA) hydrogel were used as the polymeric backbone of the constructs. The scaffold components were engineered with human bone marrow derived mesenchymal stem cells (hMSCs) and human umbilical vein endothelial cells (HUVECs), and differentiated using a dual chamber microphysiological system (MPS) bioreactor that allows the simultaneous, separate flow of media of different compositions for induced differentiation of each compartment towards a cartilaginous or osseous lineage. Within the engineered Microphysiological Vascularized Osteochondral System (microVOCS), hMSCs showed spatially distinct chondrogenic and osteogenic markers in terms of histology and gene expression. HUVECs formed a stable capillary-like network in the engineered bone compartment and enhanced both chondrogenic and osteogenic differentiation of hMSCs, resulting in the generation of anin vitrosystem that mimics a vascularized osteochondral interface tissue.
Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes
Authors: Kloub Lina , Gosselin Sean , Fullmer Matthew , Graf Joerg , Gogarten J. Peter , Bansal Mukul S. 
Published: August 2020

AbstractHorizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, calledHoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multi-gene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes.We apply HoMer to a genome-scale dataset of over 22000 gene families from 103Aeromonasgenomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multi-gene transfer. Among other insights, we find that (i) the relative frequency of HMGT increases as divergence between genomes increases, (ii) HMGTs often have conserved gene functions, and (iii) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.
The influenza A virus host shutoff factor PA-X is rapidly turned over in a strain-specific manner
Authors: Levene Rachel Emily , Shrestha Shailab D. , Gaglia Marta Maria 
Published: August 2020

ABSTRACTThe influenza A endoribonuclease PA-X regulates virulence and transmission of the virus by reducing host gene expression and thus regulating immune responses to influenza A virus. Despite this key function in viral biology, the levels of PA-X protein remain markedly low during infection, and previous results suggest that these low levels are not solely the result of regulation of the level of translation and RNA stability. How PA-X is regulated post-translationally remains unknown. We now report that the PA-X protein is rapidly turned over. PA-X from multiple viral strains are short-lived, although the half-life of PA-X ranges from ∼30 minutes to ∼3.5 hours depending on the strain. Moreover, sequences in the variable PA-X C-terminal domain are primarily responsible for regulating PA-X half-life, although the N-terminal domain also accounts for some differences among strains. Interestingly, we find that the PA-X from the 2009 pandemic H1N1 strain has a longer half-life compared to the other variants we tested. This PA-X isoform has been reported to have a higher host shutoff activity, suggesting a role for protein turnover in regulating PA-X activity. Collectively, this study reveals a novel regulatory mechanism of PA-X protein levels that may impact host shutoff activity during influenza A virus infection.IMPORTANCEThe PA-X protein from influenza A virus reduces host immune responses to infection through suppressing host gene expression, including genes encoding the antiviral response. Thus, it plays a central role in influenza A virus biology. Despite its key function, PA-X was only discovered in 2012 and much remains to be learned including how PA-X activity is regulated to promote optimal levels of viral infection. In this study, we reveal that PA-X protein levels are very low likely because of rapid turnover. We show that instability is a conserved property among PA-X variants from different strains of influenza A virus, but that the half-lives of PA-X variants differ. Moreover, the longer half-life of PA-X from the 2009 pandemic H1N1 strain correlates with its reported higher activity. Therefore, PA-X stability may be a way to regulate its activity and may contribute to the differential virulence of influenza A virus strains.
Analyzing the barriers to implementation of mass customization in Indian SMEs using integrated ISM-MICMAC and SEM
Authors: Ullah Inayat , Narain Rakesh 
Published: August 2020

PurposeThe purpose of this research is to identify the crucial barriers to the implementation of mass customization (MC) in Indian SMEs and to investigate the interactions among them so that important managerial implications could be formulated to facilitate the implementation of MC in SMEs.Design/methodology/approachThe contextual relationships and hierarchies of the barriers are established through the interpretive structural modelling (ISM) approach, and MICMAC analysis has been used to classify the barriers into different groups. Further, structural equation modelling based on partial least squares (PLS-SEM) has been applied to statistically validate the ISM model using the data collected through a questionnaire-based survey of Indian organizations.FindingsA portfolio of barriers, containing 16 items, has been identified from the literature review and a series of semi-structured interviews of practitioners. The study develops a structural model by establishing relationships and imposing directions among the barriers and classifies the barriers according to their driving and dependence power to serve as a roadmap for SMEs willing to implement MC into practice.Practical implicationsThe study highlights the critical barriers which have a significant impact on other barriers and need to be handled at priority. Also, the present research renders insights to SMEs to better prioritize their efforts and resources to overcome these barriers.Originality/valueThis research happens to be first in the MC literature that investigates the key barriers responsible for hindering the implementation of MC in SMEs and develops a statistically validated contextual model showing hierarchies and relationships of the barriers.
Remarkable lives. Lizzie Hehir in conversation with Jerome Carson
Authors: Hehir Lizzie , Carson Jerome 
Published: August 2020

Purpose
The purpose of this paper is to provide a profile of Lizzie Hehir. Lizzie tells her own story and is then interviewed by Jerome.

Design/methodology/approach
This series of papers used the case study approach. However, each paper is written collaboratively, using the person’s own words. The deeply individual nature of each person’s story reminds us of the complexities of working in mental health.

Findings
In her account, Lizzie tells us of her long-term battles with self-harm. It was a struggle that she eventually won.

Research limitations/implications
Individual stories allow us to access people’s lived experience with mental illness. No diagnostic manual can ever truly categorise this uniqueness.

Practical implications
Lizzie shows it is possible to overcome self-harm though she still experiences something of the trauma she went through when she has triggers.

Social implications
When we see burns victims, we seldom approach them asking them how they sustained their injuries, but as Lizzie points out, many people feel able to ask people who have self-harmed about their injuries.

Originality/value
Lizzie writes with conviction and humility. Now working in mental health, she is able to reach out to others who are as troubled as she once was.
Species coexist more easily if reinforcement is based on habitat preferences than on species recognition
Authors: Kyogoku Daisuke , Kokko Hanna 
Published: August 2020

Abstract

Maladaptive hybridization selects for prezygotic isolation, a process known as reinforcement. Reinforcement reduces gene flow and contributes to the final stage of speciation. Ecologically, however, coexistence of the incipient species is difficult if they initially use identical resources.

Habitat segregation offers an alternative to species discrimination as a way to reduce gene flow: production of unfit hybrids is reduced if mate encounters become rare due to differing habitat choice. Using a modelling approach, we show that hybridization avoidance alone can select for habitat specialization, even if neither of the species is intrinsically better at using a specific niche.

While habitat segregation and species discrimination both reduce the risk of producing unfit hybrids, these two isolation mechanisms differ from each other with respect to their effects on resource competition. Our model shows that, as a consequence of such differences, reinforcement evolves much more easily if hybridization is avoided based on habitat segregation than if the mechanism involves species recognition (mate choice traits).

We also examine the outcomes when both isolation mechanisms evolve jointly. The establishment of one isolation mechanism a priori weakens selection for the other. However, an asymmetry persists here too. The net effect of habitat segregation on species discrimination was typically facilitative, but not vice versa. This asymmetry arises because habitat segregation, by enhancing coexistence, secures time for the subsequent evolution of species discrimination in a mate choice context (still relevant if habitat use is not perfectly segregated). Species discrimination does not have such a stabilizing effect on coexistence.

Our results emphasize the importance of habitat segregation in reinforcement and offer a way to interpret findings where closely related taxa show similar performance on different resources or in different habitats. Studies of ecological generalization and specialization should therefore take into account that niche differences can be initiated and/or maintained by hybridization avoidance.
Soil organic carbon accumulation modes between pioneer and old‐growth forest ecosystems
Authors: Xiong Xin , Zhou Guoyi , Zhang Deqiang 
Published: August 2020

Abstract

Increasing evidence suggests that high biomass and litterfall do not necessarily bring about soil organic carbon (SOC) sinks, contrary to the assumption that higher litterfall implies higher SOC when designing carbon models. The underlying mechanism is related to the quality of litter.

We conducted 15 years (2000–2015) of consecutive field measurements of δ13C values in SOC and plants in a pioneer forest (Pinus massoniana forest, PF) and an old‐growth forest (monsoon evergreen broadleaved forest, BF), using an isotope mixing model based on mass balance to quantify the effects of vegetation on SOC stock and soil characteristics.

The carbon to nitrogen (C/N) ratio of litter in BF was lower than that in PF. The proportion of organic carbon yield input to the soil (Cinput) to the total litter carbon loss during decomposition was 38.7 ± 3.3% and 28.0 ± 2.1% in BF and PF respectively. New carbon input was higher in BF (148.7 ± 8.8 g C m−2 year−1) than PF (99.7 ± 4.5 g C m−2 year−1), though there was a non‐significant difference in annual litterfall between the two forests. Moreover, the Cinput was concentrated in the topsoil layer in PF but distributed in a more dispersed state across the whole soil profile in BF. Consequently, only the δ13C values of SOC decreased in the topsoil layer of PF, whereas these decreased at both soil depths in BF from 2000 to 2015.

Compared with PF, BF exhibited higher carbon input and a more favourable soil environment for carbon storage. It was the amount of intermediate product (i.e. Cinput) of litter decomposition, not the amount of litterfall itself, that drove the contrasting differences in SOC status.

Synthesis and applications. Litter quality controls soil organic carbon (SOC) accumulation by regulating the fate of decomposing litter, which may explain why old‐growth forests can sustainably accumulate carbon in soil. This finding questions the carbon models that predict the dependence of SOC accumulation on biomass and litter yield and suggests that litter quality should be valued in future carbon cycling models.
Continuation and replacement of Vibrio cholerae non‐O1 clonal genomic groups isolated from Plecoglossus altivelis fish in freshwaters
Authors: Kawai Mikihiko , Ota Atsushi , Takemura Taichiro , Nakai Toshihiro , Maruyama Fumito 
Published: August 2020

SummaryThe dissemination and abundances of Vibrio species in aquatic environments are of interest, as some species cause emerging diseases in humans and in aquatic organisms like fish. It is suggested that Vibrio cholerae non‐O1 infections of Plecoglossus altivelis (‘ayu’) were spread to various parts of Japan through the annual transplantation of juvenile fish. To investigate this, we used genome‐aided tracing of 17 V. cholerae strains isolated from ayu between the 1970s and 1990s in different Japanese freshwater systems. The strains formed a genomic clade distinct from all known clades, which we designate as the Ayu clade. Two clonal genomic groups identified within the clade, Ayu‐1 and Ayu‐2, persisted for a few years (between 1977 to 1979 and 1987 to 1990, respectively), and clonal replacement of Ayu‐1 by Ayu‐2 took place over an 8‐year period. Despite the high similarity between Ayu‐1 and Ayu‐2 (> 99.9% identity and > 97% fraction of genomes shared), differences in their gene repertoires were found, raising the possibility that they are phenotypically distinct. These results highlight the importance of genome‐based studies for understanding the long‐term dynamics of populations over the timescale of years.
Is lactate lower in septic patients who are prescribed beta blockers? Retrospective cohort study of an intensive care population
Authors: Pham Diem , Ward Harrison , Yong Brian , Mahendra Raj Jayanand , Awad Mariam , Harvey Martyn , Doherty Steven , Cave Grant 
Published: August 2020

AbstractObjectiveElevated serum lactate has long been considered an important marker of sepsis severity. Increasing evidence supports catecholamine‐stimulated aerobic glycolysis being a major contributor to the hyperlactataemia seen in sepsis. Beta‐blockade may blunt such catecholamine mediated rise in lactate analogous to the way it can mask tachycardia. This could impact the way we evaluate sepsis severity and adequacy of initial treatment. The objective of this study is to investigate whether septic patients who were on beta‐blocker treatment at presentation have lower serum lactate level.MethodsUsing a retrospective cohort design we gathered data on patients admitted to our base hospital intensive care unit with APACHE III diagnosis of sepsis and septic shock during the 2017 calendar year. Serum lactate, current medications, presenting vital signs, illness severity scores, laboratory data and mortality outcome were extracted from patients' medical record and the unit's clinical database.ResultsOf 189 records analysed, 49 patients were concurrently prescribed beta‐blockers. More beta‐blocked patients were male, beta‐blocked patients were older, and a greater proportion of beta blocked patients had their first lactate measured as an inpatient. After regression to correct for identified significant covariates mean serum lactate was 0.87 (95% confidence interval 0.05–1.69) mmol/L lower in those prescribed beta blockers.ConclusionsIn our cohort pre‐existing beta blocker treatment was associated with lower serum lactate measurements in patients presenting with sepsis. Pre‐existing beta blocker treatment may reduce serum lactate at presentation in patients with sepsis.
To intubate or not to intubate? Predictors of inhalation injury in burn‐injured patients before arrival at the burn centre
Authors: Dyson Kylie , Baker Paul , Garcia Nicole , Braun Anna , Aung Myat , Pilcher David , Smith Karen , Cleland Heather , Gabbe Belinda 
Published: August 2020

AbstractObjectiveInhalation injury occurs in approximately 10–20% of burn patients and is associated with increased mortality. There is no clear method of identifying patients at risk of inhalation injury or requiring intubation in the pre‐hospital setting. Our objective was to identify pre‐burn centre factors associated with inhalation injury confirmed on bronchoscopy, and to develop a prognostic model for inhalation injury.MethodsWe analysed acute admissions from the Victorian Adult Burns Service and Ambulance Victoria electronic patient care records for 1 July 2009 to 30 June 2016. We defined inhalation injury as an Abbreviated Injury Scale of >1 on bronchoscopy. A multivariable logistic regression prediction model was developed based on pre‐burn centre factors.ResultsEmergency medical services transported 1148 patients who were admitted to the burn centre. The median age of patients was 39 years and most patients had <10% total body surface area (%TBSA) burned. The prevalence of confirmed inhalation injury was 11%. Increasing %TBSA burned, flame, enclosed space, face burns, hoarse voice, soot in mouth and shortness of breath were predictive of inhalation injury. The model provided excellent discrimination (area under curve 0.87, 95% confidence interval 0.84–0.91). A lower proportion of patients intubated at a non‐burn centre had an inhalation injury (33%) compared to patients intubated by emergency medical services (54%) and in the burn centre (58%).ConclusionsA model to predict inhalation injury in burn‐injured patients was developed with excellent discrimination. This model requires prospective testing but could form an integral part of clinician decision‐making.
Workplace violence in emergency departments: The health professionals and security personnel alliance
Authors: Ramacciati Nicola , Giusti Gian Domenico 
Published: August 2020

AbstractViolence in the health sector is a widespread worldwide phenomenon. Emergency nurses and emergency physicians are among the most exposed. In violent incidents, security personnel also play an important role. Wand and colleagues on Emergency Medicine Australasia have tried to give voice to the opinions and experiences of security personnel in responding to aggression and behavioural problems. Sharing some data from our 2016 Italian National Survey on Violence towards Emergency Nurses, further elements are provided on this issue. The different perspectives of healthcare professionals and security personnel can converge in an alliance to counteract violence in the ED.
Chromosome‐level de novo genome assembly of Sarcophaga peregrina provides insights into the evolutionary adaptation of flesh flies
Authors: Ren Lipin , Shang Yanjie , Yang Li , Wang Shiwen , Wang Xiang , Chen Shan , Bao Zhigui , An Dong , Meng Fanming , Cai Jifeng , Guo Yadong 
Published: August 2020

AbstractSarcophaga peregrina is considered to be of great ecological, medical and forensic significance, and has unusual biological characteristics such as an ovoviviparous reproductive pattern and adaptation to feed on carrion. The availability of a high‐quality genome will help to further reveal the mechanisms underlying these charcateristics. Here we present a de novo‐assembled genome at chromosome scale for S. peregrina. The final assembled genome was 560.31 Mb with contig N50 of 3.84 Mb. Hi‐C scaffolding reliably anchored six pseudochromosomes, accounting for 97.76% of the assembled genome. Moreover, 45.70% of repeat elements were identified in the genome. A total of 14,476 protein‐coding genes were functionally annotated, accounting for 92.14% of all predicted genes. Phylogenetic analysis indicated that S. peregrina and S. bullata diverged ~ 7.14 million years ago. Comparative genomic analysis revealed expanded and positively selected genes related to biological features that aid in clarifying its ovoviviparous reproduction and carrion‐feeding adaptations, such as lipid metabolism, olfactory receptor activity, antioxidant enzymes, proteolysis and serine‐type endopeptidase activity. Protein‐coding genes associated with ovoviparity, such as yolk proteins, transferrin and acid sphingomyelinase, were identified. This study provides a valuable genomic resource for S. peregrina, and sheds insight into further revealing the underlying molecular mechanisms of adaptive evolution.
A systematic review of internet‐based information on dermatomyositis and polymyositis
Authors: Haque Ashraful , Cox Miriam , Sandler Robert D. , Hughes Michael 
Published: August 2020

AbstractAimPatients with rheumatic diseases are increasingly using internet‐based information to inform healthcare utilization and make treatment decisions. Our aim was to assess the readability and quality of internet‐based information on dermatomyositis (DM) and polymyositis (PM).MethodKey words “Dermatomyositis” and “Polymyositis” were searched on 3 commonly used search engines (Google, Yahoo and Bing). The first 3 pages (~30) of search results were examined from each search engine. Readability of information was assessed using 4 readability formulae (Flesch Reading Ease Score, Flesch‐Kincaid Grade Level, the Simplified Measure of Gobbledygook index, the Coleman‐Liau index). Quality of information was assessed using the DISCERN tool, Journal of The American Medical Association (JAMA) benchmark criteria and Health on The Net Code (HoN code). We also examined Google Trends® data to determine if there were obvious temporal search patterns.ResultsThirty‐two websites were included in the study after duplicates were removed and exclusion criteria were applied. The overall quality was low including DISCERN with a median overall score of 38/80 (interquartile range 12.25), only 4/32 (13%) websites fulfilled all 4 JAMA benchmark criteria, and 9/32 (28%) had HoN code. Readability of information was assessed using 4 readability formulae (Flesch Reading Ease Score, Flesch‐Kincaid Grade Level, the Simplified Measure of Gobbledygook index, the Coleman‐Liau index. There was no obvious temporal trend in searches on analysis of Google Trends® data.ConclusionThe overall quality and readability of internet‐based information relating to DM and PM is poor. Patients require appropriate information of high quality and readability throughout the course of their disease in order to make informed decisions on their condition including treatment.