bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutation analysis of the EBV‐lymphoblastoid cell line cautions their use as antigen‐presenting cells
Authors: Tan Qin , Ku Wenjing , Zhang Chaoting , Heyilimu Palashati , Tian Yuan , Ke Yang , Lu Zheming 
Published: January 2018

AbstractLymphoblastoid cell lines (LCLs) have been widely used as professional antigen‐presenting cells (APCs). However, neoantigen‐loaded LCLs could induce nonspecific T‐cell response, which could be due to expression of both Epstein–Barr virus (EBV) antigens and nonsynonymous mutations arising in LCLs. Since the number of passages could influence mutational characteristics of LCLs, and moreover extensive proliferation of LCLs in vitro is necessary to activate T cells for immunotherapy, we comprehensively profiled mutational characteristics by comparing eight sets of B cells and matched high‐passage LCLs using whole‐exome sequencing in order to assess the effect of nonsynonymous mutations arising in LCLs on nonspecific T‐cell response. We found 315 nongermline mutations (approximately 40mut/subject) randomly distributed across all chromosomes including 18 mutations in immunoglobulin V and J genes in eight LCLs, of which 137 candidate neoantigens (approximately 17mut/subject) were identified. The underlying mutational processes linked to EBV‐transformed LCLs could be attributed to activation induced cytidine deaminase gene expression which contributes to cytosine mutation clusters in LCLs through cytosine deamination. Pathways significantly enriched by nonsilent mutations of each LCL were totally different among all LCLs. In conclusion, high‐passage LCLs may not be suitable to serve as APCs due to random nonsilent mutations, particularly for presentation of neoantigens of low immunogenicity, although further experimental proofs are needed.
Looking to tomorrow’s healthcare today: a participatory health perspective
Authors: Coughlin Sheryl , Roberts David , O’Neill Kenneth , Brooks Peter 
Published: January 2018

AbstractHealth systems around the world face the issue of financial and workforce sustainability. Mobile health technologies – those devices which connect health professionals, patients, payers and the many other contributors who make up the health system offer some solutions – not just as ‘add ons’ but as enablers of real system change. This paper presents a vision for what the health system of the future could be like and emphasises the opportunities for real patient participation in clinical decision‐making if the professions can engage the technologies and patients/community in a meaningful way. Predicting the future is never easy but many of the technologies are here now – but how we will use them to make the system more patient friendly, more productive and sustainable is still for discussion. This paper should start that conversation.
Acceptability of opt‐out consent in a hospital patient population
Authors: Boulos Daniel , Morand Eric , Foo Michelle , Trivedi Janki Dhaval , Lai Ruth , Huntersmith Rachel , Zhang Karen , Stark Claire Brigid , Le Suong 
Published: January 2018

AbstractResearch has been slow to leverage digitalised medical records as a data resource. Our study assessed patient acceptability of opt‐out consent for secondary use of digital patient data. A questionnaire was distributed to patients in multiple languages and with an interpreter. Of 919 completed surveys, 33% were of non‐English speaking background, 15% self‐reported cognitive impairment and 3% were refugees. Opt‐out consent was accepted in this diverse population; 87% of participants approved, or were indifferent to opt‐out consent. Gender, employment and cognition status were not significant determinants of acceptability.
Pneumocystis jirovecii pneumonia in patients with acute myeloid leukaemia
Authors: Chang Hung , Kuo Ming‐Chung , Lin Tung‐Liang , Wu Jin‐Hou , Wang Po‐Nan 
Published: January 2018

AbstractThe association of Pneumocystis jirovecii pneumonia (PJP) and acute myeloid leukaemia (AML) is not clearly defined. In our experience of 291 patients with AML, 20 (14 males and 6 females, median age 56) developed PJP (incidence 6.8%). Thirteen patients (65%) survived until discharge from hospital. We conclude that PJP is not uncommon among patients with AML. In clinical care of AML, awareness of PJP should be heightened and prophylaxis should be considered.
Contemporaneous and Causal Relationship between Returns and Volumes: Evidence from Nifty Futures
Authors: Sampath Aravind , Garg Parth 
Published: January 2018

AbstractMotivated by the mixture of distribution hypothesis (MDH) and sequential arrival of information hypothesis (SAIH), we investigate the relationship between intraday returns and volumes using derivatives data from the emerging Indian market. Using robust statistical estimation, we document the evidence of both MDH and SAIH in one of the most traded financial markets in India (and the world). We document the presence of strong positive association between returns and volumes. We further report the evidence of strong causality from intraday returns to volumes than vice versa.
Effects of contrasting seasonal growth patterns on composition and persistence of mixed grass‐legume pastures over 5 years in a semi‐arid Australian cropping environment
Authors: Hayes R. C. , Li G. D. , Norton M. R. , Culvenor R. A. 
Published: January 2018

AbstractPerennial grass‐based pastures are uncommon in phased cropping rotations in south‐eastern Australia, where rainfall often limits production and persistence. The high reliance on pure legume‐based pastures limits overall pasture productivity and has adverse effects on environmental parameters such as weed incursion and ground cover. A field experiment was monitored over 5 years to examine the relative productivity of the temperate perennial grasses, phalaris (Phalaris aquatica) and cocksfoot (Dactylis glomerata) and determine whether contrasting seasonal activity enhances their persistence when grown in mixtures with lucerne (Medicago sativa) and annual legumes. Phalaris swards were shown to increase cumulative aboveground biomass by up to 96% and 32%, and in year 5 reduce annual grass emergence by between sevenfold and threefold compared to annual legume and lucerne/annual legume mixed swards, respectively. Only swards that included phalaris maintained ground cover above 70% in each autumn of the experimental period. Swards based on the highly summer dormant cocksfoot cultivar, Kasbah, were generally less productive over all, despite the cocksfoot showing a high level of persistence and good recovery following drought. Grass‐based swards that included lucerne were observed to produce ~35% greater legume biomass than a sward sown only to annual legumes. Cumulative legume biomass was greatest in lucerne swards in the absence of perennial grasses. The experiment was unable to demonstrate a consistent benefit in production and persistence associated with contrasting seasonal growth patterns. However, mixtures containing a range of functional types were consistently shown to enhance productivity over the duration of the experiment compared to less diverse swards. The potential to substantially increase forage productivity and ground cover, while reducing incursion by annual grass weeds, by including well‐adapted perennial grasses in mixtures with lucerne and annual legumes should be utilized.
Multivariate analysis of variations in intrinsic foot musculature among hominoids
Authors: Oishi Motoharu , Ogihara Naomichi , Shimizu Daisuke , Kikuchi Yasuhiro , Endo Hideki , Une Yumi , Soeta Satoshi , Amasaki Hajime , Ichihara Nobutsune 
Published: January 2018

AbstractComparative analysis of the foot muscle architecture among extant great apes is important for understanding the evolution of the human foot and, hence, human habitual bipedal walking. However, to our knowledge, there is no previous report of a quantitative comparison of hominoid intrinsic foot muscle dimensions. In the present study, we quantitatively compared muscle dimensions of the hominoid foot by means of multivariate analysis. The foot muscle mass and physiological cross‐sectional area (PCSA) of five chimpanzees, one bonobo, two gorillas, and six orangutans were obtained by our own dissections, and those of humans were taken from published accounts. The muscle mass and PCSA were respectively divided by the total mass and total PCSA of the intrinsic muscles of the entire foot for normalization. Variations in muscle architecture among human and extant great apes were quantified based on principal component analysis. Our results demonstrated that the muscle architecture of the orangutan was the most distinctive, having a larger first dorsal interosseous muscle and smaller abductor hallucis brevis muscle. On the other hand, the gorilla was found to be unique in having a larger abductor digiti minimi muscle. Humans were distinguished from extant great apes by a larger quadratus plantae muscle. The chimpanzee and the bonobo appeared to have very similar muscle architecture, with an intermediate position between the human and the orangutan. These differences (or similarities) in architecture of the intrinsic foot muscles among humans and great apes correspond well to the differences in phylogeny, positional behavior, and locomotion.
O‐GlcNAcylation in oral squamous cell carcinoma
Authors: Kongkaew Tassaporn , Aung Win Pa Pa , Supanchart Chayarop , Makeudom Anupong , Langsa‐ard Sarawat , Sastraruji Thanapat , Chaiyarit Ponlatham , Krisanaprakornkit Suttichai 
Published: January 2018

BackgroundTwo post‐translational mechanisms commonly demonstrated in various cancers are protein phosphorylation and glycosylation by O‐linked β‐N‐acetylglucosamine (O‐GlcNAc). However, only phosphorylation of the epidermal growth factor receptor (EGFR)/Akt pathway has been reported in oral squamous cell carcinoma (OSCC). Therefore, we aimed to determine both post‐translational modifications in OSCC tissues and in oral cancer cells compared to normal tissues and oral keratinocytes and to find correlations of these modifications with histological grading.MethodsThirty‐two OSCC and ten normal formalin‐fixed and paraffin‐embedded sections were probed with the anti‐O‐GlcNAc, anti‐O‐GlcNAc transferase (OGT), anti‐phosphorylated‐EGFRtyr1173, and anti‐phosphorylated‐Aktser473 antibodies following standard immunohistochemistry. The immunohistochemical (IHC) score was determined using the Fromowitz standard. Whole cell lysates of oral cancer cells and normal oral keratinocytes were immunoblotted with the anti‐O‐GlcNAc antibody.ResultsThe median IHC scores of O‐GlcNAc or OGT between OSCC and normal tissues were not different, whereas those of phosphorylated‐EGFRtyr1173 and phosphorylated‐Aktser473 were significantly higher in OSCC than normal tissues (P < .001 and P < .01, respectively). Similarly, expression of O‐GlcNAcylated proteins in oral cancer cells and normal oral keratinocytes did not differ. In the OSCC group, the median IHC scores of O‐GlcNAc and OGT were significantly lower than those of phosphorylated‐EGFRtyr1173 and phosphorylated‐Aktser473 (P < .01 and P < .001, respectively). The IHC scores of O‐GlcNAc or OGT were not determined to correlate with histological grading.ConclusionUnlike other types of cancers, our findings demonstrate that the levels of O‐GlcNAcylation are not significantly increased in OSCC tissues or in oral cancer cells and are not associated with the histological grading of OSCC.
Robert McKersie: Integrative Scholar
Authors: Cutcher‐Gershenfeld Joel , Kochan Thomas A. 
Published: January 2018

AbstractThis article is a tribute to Robert McKersie. It focuses on his career journey as an integrative scholar and touches on his scholarship, which among many honors included the 1995 International Association of Conflict Management (IACM) Lifetime Achievement Award. As the article suggests, Bob is integrative in multiple ways—as a teacher and facilitator integrating diverse concepts and interests; as a scholar lifting up Mary Parker Follet's concept of integration from the 1920s and, along with co‐author Richard Walton, giving it a new life in the 1965 Behavioral Theory of Labor Negotiations; and as a friend and colleague bringing out the best in everyone he encounters.
Evaluation of the use of recombinant human basic fibroblast growth factor in combination with negative pressure wound therapy with instillation and dwell time in porcine full‐thickness wound model
Authors: Saijo Hiroto , Kilpadi Deepak V. , Akita Sadanori 
Published: January 2018

AbstractNPWT with instillation and dwell time (NPWTi‐d), which combines NPWT with wound irrigation, has been clinically applied as a more effective treatment than conventional NPWT. Commercially available recombinant human basic fibroblast growth factor (rh‐bFGF) has been demonstrated to be beneficial for use over the wound beds. The objective of this study was to evaluate the effectiveness of combined treatment with NPWTi‐d and rh‐bFGF. Six pigs received 12 full‐thickness excisional skin wounds and were treated with six different treatment groups for each pair. The treatment regimens were composed NPWTi‐d, NPWT, or advanced wound care with or without rh‐bFGF. On day 6, the minimum granulation tissue thickness and blood vessel number of the group of combined treatment with NPWTi‐d and rh‐bFGF spray were significantly greater than that of the control group. Combined treatment with NPWTi‐d and rh‐bFGF spray reads to good granulation tissue formation and vascularization for accelerating wound healing.
Thermophilic Alkaline Fermentation Followed by Mesophilic Anaerobic Digestion for Efficient Hydrogen and Methane Production from Waste-Activated Sludge: Dynamics of Bacterial Pathogens as Revealed by the Combination of Metagenomic and Quantitative PCR Analyses
Authors: Wan Jingjing , Jing Yuhang , Rao Yue , Zhang Shicheng , Luo Gang 
Published: January 2018

ABSTRACT

Thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM) for hydrogen and methane production from waste-activated sludge (WAS) was investigated. The TM process was also compared to a process with mesophilic alkaline fermentation followed by a mesophilic anaerobic digestion (MM) and one-stage mesophilic anaerobic digestion (M) process. The results showed that both hydrogen yield (74.5 ml H
2
/g volatile solids [VS]) and methane yield (150.7 ml CH
4
/g VS) in the TM process were higher than those (6.7 ml H
2
/g VS and 127.8 ml CH
4
/g VS, respectively) in the MM process. The lowest methane yield (101.2 ml CH
4
/g VS) was obtained with the M process. Taxonomic results obtained from metagenomic analysis showed that different microbial community compositions were established in the hydrogen reactors of the TM and MM processes, which also significantly changed the microbial community compositions in the following methane reactors compared to that with the M process. The dynamics of bacterial pathogens were also evaluated. For the TM process, the reduced diversity and total abundance of bacterial pathogens in WAS were observed in the hydrogen reactor and were further reduced in the methane reactor, as revealed by metagenomic analysis. The results also showed not all bacterial pathogens were reduced in the reactors. For example,
Collinsella aerofaciens
was enriched in the hydrogen reactor, which was also confirmed by quantitative PCR (qPCR) analysis. The study further showed that qPCR was more sensitive for detecting bacterial pathogens than metagenomic analysis. Although there were some differences in the relative abundances of bacterial pathogens calculated by metagenomic and qPCR approaches, both approaches demonstrated that the TM process was more efficient for the removal of bacterial pathogens than the MM and M processes.

IMPORTANCE
This study developed an efficient process for bioenergy (H
2
and CH
4
) production from WAS and elucidates the dynamics of bacterial pathogens in the process, which is important for the utilization and safe application of WAS. The study also made an attempt to combine metagenomic and qPCR analyses to reveal the dynamics of bacterial pathogens in anaerobic processes, which could overcome the limitations of each method and provide new insights regarding bacterial pathogens in environmental samples.
Myxoma Virus M083 Is a Virulence Factor Which Mediates Systemic Dissemination
Authors: Wolfe A. M. , Dunlap K. M. , Smith A. C. , Bartee M. Y. , Bartee E. 
Published: January 2018

ABSTRACT

Poxviruses are large, DNA viruses whose protein capsid is surrounded by one or more lipid envelopes. Embedded into these lipid envelopes are three conserved viral proteins which are thought to mediate binding of virions to target cells. While the function of these proteins has been studied
in vitro
, their specific roles during the pathogenesis of poxviral disease remain largely unclear. Here we present data demonstrating that the putative chondroitin binding protein M083 from the leporipoxvirus myxoma virus is a significant virulence factor during infection of susceptible
Oryctolagus
rabbits. Removal of M083 results in a reduced capacity of virus to spread beyond the regional lymph nodes and completely eliminates infection-mediated mortality.
In vitro
, removal of M083 results in only minor intracellular replication defects but causes a significant reduction in the ability of myxoma virus to spread from infected epithelial cells onto primary lymphocytes. We hypothesize that the physiological role of M083 is therefore to mediate the spread of myxoma virus onto rabbit lymphocytes, allowing these cells to disseminate virus throughout infected rabbits.

IMPORTANCE
Poxviruses represent both a class of human pathogens and potential therapeutic agents for the treatment of human malignancy. Understanding the basic biology of these agents is therefore significant to human health in a variety of ways. While the mechanisms mediating poxviral binding have been well studied
in vitro
, how these mechanisms impact poxviral pathogenesis
in vivo
remains unclear. The current study advances our understanding of how poxviral binding impacts viral pathogenesis by demonstrating that the putative chondroitin binding protein M083 plays a critical role during the pathogenesis of myxoma virus in susceptible
Oryctolagus
rabbits by impacting viral dissemination through changes in the transfer of virions onto primary splenocytes.
Impact of free access to leisure facilities and community outreach on inequalities in physical activity: a quasi-experimental study
Authors: Higgerson James , Halliday Emma , Ortiz-Nunez Aurora , Brown Richard , Barr Ben 
Published: January 2018

BackgroundThere are large inequalities in levels of physical activity in the UK, and this is an important determinant of health inequalities. Little is known about the effectiveness of community-wide interventions to increase physical activity and whether effects differ by socioeconomic group.MethodsWe conducted interrupted time series and difference-in-differences analyses using local administrative data and a large national survey to investigate the impact of an intervention providing universal free access to leisure facilities alongside outreach and marketing activities in a deprived local authority area in the northwest of England. Outcomes included attendances at swimming and gym sessions, self-reported participation in gym and swim activity and any physical activity.ResultsThe intervention was associated with a 64% increase in attendances at swimming and gym sessions (relative risk 1.64, 95% CI 1.43 to 1.89, P<0.001), an additional 3.9% of the population participating in at least 30 min of moderate-intensity gym or swim sessions during the previous four weeks (95% CI 3.6 to 4.1) and an additional 1.9% of the population participating in any sport or active recreation of at least moderate intensity for at least 30 min on at least 12 days out of the last four weeks (95% CI 1.7 to 2.1). The effect on gym and swim activity and overall levels of participation in physical activity was significantly greater for the more disadvantaged socioeconomic group.ConclusionsThe study suggests that removing user charges from leisure facilities in combination with outreach and marketing activities can increase overall population levels of physical activity while reducing inequalities.
Differences in declining mortality rates due to coronary heart disease by neighbourhood deprivation
Authors: Oudin Åström Daniel , Sundquist Jan , Sundquist Kristina 
Published: January 2018

BackgroundCardiovascular disease (CVD) is the main cause of death in most industrialised countries, including those in Europe. The mortality rates due to coronary heart disease (CHD), one of the most serious CVD conditions, have been decreasing in most European countries during the last decades. However, whether the trends over time in CHD mortality rates differ depending on neighbourhood deprivation has rarely been investigated.MethodsFor each year of the study period, 1988–2012, in Sweden, age-standardised mortality rates were calculated for three different types of neighbourhoods, characterised by a Neighbourhood Deprivation Index. Joinpoint regression was used to investigate potential changes in age-standardised mortality rates by neighbourhood deprivation and over time.ResultsOver the study period, age-standardised mortality rates due to CHD were consistently the highest in the deprived neighbourhoods and the lowest in the affluent neighbourhoods. We observed a statistically significant overall decline, ranging from 67% to 59%, in the age-standardised CHD mortality rates for each level of neighbourhood deprivation. Furthermore, the decline for the affluent neighbourhoods was significantly higher compared with the decline in the deprived neighbourhoods.ConclusionAge-standardised CHD mortality rates decreased significantly in Sweden between 1988 and 2012. This decline was more pronounced in the affluent neighbourhoods, which indicates that the improvements in prevention and treatment of CHD have not benefited individuals residing in deprived neighbourhoods to an equal extent. Knowledge of time trends in CHD mortality by level of neighbourhood deprivation may help guide decision-makers in the development of appropriate healthcare policies for deprived neighbourhoods.
Lightweight, Obfuscation-Resilient Detection and Family Identification of Android Malware
Authors: Garcia Joshua , Hammad Mahmoud , Malek Sam 
Published: January 2018

The number of malicious Android apps is increasing rapidly. Android malware can damage or alter other files or settings, install additional applications, and so on. To determine such behaviors, a security analyst can significantly benefit from identifying the family to which an Android malware belongs rather than only detecting if an app is malicious. Techniques for detecting Android malware, and determining their families, lack the ability to handle certain obfuscations that aim to thwart detection. Moreover, some prior techniques face scalability issues, preventing them from detecting malware in a timely manner.
To address these challenges, we present a novel machine-learning-based Android malware detection and family identification approach, RevealDroid, that operates without the need to perform complex program analyses or to extract large sets of features. Specifically, our selected features leverage categorized Android API usage, reflection-based features, and features from native binaries of apps. We assess RevealDroid for accuracy, efficiency, and obfuscation resilience using a large dataset consisting of more than 54,000 malicious and benign apps. Our experiments show that RevealDroid achieves an accuracy of 98% in detection of malware and an accuracy of 95% in determination of their families. We further demonstrate RevealDroid’s superiority against state-of-the-art approaches.