bluuebunny/crossref_metadata_2025 huggingface dataset:
An effective ensemble classification framework using random forests and a correlation based feature selection technique
Authors: Chutia Dibyajyoti , Bhattacharyya Dhruba Kumar , Sarma Jaganath , Raju Penumetcha Narasa Lakshmi
Published: April 2017

Accurate classification of heterogeneous land surfaces with homogeneous land cover classes is a challenging task as satellite images are characterized by a large number of features in the spectral and spatial domains. The identifying relevance of a feature or feature set is an important task for designing an effective classification scheme. Here, an ensemble of random forests (RF) classifiers is realized on the basis of relevance of features. Correlation‐based Feature Selection (CFS) was utilized to assess the relevance of a subset of features by studying the individual predictive ability of each feature along with the degree of redundancy between them. Predictability of RF was greatly improved by random selection of the relevant features in each of the splits. An investigation was carried out on different types of images from the Landsat Enhanced Thematic Mapper Plus (Landsat ETM+) and QuickBird sensors. It has been observed that the performance of the RF classifier was significantly improved while using the optimal set of relevant features compared with a few of the most advanced supervised classifiers such as maximum likelihood classifier (MLC), Navie Bayes, multi‐layer perception (MLP), support vector machine (SVM) and bagging.
Comparison of administrative and survey data for estimating vitamin A supplementation and deworming coverage of children under five years of age in Sub‐Saharan Africa
Authors: Janmohamed Amynah , Doledec David
Published: April 2017

Objective

To compare administrative coverage data with results from household coverage surveys for vitamin A supplementation (VAS) and deworming campaigns conducted during 2010–2015 in 12 African countries.

Methods

Paired t‐tests examined differences between administrative and survey coverage for 52 VAS and 34 deworming dyads. Independent t‐tests measured VAS and deworming coverage differences between data sources for door‐to‐door and fixed‐site delivery strategies and VAS coverage differences between 6‐ to 11‐month and 12‐ to 59‐month age group.

Results

For VAS, administrative coverage was higher than survey estimates in 47 of 52 (90%) campaign rounds, with a mean difference of 16.1% (95% CI: 9.5–22.7; P < 0.001). For deworming, administrative coverage exceeded survey estimates in 31 of 34 (91%) comparisons, with a mean difference of 29.8% (95% CI: 16.9–42.6; P < 0.001). Mean ± SD differences in coverage between administrative and survey data were 12.2% ± 22.5% for the door‐to‐door delivery strategy and 25.9% ± 24.7% for the fixed‐site model (P = 0.06). For deworming, mean ± SD differences in coverage between data sources were 28.1% ± 43.5% and 33.1% ± 17.9% for door‐to‐door and fixed‐site distribution, respectively (P = 0.64). VAS administrative coverage was higher than survey estimates in 37 of 49 (76%) comparisons for the 6‐ to 11‐month age group and 45 of 48 (94%) comparisons for the 12‐ to 59‐month age group.

Conclusion

Reliance on health facility data alone for calculating VAS and deworming coverage may mask low coverage and prevent measures to improve programmes. Countries should periodically validate administrative coverage estimates with population‐based methods.
Systematic review of sex work interventions in sub‐Saharan Africa: examining combination prevention approaches
Authors: Awungafac George , Delvaux Therese , Vuylsteke Bea
Published: April 2017

Objective

The incidence of HIV and sexually transmitted infections is disproportionately high among sex workers (SW). We aimed to update the evidence on the effectiveness of SW interventions in sub‐Saharan Africa and to provide more insights into combination prevention.

Methods

The Systematic review followed PRISMA guidelines in a search of PUBMED and POPLINE for peer‐reviewed literature published between 1 January 2000 and 22 July 2016 (registration number on PROSPERO: CRD42016042529). We considered cohort interventions, randomised controlled trials and cross‐sectional surveys of SW programmes. A framework was used in the description and mapping of intervention to desired outcomes.

Results

Twenty‐six papers(reporting on 25 studies) were included. A strategy that empowered peer educator leaders to steer community activities showed a twofold increase in coverage of behaviour change communication and utilisation of health facility among SW. Brief alcohol harm reduction effort demonstrated a significant effect on sexual violence and engagement in sex trading. A risk reduction counselling intervention among drug‐injecting SW showed an effect on alcohol, substance use and engagement in sex work. No study on a promising intervention like PrEP among SWs was found. We observed that interventions that combined some structural components, biomedical and behavioural strategies tend to accumulate more desired outcomes.

Conclusion

The evidence base that can be considered in intervention designs to prevent HIV in SW in SSA is vast. The health sector should consider interventions to reduce binge alcohol intake and intravenous drug use among sex workers. Programmes should staunchly consider multicomponent approaches that explore community‐based structural approaches.
Bilingual creativity in Saudi stand‐up comedy
Authors: FALLATAH WAFAA
Published: April 2017

Stand‐up comedy is one of those art forms in which linguistic creativity can be seen in its most extravagant form, as stand‐up comedians mainly rely on their creative use of language to interact with their audience. This paper explores bilingual creativity in stand‐up comedy in Saudi English as an emerging variety. It investigates the form and function of bilingual creativity processes employed by Saudi comedians performing in English, and sets out to answer such questions as: What are the common forms of bilingual creativity in Saudi English stand‐up comedy and what functions do they serve; what cultural conceptualizations do these forms and functions evoke, and what are the implications of this study for researching bilingual creativity in world Englishes?
Investigation of Teacher Candidates' Opinions about Instructional Technologies and Material Usage
Authors: Orhan-Karsak Hanife Gülhan
Published: April 2017

The purpose of this study is to determine the awareness of teacher candidates about instructional technologies and materials and the ways of giving place in instruction by integrating them with different activities, to reveal opinions about their usage. Seventeen female and eight male, in total twenty five participants are sampling. The ages of the participants within the group heterogeneous between twenty two and thirty five.According to the purpose, the opinions of the teachers candidates who have been taken ‘Instructional Technology and Material Design’ lesson in the ‘Pedagogical Formation Training Certificate Program’ which is a pre-service teacher training program and have been practiced learning outputs of this lesson in other practical instruction lessons and in their lectures in the teaching internship school, were taken by writing. In this context the study is designed as a qualitative research. The findings are presented in thematically coded and supported by mind maps as visuals.It has been seen that teacher candidates are focused on different instructional technologies and materials that they learned in the Instructional Technology and Material Design’ lesson. In addition different experiences of teacher candidates about the usage of instructional technologies and materials have been identified.
Structure and function of human muscle fibres and muscle proteome in physically active older men
Authors: Brocca Lorenza , McPhee Jamie S. , Longa Emanuela , Canepari Monica , Seynnes Olivier , De Vito Giuseppe , Pellegrino Maria Antonietta , Narici Marco , Bottinelli Roberto
Published: April 2017

Key points

Loss of muscle mass and strength in the growing population of elderly people is a major health concern for modern societies. This condition, termed sarcopenia, is a major cause of falls and of the subsequent increase in morbidity and mortality.

Despite numerous studies on the impact of ageing on individual muscle fibres, the contribution of single muscle fibre adaptations to ageing‐induced atrophy and functional impairment is still unsettled.

The level of physical function and disuse is often associated with ageing.

We studied relatively healthy older adults in order to understand the effects of ageing per se without the confounding impact of impaired physical function.

We found that in healthy ageing, structural and functional alterations of muscle fibres occur. Protein post‐translational modifications, oxidation and phosphorylation contribute to such alterations more than loss of myosin and other muscle protein content.

Contradictory results have been reported on the impact of ageing on structure and functions of skeletal muscle fibres, likely to be due to a complex interplay between ageing and other phenomena such as disuse and diseases. Here we recruited healthy, physically and socially active young (YO) and elderly (EL) men in order to study ageing per se without the confounding effects of impaired physical function. In vivo analyses of quadriceps and in vitro analyses of vastus lateralis muscle biopsies were performed. In EL subjects, our results show that (i) quadriceps volume, maximum voluntary contraction isometric torque and patellar tendon force were significantly lower; (ii) muscle fibres went through significant atrophy and impairment of specific force (isometric force/cross‐sectional area) and unloaded shortening velocity; (iii) myosin/actin ratio and myosin content in individual muscle fibres were not altered; (iv) the muscle proteome went through quantitative adaptations, namely an up‐regulation of the content of several groups of proteins among which were myofibrillar proteins and antioxidant defence systems; (v) the muscle proteome went through qualitative adaptations, namely phosphorylation of several proteins, including myosin light chain‐2 slow and troponin T and carbonylation of myosin heavy chains. The present results indicate that impairment of individual muscle fibre structure and function is a major feature of ageing per se and that qualitative adaptations of muscle proteome are likely to be more involved than quantitative adaptations in determining such a phenomenon.
Discrete Linear Time Invariant Analysis of Digital Fluid Power Pump Flow Control
Authors: Johansen Per , Roemer Daniel B. , Andersen Torben O. , Pedersen Henrik C.
Published: April 2017

A fundamental part of a digital fluid power (DFP) pump is the actively controlled valves, whereby successful application of these pumps entails a need for control methods. The focus of the current paper is on a flow control method for a DFP pump. The method separates the control task concerning timing of the valve activation and the task concerning the overall flow output control. This enables application of linear control theory in the design process of the DFP pump flow controller. The linearization method is presented in a general framework and an application with a DFP pump model exemplifies the use of the method. The implementation of a discrete time linear controller and comparisons between the nonlinear model and the discrete time linear approximation shows the applicability of the control method.
Thermoacoustic Oscillations in Multipath Heated Fuel Circuits
Authors: Hunt Steven , Heister Stephen
Published: April 2017

Pressure oscillations in supercritical jet-A fuel flowing through four parallel heated tubes connected to common manifolds have been observed in this study. Tests were performed with fuel inlet temperatures ranging from 70 °F to 700 °F, and fuel pressures ranging from 360 to 700 psi. Total fuel flow rate ranged from 5 to 55 lb/h. Tubes were heated by blowing 800–950 °F nitrogen over them. Acoustic-mode oscillations, typically ranging from 100 to 500 Hz, occurred only when a large temperature gradient was created inside the heated fuel tubes. Pressure oscillation amplitudes ranged from 0.1 to 1.0 psi. Oscillations at the inlet and outlet manifolds that were caused by a mode with the characteristic length of a single fuel tube were separated by a phase lag that was a function of the manifold cross-passage diameter. A lower frequency mode was also observed, which had a characteristic length based on the summed lengths of a single fuel tube and a single manifold passage. An acoustic simulation using the comsol acoustics module was performed to predict frequencies based on geometry and flow conditions of the experiment.
Effect of Surface Roughness on Pool Boiling Heat Transfer of Water on a Superhydrophilic Aluminum Surface
Authors: Kim Jinsub , Jun Seongchul , Lee Jungho , Godinez Juan , You Seung M.
Published: April 2017

The effect of surface roughness on the pool boiling heat transfer of water was investigated on superhydrophilic aluminum surfaces. The formation of nanoscale protrusions on the aluminum surface was confirmed after immersing it in boiling water, which modified surface wettability to form a superhydrophilic surface. The effect of surface roughness was examined at different average roughness (Ra) values ranging from 0.11 to 2.93 μm. The boiling heat transfer coefficients increased with an increase in roughness owing to the increased number of cavities. However, the superhydrophilic aluminum surfaces exhibited degradation of the heat transfer coefficients when compared with copper surfaces owing to the flooding of promising cavities. The superhydrophilic aluminum surfaces exhibited a higher critical heat flux (CHF) than the copper surfaces. The CHF was 1650 kW/m2 for Ra = 0.11 μm, and it increased to 2150 kW/m2 for Ra = 0.35 μm. Surface roughness is considered to affect CHF as it improves the capillary wicking on the superhydrophilic surface. However, further increase in surface roughness above 0.35 μm did not augment the CHF, even at Ra = 2.93 μm. This upper limit of the CHF appears to result from the hydrodynamic limit on the superhydrophilic surface, because the roughest surface with Ra = 2.93 μm still showed a faster liquid spreading speed.
Life-style classification of some Phytoseiidae (Acari: Mesostigmata) species based on gnathosoma morphometrics
Authors: Liu Shan , Lv Jiale , Wang Endong , Xu Xuenong
Published: April 2017

Life style of phytoseiid species (Acari: Mesostigmata) is an important feature in evaluating their potential as biological control agents. Previous studies suggested that some morphometrics of gnathosoma are related to the feeding habits of phytoseiids. In this study, we showed it is appropriate to estimate feeding habits and/or life styles of phytoseiids based on variations in gnathosoma morphology. Scanning electron microscope pictures of 10 phytoseiid species belonging to four major life styles were taken. For each species, 23 morphometrics of gnathosoma and the length of dorsal shield were measured. Principle Component Analysis (PCA) showed that the 10 species can be divided into three groups based on the first two principle components of these parameters. The 1st group includes one specialized predators of Tetranychus species (Phytoseiulus persimilis) and two selective predators of tetranychid mites (Neoseiulus pseudolongispinosus, Neoseiulus californicus), the 2nd group includes six generalist predators (Amblyseius orientalis, Amblyseius swirskii, Amblyseius tsugawai, Neoseiulus barkeri, Neoseiulus bicaudus, Neoseiulus cucumeris), and the 3rd group includes one specialized pollen feeder (Euseius utilis). This grouping is consistent with the life style division of McMurtry & Croft (1997), except that Type I and II were not separated. However, there is a trend that both Type II species were closer to each other. Overall, species in Group II have larger chelicerae and hypostome than those of Group I and III, while species in Group III have larger lobes and angle of fixed digit than those of the other two groups.
A Question of the Head and the Heart: From Physical Education to Kinesiology in the Gymnasium and the Laboratory
Authors: Vertinsky Patricia
Published: April 2017

In this paper I view the history of kinesiology in America through the lens of a shifting academic landscape where physical culture and building acted upon each other to reflect emergent views concerning the nature of training in physical education and scientific developments around human movement. It is also an organizational history that has been largely lived in the gymnasium and the laboratory from its inception in the late nineteenth century to its current arrangements in the academy. Historians have referred to this in appropriately embodied terms as the head and the heart of physical education, and of course the impact of gender, class, and race was ever present. I conclude that the profession/discipline conundrum in kinesiology that has ebbed and flowed in the shifting spaces and carefully organized places of the academy has not gone away in the twenty-first century and that the complexities of today’s training require more fertile and flexible collaborative approaches in research, teaching, and professional training.
Draft Genome Sequence of a Biodesulfurizing Bacterium,
Gordonia
sp. Strain IITR100
Authors: Jaishankar Jananee , Singh Pooja , Srivastava Preeti
Published: April 2017

We report here the whole-genome sequence of a biodesulfurizing bacterium,
Gordonia
sp. strain IITR100. The bacterium has the unique ability to desulfurize both aliphatic and aromatic organosulfurs. The draft genome sequence will provide insights into the various genes and regulators involved in biodesulfurization and other catabolic pathways.
Draft Genome Sequence of the 1,2-Dichloroethane-Utilizing
Micrococcus
sp. Strain NDB3Y10, Isolated from an Australian Bore Well Producing Coal Seam Gas
Authors: Adelskov Joseph , Patel Bharat K. C.
Published: April 2017

Micrococcus luteus
strain NDB3Y10, which utilizes 1,2-dichloroethane as a carbon source, was isolated from a bore well that produces coal seam gas. The draft genome size of the strain was 2.49 Mb with a G+C content of 72.97%. Genes involved in the metabolism of halogenated substrates, including halogenated hydrocarbons, were identified.
Evaluation of the Accelerate Pheno System for Fast Identification and Antimicrobial Susceptibility Testing from Positive Blood Cultures in Bloodstream Infections Caused by Gram-Negative Pathogens
Authors: Marschal Matthias , Bachmaier Johanna , Autenrieth Ingo , Oberhettinger Philipp , Willmann Matthias , Peter Silke
Published: April 2017

Bloodstream infections (BSI) are an important cause of morbidity and mortality. Increasing rates of antimicrobial-resistant pathogens limit treatment options, prompting an empirical use of broad-range antibiotics. Fast and reliable diagnostic tools are needed to provide adequate therapy in a timely manner and to enable a de-escalation of treatment. The Accelerate Pheno system (Accelerate Diagnostics, USA) is a fully automated test system that performs both identification and antimicrobial susceptibility testing (AST) directly from positive blood cultures within approximately 7 h. In total, 115 episodes of BSI with Gram-negative bacteria were included in our study and compared to conventional culture-based methods. The Accelerate Pheno system correctly identified 88.7% (102 of 115) of all BSI episodes and 97.1% (102 of 105) of isolates that are covered by the system's identification panel. The Accelerate Pheno system generated an AST result for 91.3% (95 of 104) samples in which the Accelerate Pheno system identified a Gram-negative pathogen. The overall category agreement between the Accelerate Pheno system and culture-based AST was 96.4%, the rates for minor discrepancies 1.4%, major discrepancies 2.3%, and very major discrepancies 1.0%. Of note, ceftriaxone, piperacillin-tazobactam, and carbapenem resistance was correctly detected in blood culture specimens with extended-spectrum beta-lactamase-producingEscherichia coli(n= 7) and multidrug-resistantPseudomonas aeruginosa(n= 3) strains. The utilization of the Accelerate Pheno system reduced the time to result for identification by 27.49 h (P< 0.0001) and for AST by 40.39 h (P< 0.0001) compared to culture-based methods in our laboratory setting. In conclusion, the Accelerate Pheno system provided fast, reliable results while significantly improving turnaround time in blood culture diagnostics of Gram-negative BSI.
Diagnostic Value of Galactomannan Antigen Test in Serum and Bronchoalveolar Lavage Fluid Samples from Patients with Nonneutropenic Invasive Pulmonary Aspergillosis
Authors: Zhou Wei , Li Hongxing , Zhang Yan , Huang Mei , He Qian , Li Pei , Zhang Fang , Shi Yi , Su Xin
Published: April 2017

The objective of this study was to compare the diagnostic value of galactomannan (GM) detection in bronchoalveolar lavage fluid (BALF) and serum samples from nonneutropenic patients with invasive pulmonary aspergillosis (IPA) and determine the optimal BALF GM cutoff value for pulmonary aspergillosis. GM detection in BALF and serum samples was performed by enzyme-linked immunosorbent assay (ELISA) in 128 patients with clinically suspected nonneutropenic pulmonary aspergillosis between June 2014 and June 2016. On the basis of the clinical and pathological diagnoses, 8 patients were excluded because their diagnosis was uncertain. The remaining 120 patients were diagnosed with either IPA (
n
= 37), community-acquired pneumonia (CAP;
n
= 59), noninfectious diseases (
n
= 19), or tuberculosis (
n
= 5). At a cutoff optical density index (ODI) value of ≥0.5, the sensitivity of BALF GM detection was much higher than that of serum GM detection (75.68% versus 37.84%;
P
= 0.001), but there was no significant difference between their specificities (80.72% versus 87.14%;
P
= 0.286). At a cutoff value of ≥1.0, the sensitivity of BALF GM detection was still much higher than that of serum GM detection (64.86% versus 24.32%;
P
< 0.001), and their specificities were similar (90.36% versus 95.71%;
P
= 0.202). Receiver operating characteristic (ROC) curve analysis showed that when the BALF GM detection cutoff value was 0.7, its diagnostic value for pulmonary aspergillosis was optimized, and the sensitivity and specificity reached 72.97% and 89.16%, respectively. BALF GM detection was valuable for the diagnosis of IPA in nonneutropenic patients, and its diagnostic value was superior to that of serum GM detection. The optimal BALF GM cutoff value was 0.7.
Serine 235 Is the Primary NS5A Hyperphosphorylation Site Responsible for Hepatitis C Virus Replication
Authors: Hsu Shih-Chin , Lo Chieh-Wen , Pan Ting-Chun , Lee Kuan-Ying , Yu Ming-Jiun
Published: April 2017

The nonstructural protein 5A (NS5A) of the hepatitis C virus (HCV) is a phosphoprotein with two phosphorylation states: hypo- and hyperphosphorylation. Genetic mutation studies have demonstrated a cluster of serine residues responsible for NS5A hyperphosphorylation and functions in viral replication and assembly; however, the phosphorylation levels and potential interactions among the serine residues are unclear. We used three specific antibodies to measure NS5A phosphorylation at S222, S235, and S238 that were identified in our previous proteomics study. In the HCV (J6/JFH-1)-infected Huh7.5.1 cells, S222 phosphorylation was barely detected, whereas S235 phosphorylation and S238 phosphorylation were always detected in parallel in time and intracellular spaces. S235A mutation eliminated S238 phosphorylation whereas S238A mutation did not affect S235 phosphorylation, indicating that S235 phosphorylation occurs independently of S238 phosphorylation while S238 phosphorylation depends on S235 phosphorylation. In line with this, immunoprecipitation coupled with immunoblotting showed that S235 phosphorylation existed alone without S238 phosphorylation, whereas S238 phosphorylation existed only when S235 was phosphorylated on the same NS5A molecule. S235-phosphorylated NS5A constituted the primary hyperphosphorylated NS5A species. S235A mutation blunted viral replication, whereas S238A mutation did not affect replication. We concluded that S235 is the primary NS5A hyperphosphorylation site required for HCV replication. S238 is likely phosphorylated by casein kinase Iα, which requires a priming phosphorylation at S235.

IMPORTANCEIt has been known for years that the hepatitis C virus nonstructural protein 5A (NS5A) undergoes transition between two phosphorylation states: hypo- and hyperphosphorylation. It is also known that a cluster of serine residues is responsible for NS5A hyperphosphorylation and functions; however, the primary serine residue responsible for NS5A hyperphosphorylation is not clear. Here, we show for the first time that serine 235-phosphorylated NS5A constitutes the primary hyperphosphorylated NS5A species required for viral replication. We also show that NS5A phosphorylation among the serine residues is interdependent and occurs in a directional manner, i.e., phosphorylation at serine 235 leads to phosphorylation at serine 238. Our data provide the first proof-of-principle evidence that NS5A undergoes a sequential phosphorylation cascade.
Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses
Authors: Andreani Julien , Khalil Jacques Yaacoub Bou , Sevvana Madhumati , Benamar Samia , Di Pinto Fabrizio , Bitam Idir , Colson Philippe , Klose Thomas , Rossmann Michael G. , Raoult Didier , La Scola Bernard
Published: April 2017

African swine fever virus
, a double-stranded DNA virus that infects pigs, is the only known member of the
Asfarviridae
family. Nevertheless, during our isolation and sequencing of the complete genome of faustovirus, followed by the description of kaumoebavirus, carried out over the past 2 years, we observed the emergence of previously unknown related viruses within this group of viruses. Here we describe the isolation of pacmanvirus, a fourth member in this group, which is capable of infecting
Acanthamoeba castellanii
. Pacmanvirus A23 has a linear compact genome of 395,405 bp, with a 33.62% G+C content. The pacmanvirus genome harbors 465 genes, with a high coding density. An analysis of reciprocal best hits shows that 31 genes are conserved between
African swine fever virus
, pacmanvirus, faustovirus, and kaumoebavirus. Moreover, the major capsid protein locus of pacmanvirus appears to be different from those of kaumoebavirus and faustovirus. Overall, comparative and genomic analyses reveal the emergence of a new group or cluster of viruses encompassing
African swine fever virus
, faustovirus, pacmanvirus, and kaumoebavirus.

IMPORTANCE
Pacmanvirus is a newly discovered icosahedral double-stranded DNA virus that was isolated from an environmental sample by amoeba coculture. We describe herein its structure and replicative cycle, along with genomic analysis and genomic comparisons with previously known viruses. This virus represents the third virus, after faustovirus and kaumoebavirus, that is most closely related to classical representatives of the
Asfarviridae
family. These results highlight the emergence of previously unknown double-stranded DNA viruses which delineate and extend the diversity of a group around the asfarvirus members.
Disparate Contributions of Human Retrovirus Capsid Subdomains to Gag-Gag Oligomerization, Virus Morphology, and Particle Biogenesis
Authors: Martin Jessica L. , Mendonça Luiza M. , Angert Isaac , Mueller Joachim D. , Zhang Wei , Mansky Louis M.
Published: April 2017

The capsid domain (CA) of the retroviral Gag protein is a primary determinant of Gag oligomerization, which is a critical step for immature Gag lattice formation and virus particle budding. Although the human immunodeficiency virus type 1 (HIV-1) CA carboxy-terminal domain (CTD) is essential for CA-CA interactions, the CA CTD has been suggested to be largely dispensable for human T-cell leukemia virus type 1 (HTLV-1) particle biogenesis. To more clearly define the roles of the HTLV-1 CA amino-terminal domain (NTD) and CA CTD in particle biogenesis, we generated and analyzed a panel of Gag proteins with chimeric HIV-1/HTLV-1 CA domains. Subcellular distribution and protein expression levels indicated that Gag proteins with a chimeric HIV-1 CA NTD/HTLV-1 CA CTD did not result in Gag oligomerization regardless of the parent Gag background. Furthermore, chimeric Gag proteins with the HTLV-1 CA NTD produced particles phenotypically similar to HTLV-1 immature particles, highlighting the importance of the HTLV-1 CA NTD in HTLV-1 immature particle morphology. Taken together, these observations support the conclusion that the HTLV-1 CA NTD can functionally replace the HIV-1 CA CTD, but the HIV-1 CA NTD cannot replace the HTLV-1 CA CTD, indicating that the HTLV-1 CA subdomains provide distinct contributions to Gag-Gag oligomerization, particle morphology, and biogenesis. Furthermore, we have shown for the first time that HIV-1 and HTLV-1 Gag domains outside the CA (e.g., matrix and nucleocapsid) impact Gag oligomerization as well as immature particle size and morphology.

IMPORTANCE
A key aspect in virus replication is virus particle assembly, which is a poorly understood process for most viruses. For retroviruses, the Gag structural protein is the primary driver of virus particle biogenesis, and the CA CTD is the primary determinant of Gag-Gag interactions for HIV-1. In this study, the HTLV-1 capsid amino-terminal domain was found to provide distinct contributions to Gag-Gag oligomerization, particle morphology, and biogenesis. This study provides information that will aid efforts for discovery of therapeutic targets for intervention.
Analysis of Competing HIV-1 Splice Donor Sites Uncovers a Tight Cluster of Splicing Regulatory Elements within Exon 2/2b
Authors: Brillen Anna-Lena , Walotka Lara , Hillebrand Frank , Müller Lisa , Widera Marek , Theiss Stephan , Schaal Heiner
Published: April 2017

The HIV-1 accessory protein Vif is essential for viral replication by counteracting the host restriction factor APOBEC3G (A3G), and balanced levels of both proteins are required for efficient viral replication. Noncoding exons 2/2b contain the Vif start codon between their alternatively used splice donors 2 and 2b (D2 and D2b). For
vif
mRNA, intron 1 must be removed while intron 2 must be retained. Thus, splice acceptor 1 (A1) must be activated by U1 snRNP binding to either D2 or D2b, while splicing at D2 or D2b must be prevented. Here, we unravel the complex interactions between previously known and novel components of the splicing regulatory network regulating HIV-1 exon 2/2b inclusion in viral mRNAs. In particular, using RNA pulldown experiments and mass spectrometry analysis, we found members of the heterogeneous nuclear ribonucleoparticle (hnRNP) A/B family binding to a novel splicing regulatory element (SRE), the exonic splicing silencer ESS2b, and the splicing regulatory proteins Tra2/SRSF10 binding to the nearby exonic splicing enhancer ESE2b. Using a minigene reporter, we performed bioinformatics HEXplorer-guided mutational analysis to narrow down SRE motifs affecting splice site selection between D2 and D2b. Eventually, the impacts of these SREs on the viral splicing pattern and protein expression were exhaustively analyzed in viral particle production and replication experiments. Masking of these protein binding sites by use of locked nucleic acids (LNAs) impaired Vif expression and viral replication.

IMPORTANCE
Based on our results, we propose a model in which a dense network of SREs regulates
vif
mRNA and protein expression, crucial to maintain viral replication within host cells with varying A3G levels and at different stages of infection. This regulation is maintained by several serine/arginine-rich splicing factors (SRSF) and hnRNPs binding to those elements. Targeting this cluster of SREs with LNAs may lead to the development of novel effective therapeutic strategies.
Dense Array of Spikes on HIV-1 Virion Particles
Authors: Stano Armando , Leaman Daniel P. , Kim Arthur S. , Zhang Lei , Autin Ludovic , Ingale Jidnyasa , Gift Syna K. , Truong Jared , Wyatt Richard T. , Olson Arthur J. , Zwick Michael B.
Published: April 2017

HIV-1 is rare among viruses for having a low number of envelope glycoprotein (Env) spikes per virion, i.e., ∼7 to 14. This exceptional feature has been associated with avoidance of humoral immunity, i.e., B cell activation and antibody neutralization. Virus-like particles (VLPs) with increased density of Env are being pursued for vaccine development; however, these typically require protein engineering that alters Env structure. Here, we used instead a strategy that targets the producer cell. We employed fluorescence-activated cell sorting (FACS) to sort for cells that are recognized by trimer cross-reactive broadly neutralizing antibody (bnAb) and not by nonneutralizing antibodies. Following multiple iterations of FACS, cells and progeny virions were shown to display higher levels of antigenically correct Env in a manner that correlated between cells and cognate virions (P= 0.027). High-Env VLPs, or hVLPs, were shown to be monodisperse and to display more than a 10-fold increase in spikes per particle by electron microscopy (average, 127 spikes; range, 90 to 214 spikes). Sequencing revealed a partial truncation in the C-terminal tail of Env that had emerged in the sort; however, iterative rounds of “cell factory” selection were required for the high-Env phenotype. hVLPs showed greater infectivity than standard pseudovirions but largely similar neutralization sensitivity. Importantly, hVLPs also showed superior activation of Env-specific B cells. Hence, high-Env HIV-1 virions, obtained through selection of producer cells, represent an adaptable platform for vaccine design and should aid in the study of native Env.

IMPORTANCEThe paucity of spikes on HIV is a unique feature that has been associated with evasion of the immune system, while increasing spike density has been a goal of vaccine design. Increasing the density of Env by modifying it in various ways has met with limited success. Here, we focused instead on the producer cell. Cells that stably express HIV spikes were screened on the basis of high binding by bnAbs and low binding by nonneutralizing antibodies. Levels of spikes on cells correlated well with those on progeny virions. Importantly, high-Env virus-like particles (hVLPs) were produced with a manifest array of well-defined spikes, and these were shown to be superior in activating desirable B cells. Our study describes HIV particles that are densely coated with functional spikes, which should facilitate the study of HIV spikes and their development as immunogens.
Minute Virus of Mice Inhibits Transcription of the Cyclin B1 Gene during Infection
Authors: Fuller Matthew S. , Majumder Kinjal , Pintel David J.
Published: April 2017

Replication of minute virus of mice (MVM) induces a sustained cellular DNA damage response (DDR) which the virus then exploits to prepare the nuclear environment for effective parvovirus takeover. An essential aspect of the MVM-induced DDR is the establishment of a potent premitotic block, which we previously found to be independent of activated p21 and ATR/Chk1 signaling. This arrest, unlike others reported previously, depends upon a significant, specific depletion of cyclin B1 and its encoding RNA, which precludes cyclin B1/CDK1 complex function, thus preventing mitotic entry. We show here that while the stability of cyclin B1 RNA was not affected by MVM infection, the production of nascent cyclin B1 RNA was substantially diminished at late times postinfection. Ectopic expression of NS1 alone did not reduce cyclin B1 expression. MVM infection also reduced the levels of cyclin B1 protein, and RNA levels normally increased in response to DNA-damaging reagents. We demonstrated that at times of reduced cyclin B1 expression during infection, there was a significantly reduced occupancy of RNA polymerase II and the essential mitotic transcription factor FoxM1 on the cyclin B1 gene promoter. Additionally, while total FoxM1 levels remained constant, there was a significant decrease of the phosphorylated, likely active, forms of FoxM1. Targeting of a constitutively active FoxM1 construct or the activation domain of FoxM1 to the cyclin B1 gene promoter via clustered regularly interspaced short palindromic repeats (CRISPR)-enzymatically inactive Cas9 in MVM-infected cells increased both cyclin B1 protein and RNA levels, implicating FoxM1 as a critical target for cyclin B1 inhibition during MVM infection.

IMPORTANCE
Replication of the parvovirus minute virus of mice (MVM) induces a sustained cellular DNA damage response (DDR) which the virus exploits to prepare the nuclear environment for effective takeover. An essential aspect of the MVM-induced DDR is establishment of a potent premitotic block. This block depends upon a significant, specific depletion of cyclin B1 and its encoding RNA that precludes cyclin B1/CDK1 complex functions necessary for mitotic entry. We show that reduced cyclin B1 expression is controlled primarily at the level of transcription initiation. Additionally, the essential mitotic transcription factor FoxM1 and RNA polymerase II were found to occupy the cyclin B1 gene promoter at reduced levels during infection. Recruiting a constitutively active FoxM1 construct or the activation domain of FoxM1 to the cyclin B1 gene promoter via CRISPR-catalytically inactive Cas9 (dCas9) in MVM-infected cells increased expression of both cyclin B1 protein and RNA, implicating FoxM1 as a critical target mediating MVM-induced cyclin B1 inhibition.
Acupuncture Upregulates G Protein Coupled Activity in Samp8 Mice
Authors: Luo Benhua , Zhao Lan , Zhang Xuezhu , Kan Bohong , Liu Yunhe , Jia Yujie , Han Jingxian , Yu Jianchun
Published: April 2017

Background

Transmembrane and intracellular signal transduction of G protein is closely related to the pathophysiology of Alzheimer's disease (AD).

Objective

To explore the effects of Sanjiao acupuncture on G protein signal transduction pathways in the pathogenesis of AD.

Methods

36 senescence-accelerated (SAM) prone 8 mice were divided into three groups that remained untreated (SAMP8, n=12) or received Sanjiao acupuncture (SAMP8+SA, n=12) or control acupuncture (SAMP8+CA, n=12). An additional control group of SAM resistant 1 mice was included (SAMR1 group, n=12). Morris water maze tests were used to investigate learning and memory abilities. Immunoprecipitation and Western blotting were used to study expression of G protein subunits and their activities in the cortex/hippocampus.

Results

Behavioural analysis showed that acupuncture attenuated the severe cognitive deficits observed in untreated/CA-treated SAMP8 mice. The findings of the G protein activation assays via immunoprecipitation and Western blots were that the physiologically coupled activation rate (PCAR) and maximal coupled activation rate (MCAR) of Gαs and Gαi were decreased in the cortex of SAMP8 vs SAMR1 mice. Sanjiao acupuncture induced an upregulation in the PCAR of Gαs and Gαi. In the hippocampus of untreated SAMP8 mice, the PCAR of Gαs and MCAR of both Gαs and Gαi declined, and Sanjiao acupuncture was associated with an upregulation in the MCAR of Gαs and Gαi. There were no significant differences in Gαs and Gαi expression between the groups.

Conclusions

Sanjiao acupuncture attenuates cognitive deficits in a mouse model of AD via upregulation of G protein activity and stabilisation of the cellular signal.
Injuries impair the chance of successful performance by sportspeople: a systematic review
Authors: Drew Michael K , Raysmith Ben P , Charlton Paula C
Published: April 2017

Background

Cost–benefit analyses have been proposed for determining acceptable risk of injury regarding training and competition participation. Currently, there is no best evidence synthesis of the literature evaluating the relationship between injury/illness and chance of success or failure.

Objective

To evaluate the relationship between injury and/or illness and success and/or failure in athletic populations (individual and team sports).

Methods

This review was prospectively registered (PROSPERO CRD42016036729) and a systematic electronic search was conducted in May 2016. Inclusion criterion was any study design describing the association between injury and/or illness and success or failure in athletic performance. Two independent authors screened search results, performed data extraction and assessed methodological quality and strength of evidence using a modified Downs and Black appraisal tool and a modified van Tulder method, respectively.

Results

Of 10 546 titles identified, 14 satisfied the inclusion criteria and 7 had low risk of bias. Outcome measures associated with success and/or failure included: (1) availability of team members, (2) injury incidence, (3) injury burden, (4) squad utilisation and (5, 6) precompetition and in-competition injury. There was strong evidence that (1) increased availability of team members/athletes decreased the risk of failure and (2) precompetition and in-competition injuries were associated with increased risk of failure.

Conclusions

Injuries have a detrimental impact on team and individual athletic success. Increased player availability improves chances of success. Conversely, injuries sustained both prior to and during competition may increase risk of failure. Injury prevention should therefore be a priority for maximising athletic performance.
MerTK expressing hepatic macrophages promote the resolution of inflammation in acute liver failure
Authors: Triantafyllou Evangelos , Pop Oltin T , Possamai Lucia A , Wilhelm Annika , Liaskou Evaggelia , Singanayagam Arjuna , Bernsmeier Christine , Khamri Wafa , Petts Gemma , Dargue Rebecca , Davies Scott P , Tickle Joseph , Yuksel Muhammed , Patel Vishal C , Abeles Robin D , Stamataki Zania , Curbishley Stuart M , Ma Yun , Wilson Ian D , Coen Muireann , Woollard Kevin J , Quaglia Alberto , Wendon Julia , Thursz Mark R , Adams David H , Weston Chris J , Antoniades Charalambos G
Published: April 2017

Objective

Acute liver failure (ALF) is characterised by overwhelming hepatocyte death and liver inflammation with massive infiltration of myeloid cells in necrotic areas. The mechanisms underlying resolution of acute hepatic inflammation are largely unknown. Here, we aimed to investigate the impact of Mer tyrosine kinase (MerTK) during ALF and also examine how the microenvironmental mediator, secretory leucocyte protease inhibitor (SLPI), governs this response.

Design

Flow cytometry, immunohistochemistry, confocal imaging and gene expression analyses determined the phenotype, functional/transcriptomic profile and tissue topography of MerTK+ monocytes/macrophages in ALF, healthy and disease controls. The temporal evolution of macrophage MerTK expression and its impact on resolution was examined in APAP-induced acute liver injury using wild-type (WT) and Mer-deficient (Mer−/−) mice. SLPI effects on hepatic myeloid cells were determined in vitro and in vivo using APAP-treated WT mice.

Results

We demonstrate a significant expansion of resolution-like MerTK+HLA-DRhigh cells in circulatory and tissue compartments of patients with ALF. Compared with WT mice which show an increase of MerTK+MHCIIhigh macrophages during the resolution phase in ALF, APAP-treated Mer−/− mice exhibit persistent liver injury and inflammation, characterised by a decreased proportion of resident Kupffer cells and increased number of neutrophils. Both in vitro and in APAP-treated mice, SLPI reprogrammes myeloid cells towards resolution responses through induction of a MerTK+HLA-DRhigh phenotype which promotes neutrophil apoptosis and their subsequent clearance.

Conclusions

We identify a hepatoprotective, MerTK+, macrophage phenotype that evolves during the resolution phase following ALF and represents a novel immunotherapeutic target to promote resolution responses following acute liver injury.
British Society of Gastroenterology position statement on serrated polyps in the colon and rectum
Authors: East James E , Atkin Wendy S , Bateman Adrian C , Clark Susan K , Dolwani Sunil , Ket Shara N , Leedham Simon J , Phull Perminder S , Rutter Matt D , Shepherd Neil A , Tomlinson Ian , Rees Colin J
Published: April 2017

Serrated polyps have been recognised in the last decade as important premalignant lesions accounting for between 15% and 30% of colorectal cancers. There is therefore a clinical need for guidance on how to manage these lesions; however, the evidence base is limited. A working group was commission by the British Society of Gastroenterology (BSG) Endoscopy section to review the available evidence and develop a position statement to provide clinical guidance until the evidence becomes available to support a formal guideline. The scope of the position statement was wide-ranging and included: evidence that serrated lesions have premalignant potential; detection and resection of serrated lesions; surveillance strategies after detection of serrated lesions; special situations—serrated polyposis syndrome (including surgery) and serrated lesions in colitis; education, audit and benchmarks and research questions. Statements on these issues were proposed where the evidence was deemed sufficient, and re-evaluated modified via a Delphi process until >80% agreement was reached. The Grading of Recommendations, Assessment, Development and Evaluations (GRADE) tool was used to assess the strength of evidence and strength of recommendation for finalised statements.Key recommendation: we suggest that until further evidence on the efficacy or otherwise of surveillance are published, patients with sessile serrated lesions (SSLs) that appear associated with a higher risk of future neoplasia or colorectal cancer (SSLs ≥10 mm or serrated lesions harbouring dysplasia including traditional serrated adenomas) should be offered a one-off colonoscopic surveillance examination at 3 years (weak recommendation, low quality evidence, 90% agreement).
Frequent hypomorphic alleles account for a significant fraction of ABCA4 disease and distinguish it from age-related macular degeneration
Authors: Zernant Jana , Lee Winston , Collison Frederick T , Fishman Gerald A , Sergeev Yuri V , Schuerch Kaspar , Sparrow Janet R , Tsang Stephen H , Allikmets Rando
Published: April 2017

Background

Variation in theABCA4gene is causal for, or associated with, a wide range of phenotypes from early onset Mendelian retinal dystrophies to late-onset complex disorders such as age-related macular degeneration (AMD). Despite substantial progress in determining the causal genetic variation, even complete sequencing of the entire open reading frame and splice sites ofABCA4identifies biallelic mutations in only 60%–70% of cases; 20%–25% remain with one mutation and no mutations are found in 10%–15% of cases with clinically confirmed ABCA4 disease. This study was designed to identify missing causal variants specifically in monoallelic cases of ABCA4 disease.

Methods

Direct sequencing and analysis were performed in a large familial ABCA4 disease cohort of predominately European descent (n=643). Patient phenotypes were assessed from clinical and retinal imaging data.

Results

We determined that a hypomorphicABCA4variant c.5603A>T (p.Asn1868Ile), previously considered benign due to high minor allele frequency (MAF) (~7%) in the general population, accounts for 10% of the disease, >50% of the missing causal alleles in monoallelic cases, ~80% of late-onset cases and distinguishes ABCA4 disease from AMD. It results in a distinct clinical phenotype characterised by late-onset of symptoms (4th decade) and foveal sparing (85%). Intragenic modifying effects involving this variant and another, c.2588G>C (p.Gly863Ala) allele, were also identified.

Conclusions

These findings substantiate the causality of frequent missense variants and their phenotypic outcomes as a significant contribution to ABCA4 disease, particularly the late-onset phenotype, and its clinical variation. They also suggest a significant revision of diagnostic screening and assessment ofABCA4variation in aetiology of retinal diseases.