bluuebunny/crossref_metadata_2025 huggingface dataset:
Caffeine and resistance exercise: the effects of two caffeine doses and the influence of individual perception of caffeine
Authors: Polito Marcos Doederlein , Grandolfi Kamila , de Souza Diego Brito
Published: April 2019

Although caffeine is a widely used ergogenic resource, some information regarding its effects on resistance exercises is still lacking. The objective of the present study was to verify the acute effect of the ingestion of two different doses of caffeine on performance during a session of resistance exercises and to analyze the perception of the subjects in relation to the intake of caffeine. Following a double‐blind, randomised, cross‐over, controlled, and non‐placebo design, 14 trained and healthy men (24.7 ± 6.8 years; 79.8 ± 9.8 kg; 177.3 ± 8.5 cm) performed a training session in chest‐press, shoulder‐press, and biceps curl exercises (3 sets until exhaustion; 70% 1RM; 3 min rest interval; 2 s for each concentric and eccentric phase) on three non‐consecutive days after ingestion of 3 mg.kg−1 caffeine (CAF3), 6 mg.kg−1 caffeine (CAF6), or no substance (CON). Subjects were informed that one of the caffeine doses would be placebo. The total number of repetitions performed in CON (93.6 ± 22.4) was significantly lower than in CAF3 (108.0 ± 19.9, P = 0.02) and in CAF6 (109.3 ± 19.8, P = 0.03) and there were no differences between caffeine doses. Eight subjects noticed that caffeine was in CAF3 and six in CAF6 and there were no differences in the number of repetitions between sessions in which the subjects perceived and did not perceive caffeine. In conclusion, caffeine doses of 3 or 6 mg.kg−1 similarly increased performance in resistance upper limb exercises, independent of the subject's perception of substance ingestion.
Fatigue reduces the complexity of knee extensor torque during fatiguing sustained isometric contractions
Authors: Pethick Jamie , Winter Samantha L. , Burnley Mark
Published: April 2019

The temporal structure, or complexity, of muscle torque output reflects the adaptability of motor control to changes in task demands. This complexity is reduced by neuromuscular fatigue during intermittent isometric contractions. We tested the hypothesis that sustained fatiguing isometric contractions would result in a similar loss of complexity. To that end, nine healthy participants performed, on separate days, sustained isometric contractions of the knee extensors at 20% MVC to task failure and at 100% MVC for 60 s. Torque and surface EMG signals were sampled continuously. Complexity and fractal scaling were quantified by calculating approximate entropy (ApEn) and the detrended fluctuation analysis (DFA) α scaling exponent. Global, central and peripheral fatigue were quantified using maximal voluntary contractions (MVCs) with femoral nerve stimulation. Fatigue reduced the complexity of both submaximal (ApEn from 1.02 ± 0.06 to 0.41 ± 0.04, P < 0.05) and maximal contractions (ApEn from 0.34 ± 0.05 to 0.26 ± 0.04, P < 0.05; DFA α from 1.41 ± 0.04 to 1.52 ± 0.03, P < 0.05). The losses of complexity were accompanied by significant global, central and peripheral fatigue (all P < 0.05). These results demonstrate that a fatigue‐induced loss of torque complexity is evident not only during fatiguing intermittent isometric contractions, but also during sustained fatiguing contractions.
A season long investigation into the effects of injury, match selection and training load on mental wellbeing in professional under 23 soccer players: A team case study
Authors: Abbott Will , Brownlee Thomas E. , Harper Liam D. , Naughton Robert J. , Richardson Andy , Clifford Tom
Published: April 2019

This study examined the influence of injury, match selection and training load on mental wellbeing (MW) in a squad of professional soccer players. Using a longitudinal design, twenty‐five male soccer players (age, 20 ± 1 years, height, 1.80 ± 5.79 m, body mass 76.33 ± 7.52 kg) from the under 23 squad playing in the Premier League 2 division in the UK completed the Warwick–Edinburgh Mental Well‐being Scale (WEMWBS) each week of the 2017/2018 season (37 weeks in total). Injury and non‐selection for the match squad were the only significant predictors of MW (P < 0.05). Injury had the biggest influence on MW that was lower when injured vs. not injured (43.6 ± 5.0 vs. 49.9 ± 3.5, respectively, P = 0.001, ES = 1.48), accounting for 40% of the variation in MW. This increased to 50% when not being selected to play games was also considered. Weekly training loads measured by GPS (total distance, sprint distance and total duration) and individual player win rate did not influence MW (P > 0.05). These findings highlight the importance of monitoring MW in professional soccer players and suggest that injured players and those rarely selected for the match squad should be educated on the strategies available for managing their mental health and wellbeing.
Deposition of Host Matrix Proteins on Breast Implant Surfaces Facilitates Staphylococcus Epidermidis Biofilm Formation: In Vitro Analysis
Authors: Walker Jennifer N , Pinkner Chloe L , Lynch Aaron J L , Ortbal Sarah , Pinkner Jerome S , Hultgren Scott J , Myckatyn Terence M
Published: April 2019

Background

Staphylococcus epidermidis is a primary cause of breast implant-associated infection. S epidermidis possesses several virulence factors that enable it to bind both abiotic surfaces and host factors to form a biofilm. In addition S epidermidis colocalizes with matrix proteins coating explanted human breast implants.

Objectives

The authors sought to identify matrix proteins that S epidermidis may exploit to infect various breast implant surfaces in vitro.

Methods

A combination of in vitro assays was used to characterize S epidermidis strains isolated from human breast implants to gain a better understanding of how these bacteria colonize breast implant surfaces. These included determining the (1) minimum inhibitory and bactericidal concentrations for irrigation solutions commonly used to prevent breast implant contamination; (2) expression and carriage of polysaccharide intercellular adhesin and serine-aspartate repeat proteins, which bind fibrinogen (SdrG) and collagen (SdrF), respectively; and (3) biofilm formation on varying implant surface characteristics, in different growth media, and supplemented with fibrinogen and Types I and III collagen. Scanning electron microscopy and immunofluorescence staining analyses were performed to corroborate findings from these assays.

Results

Textured breast implant surfaces support greater bacterial biofilm formation at baseline, and the addition of collagen significantly increases biomass on all surfaces tested. We found that S epidermidis isolated from breast implants all encoded SdrF. Consistent with this finding, these strains had a clear affinity for Type I collagen, forming dense, highly structured biofilms in its presence.

Conclusions

The authors found that S epidermidis may utilize SdrF to interact with Type I collagen to form biofilm on breast implant surfaces.

Level of Evidence: 5
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction
Authors: Mei Shutao , Li Fuyi , Leier André , Marquez-Lago Tatiana T , Giam Kailin , Croft Nathan P , Akutsu Tatsuya , Smith A Ian , Li Jian , Rossjohn Jamie , Purcell Anthony W , Song Jiangning
Published: April 2019

Human leukocyte antigen class I (HLA-I) molecules are encoded by major histocompatibility complex (MHC) class I loci in humans. The binding and interaction between HLA-I molecules and intracellular peptides derived from a variety of proteolytic mechanisms play a crucial role in subsequent T-cell recognition of target cells and the specificity of the immune response. In this context, tools that predict the likelihood for a peptide to bind to specific HLA class I allotypes are important for selecting the most promising antigenic targets for immunotherapy. In this article, we comprehensively review a variety of currently available tools for predicting the binding of peptides to a selection of HLA-I allomorphs. Specifically, we compare their calculation methods for the prediction score, employed algorithms, evaluation strategies and software functionalities. In addition, we have evaluated the prediction performance of the reviewed tools based on an independent validation data set, containing 21 101 experimentally verified ligands across 19 HLA-I allotypes. The benchmarking results show that MixMHCpred 2.0.1 achieves the best performance for predicting peptides binding to most of the HLA-I allomorphs studied, while NetMHCpan 4.0 and NetMHCcons 1.1 outperform the other machine learning-based and consensus-based tools, respectively. Importantly, it should be noted that a peptide predicted with a higher binding score for a specific HLA allotype does not necessarily imply it will be immunogenic. That said, peptide-binding predictors are still very useful in that they can help to significantly reduce the large number of epitope candidates that need to be experimentally verified. Several other factors, including susceptibility to proteasome cleavage, peptide transport into the endoplasmic reticulum and T-cell receptor repertoire, also contribute to the immunogenicity of peptide antigens, and some of them can be considered by some predictors. Therefore, integrating features derived from these additional factors together with HLA-binding properties by using machine-learning algorithms may increase the prediction accuracy of immunogenic peptides. As such, we anticipate that this review and benchmarking survey will assist researchers in selecting appropriate prediction tools that best suit their purposes and provide useful guidelines for the development of improved antigen predictors in the future.
A coordinate descent approach for sparse Bayesian learning in high dimensional QTL mapping and genome-wide association studies
Authors: Wang Meiyue , Xu Shizhong
Published: April 2019

Motivation

Genomic scanning approaches that detect one locus at a time are subject to many problems in genome-wide association studies and quantitative trait locus mapping. The problems include large matrix inversion, over-conservativeness for tests after Bonferroni correction and difficulty in evaluation of the total genetic contribution to a trait’s variance. Targeting these problems, we take a further step and investigate a multiple locus model that detects all markers simultaneously in a single model.

Results

We developed a sparse Bayesian learning (SBL) method for quantitative trait locus mapping and genome-wide association studies. This new method adopts a coordinate descent algorithm to estimate parameters (marker effects) by updating one parameter at a time conditional on current values of all other parameters. It uses an L2 type of penalty that allows the method to handle extremely large sample sizes (>100 000). Simulation studies show that SBL often has higher statistical powers and the simulated true loci are often detected with extremely small P-values, indicating that SBL is insensitive to stringent thresholds in significance testing.

Availability and implementation

An R package (sbl) is available on the comprehensive R archive network (CRAN) and https://github.com/MeiyueComputBio/sbl/tree/master/R%20packge.

Supplementary information

Supplementary data are available at Bioinformatics online.
Evolution of prodromal Parkinson’s disease and dementia with Lewy bodies: a prospective study
Authors: Fereshtehnejad Seyed-Mohammad , Yao Chun , Pelletier Amelie , Montplaisir Jacques Y , Gagnon Jean-François , Postuma Ronald B
Published: April 2019

Parkinson’s disease has a long prodromal stage with various subclinical motor and non-motor manifestations; however, their evolution in the years before Parkinson’s disease is diagnosed is unclear. We traced the evolution of early motor and non-motor manifestations of synucleinopathy from the stage of idiopathic rapid eye movement (REM) sleep behaviour disorder until defined neurodegenerative disease. During 2004–16, we recruited and then annually followed 154 polysomnography-proven patients with idiopathic REM sleep behaviour disorder, of whom 55 phenoconverted to defined parkinsonism or dementia. Longitudinal data on multiple prodromal features, including the Unified Parkinson’s Disease Rating Scale parts I–III, quantitative motor tests, olfaction, colour vision, cognition, and autonomic functions were gathered annually (average = five follow-up visits, range: 2–12 years). The same measures were also assessed in 102 age- and sex-matched healthy control subjects. By looking backward from the time of dementia or parkinsonism diagnosis, we examined trajectories of each prodromal feature using mixed effect models. Based on analysis, olfactory loss was first to develop, with predicted onset >20 years before phenoconversion. This was followed by impaired colour vision, constipation, and erectile dysfunction, starting 10–16 years prior to phenoconversion. At 7–9 years before phenoconversion, slight urinary dysfunction and subtle cognitive decline could be detected. Among motor symptoms altered handwriting, turning in bed, walking, salivation, speech, and facial expression began to be disrupted starting 7–11 years prior to parkinsonism diagnosis, but remained mild until soon before phenoconversion. Motor examination abnormalities began 5–7 years before phenoconversion, with the alternate tap test having the longest interval (8 years before phenoconversion). Among cardinal motor phenotypes, bradykinesia appeared first, ∼5–6 years prior to phenoconversion, followed by rigidity (Year −3) and tremor (Year −2). With direct prospective evaluation of an idiopathic REM sleep behaviour disorder cohort during phenoconversion, we documented an evolution of prodromal manifestations similar to that predicted by pathological staging models, with predicted prodromal intervals as long as 20 years.
Real-Time Topic Detection with Dynamic Windows
Authors: Su Na , Ji Shujuan , Liu Jimin
Published: April 2019

Microblog is a popular social network in which hot topics propagate online rapidly. Real-time topic detection can not only understand public opinion well but also bring high commercial value. We design a method for real-time microblog data analysis in order to detect popular long lasting events as well as emerging events. Firstly, a mining frequent items algorithm on microblog data stream is proposed to count approximate word frequency. This mining frequent items algorithm can find the frequent words for some time. Secondly, the windows size of the monitored words is adjusted dynamically according to the duration time and the evolution of events. Lastly, new topics and trends of existing topics can be detected by using dynamic clustering algorithm based on vector space model. Experimental results show that the proposed algorithms can improve performance in terms of running time and accuracy.
piRDisease v1.0: a manually curated database for piRNA associated diseases
Authors: Muhammad Azhar , Waheed Ramay , Khan Nauman Ali , Jiang Hong , Song Xiaoyuan
Published: April 2019

In recent years, researches focusing on PIWI-interacting RNAs (piRNAs) have increased rapidly. It has been revealed that piRNAs have strong association with a wide range of diseases; thus, it becomes very important to understand piRNAs’ role(s) in disease diagnosis, prognosis and assessment of treatment response. We searched more than 2500 articles using keywords, such as `PIWI-interacting RNAs’ and `piRNAs’, and further scrutinized the articles to collect piRNAs-disease association data. These data are highly complex and heterogeneous due to various types of piRNA idnetifiers (IDs) and different reference genome versions. We put considerable efforts into removing redundancy and anomalies and thus homogenized the data. Finally, we developed the piRDisease database, which incorporates experimentally supported data for piRNAs’ relationship with wide range of diseases. The piRDisease (piRDisease v1.0) is a novel, comprehensive and exclusive database resource, which provides 7939 manually curated associations of experimentally supported 4796 piRNAs involved in 28 diseases. piRDisease facilitates users by providing detailed information of the piRNA in respective disease, explored by experimental support, brief description, sequence and location information. Considering piRNAs’ role(s) in wide range of diseases, it is anticipated that huge amount of data would be produced in the near future. We thus offer a submitting page, on which users or researches can contribute in to update our piRDisease database.
Cloning and analysis of Ophiocordyceps xuefengensis mating type (MAT) loci
Authors: Zou Juan , Zeng Ting-Ting , He Zheng-Mi , Zhang Ping , Chen Zuo-Hong
Published: April 2019

The entomopathogenic fungus Ophiocordyceps xuefengensis, a recently described species and identified as the sister taxon of Ophiocordyceps sinensis, is a desirable alternative to O. sinensis. The mating systems of fungi play a vitally important role in the regulation of sexual reproduction and evolution, but the mating type loci of O. xuefengensis were completely unknown. In this study, the mating systems of O. xuefengensis were analyzed. The conserved α-box region of the MAT1-1-1 and HMG-box of MAT1-2-1 were successfully obtained by PCR amplification. The distribution of both mating types in different tissues of wild and cultivated O. xuefengensis growth was detected and analyzed. The results showed that the asci always harbored both mating types, whereas the sclerotium, the stipe and each isolated strain of wild O. xuefengensis always had only one idiomorph, either MAT1-1 or MAT1-2, which confirmed that O. xuefengensis is heterothallic. The MAT1-1 locus of O. xuefengensis harbors MAT1-1-1, MAT1-1-2 and MAT1-1-3, and MAT1-2 contains the MAT1–2-1 gene. Southern blot analysis showed the MAT-1-1-1 and MAT-1-2-1 genes were single-copy in O. xuefengensis. These results will help to understand its life cycle and support artificial cultivation of O. xuefengensis.
The Cryptococcus neoformans monocarboxylate transporter Jen4 is responsible for increased 3-bromopyruvate sensitivity
Authors: Niedźwiecka Katarzyna , Ribas David , Casal Margarida , Ułaszewski Stanisław
Published: April 2019

In the last decades, 3-bromopyruvate (3BP) has been intensively studied as a promising anticancer and antimicrobial agent. The transport of this drug inside the cell is a critical step for its toxicity in cancer and microorganisms. The Cryptococcus neoformans is the most sensitive species of microorganisms toward 3BP. Its cells exhibit the highest uptake rate of 3BP among all tested fungal strains. In Saccharomyces cerevisiae cells, the Jen1 transporter was found to be responsible for 3BP sensitivity. The deletion of Jen1 resulted in the abolishment of 3BP mediated transport. We functionally characterized the Jen4 protein, a Jen1 homologue of C. neoformans, and its role in the phenotypic 3BP sensitivity. The deletion of the CNAG_04704 gene, which encodes Jen4, was found to impair the mediated transport of 3BP and decrease 3BP sensitivity. Further heterologous expression of Jen4 in the S. cerevisiae jen1Δ ady2Δ strain restored the mediated transport of 3BP. The application of a green fluorescent protein fusion tag with the CNAG_04704, revealed the Jen4 labeled on the plasma membrane. The identification of 3BP transporters in pathogen cells is of great importance for understanding the mechanisms of 3BP action and to anticipate the application of this compound as an antimicrobial drug.
A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis
Authors: Arimoto Asuka , Hikosaka-Katayama Tomoe , Hikosaka Akira , Tagawa Kuni , Inoue Toyoshige , Ueki Tatsuya , Yoshida Masa-aki , Kanda Miyuki , Shoguchi Eiichi , Hisata Kanako , Satoh Noriyuki
Published: April 2019

Background

Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis.

Findings

To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired-end and mate-pair libraries) and PacBio sequencing. RNA sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ~17–kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was ~656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although ~70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, ~99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules.

Conclusions

Our present sequencing and assembly of the P. naikaiensis nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.
Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch)
Authors: Chen Wenbo , Shakir Sara , Bigham Mahdiyeh , Richter Annett , Fei Zhangjun , Jander Georg
Published: April 2019

Background

The corn leaf aphid (Rhopalosiphum maidis Fitch) is the most economically damaging aphid pest on maize (Zea mays), one of the world's most important grain crops. In addition to causing direct damage by removing photoassimilates, R. maidis transmits several destructive maize viruses, including maize yellow dwarf virus, barley yellow dwarf virus, sugarcane mosaic virus, and cucumber mosaic virus.

Findings

The genome of a parthenogenetically reproducing R. maidis clone was assembled with a combination of Pacific Biosciences (207-fold coverage) and Illumina (83-fold coverage) sequencing. The 689 assembled contigs, which have an N50 size of 9.0 megabases (Mb) and a low level of heterozygosity, were clustered using Phase Genomics Hi-C interaction maps. Consistent with the commonly observed 2n = 8 karyotype of R. maidis, most of the contigs (473 spanning 321 Mb) were successfully oriented into 4 scaffolds. The genome assembly captured the full length of 95.8% of the core eukaryotic genes, indicating that it is highly complete. Repetitive sequences accounted for 21.2% of the assembly, and a total of 17,629 protein-coding genes were predicted with integrated evidence from ab initio and homology-based gene predictions and transcriptome sequences generated with both Pacific Biosciences and Illumina. An analysis of likely horizontally transferred genes identified 2 from bacteria, 7 from fungi, 2 from protozoa, and 9 from algae. Repeat elements, transposons, and genes encoding likely detoxification enzymes (cytochrome P450s, glutathione S-transferases, carboxylesterases, uridine diphosphate–glucosyltransferases, and ABC transporters) were identified in the genome sequence. Other than Buchnera aphidicola (642,929 base pairs, 602 genes), no endosymbiont bacteria were found in R. maidis.

Conclusions

A high-quality R. maidis genome was assembled at the chromosome level. This genome sequence will enable further research related to ecological interactions, virus transmission, pesticide resistance, and other aspects of R. maidis biology. It also serves as a valuable resource for comparative investigation of other aphid species.
On the robustness of attenuation measurements on teleseismic P waves: insights from micro-array analysis of the 2017 North Korean nuclear test
Authors: Bezada M J , Byrnes J , Eilon Z
Published: April 2019

Despite their importance as a fundamental constraint on Earth properties, regional-scale measurements of body-wave seismic attenuation are scarce. This is partially a result of the difficulty in producing robust estimates of attenuation. In this paper, we focus on measuring differential attenuation on records of teleseismic P waves. We examine a unique data set of five records of the North Korean nuclear test of 2017 measured at five broad-band seismic stations deployed within a few metres of each other but using different installation procedures. Given their extreme proximity, we expect zero differential intrinsic attenuation between the different records. However, we find that different attenuation measurement methods and implementation parameters in fact produce significant apparent differential attenuation (Δt*). Frequency-domain methods yield a wide range of Δt* estimates between stations, depending on measurement bandwidth and nuances of signal processing. This measurement instability increases for longer time windows. Time domain methods are largely insensitive to the frequency band being considered but are sensitive to the time window that is chosen. We determine that signal-generated noise can affect measurements in both the frequency and time domain. In some cases, the range of results amounts to a significant fraction of the range of differential attenuation across the conterminous United States as determined by a recent study. We suggest some approaches to manage the inherent instability in these measurements and recommend best practices to confidently estimate body wave attenuation.
Value and effectiveness of National Immunization Technical Advisory Groups in low- and middle-income countries: a qualitative study of global and national perspectives
Authors: Bell Sadie , Blanchard Laurence , Walls Helen , Mounier-Jack Sandra , Howard Natasha
Published: April 2019

The Global Vaccine Action Plan proposes that every country establish or have access to a National Immunization Technical Advisory Group (NITAG) by 2020. The NITAG role is to produce evidence-informed recommendations that incorporate local context, to guide national immunization policies and practice. This study aimed to explore the value and effectiveness of NITAGs in low- and middle-income countries (LMICs), identifying areas in which NITAGs may require further support to improve their functionality and potential barriers to global investment. A multi-methods study design was used, comprising 134 semi-structured interviews and 82 literature review sources that included 38 countries. Interviews were conducted with 53 global/regional and 81 country-level participants able to provide insight into NITAG effectiveness, including NITAG members, national immunization programme staff, and global agency representatives (e.g. the World Health Organisation, the Bill and Melinda Gates Foundation, Gavi the Vaccine Alliance). The review, including published and unpublished sources on NITAGs in LMICs, was conducted to supplement and corroborate interview findings. Data were analysed thematically. NITAGs were described as valuable in promoting evidence-informed vaccination decision-making, with NITAG involvement enhancing national immunization programme strength and sustainability. Challenges to NITAG effectiveness included: (1) unreliable funding; (2) insufficient diversity of member expertise; (3) inadequate conflicts of interest management procedures; (4) insufficient capacity to access and use evidence; (5) lack of transparency; and (6) limited integration with national decision-making processes that reduced the recognition and incorporation of NITAG recommendations. LMIC NITAGs have developed significantly in the past decade. Well-functioning NITAGs were trusted national resources that enhanced country ownership of immunization provision. However, many LMIC NITAGs require additional technical and funding support to strengthen quality and effectiveness, while maintaining impartiality and ensuring sufficient integration with national decision-making processes. Barriers to sustainable global support need to be addressed for LMIC NITAGs to both continue and develop further.
Emergence of NDM-1-producing Klebsiella pneumoniae in Greece: evidence of a widespread clonal outbreak
Authors: Politi Lida , Gartzonika Konstantina , Spanakis Nicholas , Zarkotou Olympia , Poulou Aggeliki , Skoura Lemonia , Vrioni Georgia , Tsakris Athanasios
Published: April 2019

Objectives

NDM-producing Enterobacteriaceae clinical isolates remain uncommon in the European region. We describe the emergence and broad dissemination of one successful NDM-1-producing Klebsiella pneumoniae clone in Greek hospitals.

Methods

During a 4 year survey (January 2013–December 2016), 480 single-patient carbapenem non-susceptible K. pneumoniae isolates, phenotypically MBL positive, were consecutively recovered in eight Greek hospitals from different locations and subjected to further investigation. Antimicrobial susceptibility testing, combined-disc test, identification of resistance genes by PCR and sequencing, molecular fingerprinting by PFGE, plasmid profiling, replicon typing, conjugation experiments and MLST were performed.

Results

Molecular analysis confirmed the presence of the blaNDM-1 gene in 341 (71%) K. pneumoniae isolates. A substantially increasing trend of NDM-1-producing K. pneumoniae was noticed during the survey (R2 = 0.9724). Most blaNDM-1-carrying isolates contained blaCTX-M-15, blaOXA-1, blaOXA-2 and blaTEM-1 genes. PFGE analysis clustered NDM-1 producers into five distinct clonal types, with five distinct STs related to each PFGE clone. The predominant ST11 PFGE clonal type was detected in all eight participating hospitals, despite adherence to the national infection control programme; it was identical to that observed in the original NDM-1 outbreak in Greece in 2011, as well as in a less-extensive NDM-1 outbreak in Bulgaria in 2015. The remaining four ST clonal types (ST15, ST70, ST258 and ST1883) were sporadically detected. blaNDM-1 was located in IncFII-type plasmids in all five clonal types.

Conclusions

This study gives evidence of possibly the largest NDM-1-producing K. pneumoniae outbreak in Europe; it may also reinforce the hypothesis of an NDM-1 clone circulating in the Balkans.
Helicoverpa zea (Lepidoptera: Noctuidae) Preference for Plant Structures, and Their Location, Within Bt Cotton Under Different Nitrogen and Irrigation Regimes
Authors: Braswell Lewis R , Reisig Dominic D , Sorenson Clyde E , Collins Guy D
Published: April 2019

Helicoverpa zea Boddie is a common economic pest of cotton (Gossypium hirsutum L.), including transgenic cotton varieties that express Bacillus thuringiensis (Bt). Helicoverpa zea oviposition is similar in Bt and non-Bt cotton, but behavior of H. zea larvae can be different in the presence of Bt, with neonates moving away from terminals faster in single-toxin Bt than non-Bt cotton or avoiding Bt-treated diet in the lab. We quantified H. zea oviposition and larval distribution on structures within cotton plants in small plot experiments of Cry1Ac + Cry1F cotton for 2 yr under different irrigation and nitrogen treatments. More eggs were oviposited on plants receiving nitrogen application during 2016 and on leaves in the top section of irrigated plants during 2017, but other treatment effects on eggs or larvae were minimal. Helicoverpa zea eggs were most common on leaves in the top third of plants at position zero and middle section of cotton plants throughout the season, but some oviposition occurred on fruiting structures as well. First and second instars were more common on squares in the top section of plants during 2016 and bolls in the middle and lower sections during 2017 due to oviposition lower in the canopy during 2017. During both years, third through fifth instars were more common on bolls in the middle and lower section of plants closer to the main stem. These findings have resistance management implications as extended larval feeding on bolls could optimize nutrition, decrease Bt susceptibility, and potentially influence behavioral resistance.
A Microinjection Method for Infecting the Planthopper Sogatella furcifera (Hemiptera: Delphacidae) with the Southern Rice Black-Streaked Dwarf Virus
Authors: Hu Kui , Qiu Lin , Zhang Yurong , Du Yu , He Hualiang , Ding Wenbing , Li Youzhi
Published: April 2019

The southern rice black-streaked dwarf virus (SRBSDV) causes significant economic damage to rice crops. This virus is transmitted to rice plants by the planthopper Sogatella furcifera (Horváth) in a persistent, circular, and propagative manner. Researchers currently lack suitable methods for assaying the activity of SRBSDV in vitro and preserving the virus all year. We used a microinjection method to directly inject SRBSDV extracts into the hemocoel of S. furcifera nymphs. SRBSDV was subsequently detected by Reverse Transcription-Polymerase Chain Reaction in more than 56.7% of the insects after 5 d and 60% of healthy rice plants fed by these insects also became SRBSDV infected. Moreover, injecting planthopper with an extract of SRBSDV-infected rice plant that had been frozen at −80°C for 220 d caused 63.3% to become viruliferous. These results indicate that SRBSDV can be successfully transmitted to S. furcifera by microinjection, and that extracts of SRBSDV-infected rice plants frozen at −80°C for 220 d still contain sufficient active SRBSDV to infect S. furcifera. We provide a novel way to preserve SRBSDV all year by injecting S. furcifera with the SRBSDV extract.
Magnetic domains characterization of crystalline Fe3O4 under DC and AC magnetic field
Authors: Li Xiang , Zhu Xiaojuan , Pan Dong , Xue Yan , Jia Qingqing , Liu Fang , Li Zhenghua
Published: April 2019

Fe3O4 nanoparticles with crystallite sizes around 10 nm were synthesized by an emulsion method. X-ray diffractometer (XRD) shows that nanocrystalline Fe3O4 possesses face center cubic structure. The magnetic characteristics are investigated by magnetic force microscopy (MFM). Magnetic field directions were applied parallel and perpendicular to the Fe3O4 sample surface for magnetic measurements. Under the perpendicular magnetic field, the phase images of most magnetic nanoparticles exhibit bright or dark MFM contrast. In comparison, the parallel field phase images display a bright–dark dipole MFM contrast, with in-plane magnetic domain configurations. Furthermore, the investigation of strip domains inside Fe3O4 particles under altering magnetic fields indicates the existence of magnetic anisotropy energies, dipole energies as well as inter-grain coupling energies inside the clusters. This approach for probing magnetic responses on nanoscale magnetic domains can be further extended to the analysis of local physical features.
Cognitive Function in Sickle Cell Disease Across Domains, Cerebral Infarct Status, and the Lifespan: A Meta-Analysis
Authors: Prussien Kemar V , Jordan Lori C , DeBaun Michael R , Compas Bruce E
Published: April 2019

Objective

To provide a comprehensive quantitative review of neurocognitive function in sickle cell disease (SCD) across multiple domains, cerebral infarct status, and the lifespan.

Methods

One hundred and ten studies were identified in PubMed, MedLine, and PsycINFO involving 110 studies of 3,600 participants with SCD and 1,127 sibling or health controls.

Results

Meta-analytic findings indicate significant deficits across all neurocognitive domains, age groups, and infarct status. Significant deficits relative to the normative mean ranged from Hedges’ g = −.39 to g = −.63 in preschool children, g = −.83 to g = −1.18 in school-aged children and adolescents, and g = −.46 to g = −.86 in adults. Deficits in full scale IQ (FSIQ), verbal reasoning, perceptual reasoning, and executive function increased from preschool to school-aged samples. However, findings also showed that deficits were smaller in adult samples relative to school-aged samples, likely due to sampling bias in adult studies. Findings across infarct status in sickle cell anemia showed that deficits ranged from g = −.54 to g = −.65 in samples without infarcts, g = −.52 to g = −1.03 in samples with silent cerebral infarct, and g = −1.35 to g = −1.82 in samples with stroke. Deficits in each domain increased in magnitude from no infarct or stroke, to silent cerebral infarct, to overt stroke.

Conclusion

Individuals with SCD are at risk for cognitive deficits across domains, infarct status, and the lifespan. More research is necessary to determine unbiased effects for cognitive function in adults with SCD.
The decommissioning of oil and gas fields: Egyptian law and policy
Authors: Elshazly Mostafa
Published: April 2019

Legal issues around the decommissioning of oil and gas fields have generally been given insufficient attention by energy lawyers in most jurisdictions worldwide. Oil and gas lawyers, and other stakeholders in Egypt, face the same challenge. This article discusses the topic of the decommissioning of oil and gas fields in the context of the legal aspects and the regulatory framework for decommissioning in Egypt, demonstrating the main challenges relating to the legal framework for decommissioning arrangements in the country. At the heart of the legal challenges associated with the decommissioning of oil and gas fields in Egypt lies the most important question: who should pay the associated costs, and when? This article also presents some recommendations to enhance the current regulatory framework for the decommissioning of oil and gas fields in Egypt, to maintain the balance of interests between international oil companies and national oil companies active in Egypt.
The association between BMI and BSA–temozolomide-induced myelosuppression toxicities: a correlative analysis of NRG oncology RTOG 0525
Authors: Robins H Ian , Eickhoff Jens , Gilbert Mark R , Armstrong Terri S , Shi Wenyin , De Groot John F , Schultz Christopher J , Hunter Grant K , Valeinis Egils , Roach Mack , Youssef Emad F , Souhami Luis , Howard Steve P , Lieberman Frank S , Herman James G , Zhang Peixin , Mehta Minesh P
Published: April 2019

Background

Fearing increased myelotoxicity, many practitioners adjust the body surface area (BSA)-calculated doses in obese patients. Regarding temozolomide (TMZ), a prior study suggested men with a BSA >2 m2 may experience increased toxicity; however, surprisingly, the inverse observation was noted in women, ie, BSA <2 m2 was associated with higher toxicity. To further clarify this issue, data derived from a large clinical trial were analyzed.

Methods

The incidence of grade 3 and 4 myelotoxicity in a newly diagnosed glioblastoma phase 3 trial (RTOG 0525) was statistically correlated with BMI and separately with BSA. All patients received radiation and TMZ followed by adjuvant standard dose TMZ vs dose-dense TMZ; dosing regimen-associated myelotoxicity and BMI/BSA were analyzed separately. Obesity was defined as a BMI ≥30.

Results

There was no statistically significant correlation between gender and BSA and the occurrence of myotoxicities. For the standard arm, surprisingly the incidence of grade 3/4 myotoxicities in patients with a BMI <30 was significantly higher than in patients with a BMI ≥30 (12% vs 1%, odds ratio [OR] 12.5, P < .001). There was no significant difference between obese and nonobese patients (BMI “cut-point” of 30) in the dose-dense arm (OR = 0.9, 95% confidence interval: 0.4–1.6). The grade hematological 3/4 toxicity rate was significantly higher in women vs men (14% vs 8%) P = .009 in spite of the lack of association between gender and BSA or BMI.

Conclusion

TMZ dosing based on actual BSA is recommended with the caveat that woman are likely at higher toxicity risk.
Universal bound on sampling bosons in linear optics and its computational implications
Authors: Yung Man-Hong , Gao Xun , Huh Joonsuk
Published: April 2019

In linear optics, photons are scattered in a network through passive optical elements including beam splitters and phase shifters, leading to many intriguing applications in physics, such as Mach–Zehnder interferometry, the Hong–Ou–Mandel effect, and tests of fundamental quantum mechanics. Here we present the fundamental limit in the transition amplitudes of bosons, applicable to all physical linear optical networks. Apart from boson sampling, this transition bound results in many other interesting applications, including behaviors of Bose–Einstein condensates (BEC) in optical networks, counterparts of Hong–Ou–Mandel effects for multiple photons, and approximating permanents of matrices. In addition, this general bound implies the existence of a polynomial-time randomized algorithm for estimating the transition amplitudes of bosons, which represents a solution to an open problem raised by Aaronson and Hance (Quantum Inf Comput 2012; 14: 541–59). Consequently, this bound implies that computational decision problems encoded in linear optics, prepared and detected in the Fock basis, can be solved efficiently by classical computers within additive errors. Furthermore, our result also leads to a classical sampling algorithm that can be applied to calculate the many-body wave functions and the S-matrix of bosonic particles.
Comparing fatal occupational accidents in Denmark and Sweden 1993–2012
Authors: Hansen C D
Published: April 2019

Background

Denmark and Sweden are in many respects two very similar countries with similar welfare state systems and work environment authorities. Nevertheless, marked differences in the incidence of fatal occupational accidents have been found in earlier comparisons of the two countries.

Aims

To investigate differences in the incidence of fatal occupational accidents in the period from 1993 to 2012 to establish to what extent characteristics of the deceased can explain some of the difference between the two countries.

Methods

Analyses of the accident registers of the two countries’ national work environment authorities with supplemental linkages to official registers on employment status are used to determine the incidence of fatal occupational accidents for different groups. The analysis is based on 2375 accidents (1068 in Denmark and 1307 in Sweden) over the period of 20 years. Poisson regression is used to derive incidence rates over time for specific groups.

Results

In the study period, the incidence of fatal occupational accidents decreased in both countries (incidence rate ratio [IRR]: 0.95), although the incidence was on average higher in Denmark (IRR: 1.20) and grew larger over time. This difference did not disappear after adjusting for age, sex and industry among the deceased (IRR: 1.12).

Conclusions

The incidence of fatal occupational accidents was slightly higher in Denmark in the entire period. The difference could not be explained completely by sociodemographic differences or differences related to the labour market structure in the two countries, i.e. other factors (e.g. cultural) may play a role in producing the difference.
Efficacy and safety of switching from rituximab to biosimilar CT-P10 in rheumatoid arthritis: 72-week data from a randomized Phase 3 trial
Authors: Shim Seung Cheol , Božić-Majstorović Ljubinka , Berrocal Kasay Alfredo , El-Khouri Elias Chalouhi , Irazoque-Palazuelos Fedra , Cons Molina Francisco Fidencio , Medina-Rodriguez Francisco G , Miranda Pedro , Shesternya Pavel , Chavez-Corrales Jose , Wiland Piotr , Jeka Slawomir , Garmish Olena , Hrycaj Pawel , Fomina Natalia , Park Won , Suh Chang-Hee , Lee Sang Joon , Lee Sung Young , Bae Yun Ju , Yoo Dae Hyun
Published: April 2019

Objective

To evaluate the efficacy and safety of CT-P10, a rituximab biosimilar after a single switch, during a multinational, randomized, double-blind Phase 3 trial involving patients with RA.

Methods

Patients received 48 weeks’ treatment with CT-P10 or United States- or European Union-sourced reference rituximab (US-RTX and EU-RTX, respectively). Patients entering the extension period (weeks 48–72) remained on CT-P10 (CT-P10/CT-P10; n = 122) or US-RTX (US-RTX/US-RTX; n = 64), or switched to CT-P10 from US-RTX (US-RTX/CT-P10; n = 62) or EU-RTX (EU-RTX/CT-P10; n = 47) for an additional course. Efficacy endpoints included Disease Activity Score using 28 joints (DAS28), American College of Rheumatology (ACR) response rates, and quality of life-related parameters. Pharmacodynamics, immunogenicity and safety were also assessed.

Results

At week 72, similar improvements were observed by disease activity parameters including DAS28 and ACR response rate in the four extension period treatment groups. Quality of life improvements at week 72 vs baseline were similarly shown during the extension period in all groups. Newly developed anti-drug antibodies were detected in two patients following study drug infusion in the extension period. Similar pharmacodynamic and safety profiles were observed across groups.

Conclusion

Long-term use of CT-P10 up to 72 weeks was effective and well tolerated. Furthermore, switching from reference rituximab to CT-P10 in RA was well tolerated and did not result in any clinically meaningful differences in terms of efficacy, pharmacodynamics, immunogenicity and safety.

Trail registration

ClinicalTrials.gov, http://clinicaltrials.gov, NCT02149121.
Sirt1 ameliorates monosodium urate crystal–induced inflammation by altering macrophage polarization via the PI3K/Akt/STAT6 pathway
Authors: Liu Lei , Zhu Xiaoxia , Zhao Tianyi , Yu Yiyun , Xue Yu , Zou Hejian
Published: April 2019

Objectives

Acute gout is an inflammatory response to MSU crystals. In our previous research, Sirt1 was shown to have an effect in preventing acute gouty inflammation. In the current study, we aimed to investigate the underlying mechanism involving Sirt1 in acute gout.

Methods

The cytological changes and Sirt1 expression in the synovium were observed in patients with acute or intermittent gout. The effect of Sirt1 and its mechanism in gout were studied in macrophages, C57BL/6 mice and Sirt1+/− mice.

Results

Sirt1 expression was increased in the peripheral blood mononuclear cells (PBMCs) of patients with acute gout but not in the chronic tophus tissue. The arthritis score and numbers of inflammatory cells in injured paw tissue from murine gout models were upregulated in Sirt1+/− mice compared with wild-type mice. A PCR array of the paw tissue from murine gout models indicated that Sirt1 activation might attenuate MSU-induced inflammation by altering the polarization state of macrophages. Furthermore, in patients with acute gout, the phagocytosis of MSU crystals by a macrophage was found in a smear of the joint fluid and large amounts of macrophages were also found in the synovium. The activation of Sirt1 in gouty mice actually decreased the tendency toward M1 polarization. The inhibition of PI3K/Akt partially blocked the anti-inflammatory effect of Sirt1 and the translocation of STAT6, and phosphorylated STAT6 expression was decreased in RAW 264.7 cells treated with MSU crystals.

Conclusion

Our studies revealed that Sirt1 ameliorates MSU-induced inflammation by altering macrophage polarization via the PI3K/Akt/STAT6 pathway.