bluuebunny/crossref_metadata_2025 huggingface dataset:
Gas-phase deposited plasmonic nanoparticles supported on 3D-graphene/nickel foam for highly SERS detection
Authors: Mao Peng , Chen Qiang , Wang Guang-hou , Han Min
Published: May 2019

In this work, we proposed a novel three-dimensional (3D) plasmonic nanostructure based on porous graphene/nickel foam (GNF) and gas-phase deposited Ag nanoparticles (NPs). Ag NPs with high density were directly deposited on the surface of 3D GNF by performing a novel cluster beam deposition approach. In comparison with traditional Ag substrate (SiO2/Ag), such hot-spots enriched 3D nanostructure showed extremely high electromagnetic field enhancement under incident light irradiation which could be used as a sensitive chemical sensor based on surface enhanced Raman scattering (SERS). The experimental results demonstrated that the proposed nanostructure showed superior SERS performance in terms of Raman signal reproducibility and sensitivity for the probe molecules. 3D full-wave simulation showed that the enhanced SERS performance in this 3D hierarchical plasmonic nanostructure was mainly obtained from the hot-spots between Ag NPs and the near-field coupling between Ag NPs and GNF scaffolds. This work can provide a novel assembled SERS substrate as a SERS-based chemical sensor in practical applications.
CO oxidation by neutral gold-vanadium oxide clusters
Authors: Ou Shu-hua , Chen Jiao-jiao , Li Xiao-na , Wang Li-na , Ma Tong-mei , He Sheng-gui
Published: May 2019

Oxidation of CO by gas-phase atomic clusters is being actively studied to understand the molecular-level mechanisms of heterogeneous CO oxidation over related catalytic surfaces. However, it is experimentally challenging to study CO oxidation by neutral heteronuclear metal oxide clusters because of the difficulty of cluster ionization and detection without fragmentation. Herein, the neutral AuVO2−4 clusters were experimentally generated and their reactions with CO and O2 were studied. The experimental results showed that CO adsorption is the dominant channel on the interactions of AuVO4 and AuVO3 with CO, and AuVO2 can pick up an O2 molecule to generate AuVO4. Theoretical studies indicated that the oxidation of the trapped CO in AuVO3,4CO into CO2 is exothermic while the reaction barriers have to be overcome at the elevated temperatures. A catalytic cycle for CO oxidation by AuVO2−4 is proposed.
van der Waals interactions in bimolecular reactions
Authors: Cao Jian-wei , Li Feng-yi , Xia Wen-sha , Bian Wen-sheng
Published: May 2019

The van der Waals (vdW) interaction is very important in fields of physics, biology and chemistry, and its role in reaction dynamics is an issue of great interest. In this review, we focus on the recent progresses in the theoretical and experimental studies on the vdW interaction in bimolecular reactions. In particular, we review those studies that have advanced our understanding of how the vdW interaction can strongly influence the dynamics in both direct activated and complex-forming reactions, and further extend the discussion to the polyatomic reactions involving more atoms and those occurring at cold and ultracold temperatures. We indicate that an accurate description of the delicate vdW structure and long-range potential remains a challenge nowadays in either ab initio calculations or the fitting of the potential energy surfaces. We also present an explanation on the concept of vdW saddle proposed by us recently which may have general importance.
RETRACTED ARTICLE: Single joint exercises do not provide benefits in performance and anthropometric changes in recreational bodybuilders
Authors: Barbalho Matheus , Coswig Victor , Raiol Rodolfo , Fisher James , Steele James , Bianco Antonino , Gentil Paulo
Published: May 2019

We, the Editor‐in‐Chief and Publishers of the European Journal of Sport Science, retract the following article:

Matheus Barbalho, Victor Coswig, Rodolfo Raiol, James Fisher, James Steele, Antonino Bianco, Paulo Gentil, ‘Single joint exercises do not provide benefits in performance and anthropometric changes in recreational bodybuilders’, European Journal of Sport Science, 20:1, 72‐79, DOI: 10.1080/17461391.2019.1611932

Two authors of the original article (James Fisher, and James Steele) raised questions regarding the data integrity and requested that it be retracted. Following data concerns raised in the published White Paper below, an external statistical review was undertaken.

Vigotsky, A. D., Nuckols, G. L., Fisher, J., Heathers, J., Krieger, J., Schoenfeld, B. J., Giessing, J., Steele, J. (2020, July 18). Improbable data patterns in the work of Barbalho et al. https://doi.org/10.31236/osf.io/sg3wm

The White Paper includes two authors who are also co‐authors of the above paper by Barbalho et al., published in the European Journal of Sport Science (James Fisher, and James Steele). We informed all of the authors, as well as the first author's institution, about these concerns, and invited them to respond. Having considered the evaluation report from the external review, as well as author and institutional responses, we find the data and findings in the article to be unreliable and invalid.

All authors have been informed of our decision to retract this article. The authors James Fisher, James Steele, and Antonino Bianco wish to record their agreement with the decision to retract to be noted within this retraction statement.

We have been informed in our decision‐making by our policy on publishing ethics and integrity and the guidance of COPE guidelines on retractions.

The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
Nanosecond Pulse Generation with Silver Nanoparticle Saturable Absorber*
Authors: Rosdin R. Z. R. R. , Ahmad M. T. , Muhammad A. R. , Jusoh Z. , Arof H. , Harun S. W.
Published: May 2019

Nanosecond pulse generation in an erbium-doped fiber laser (EDFL) passively mode-locked by a silver nanoparticle (SNP)-based saturable absorber (SA) is experimentally demonstrated. The SA is fabricated by depositing a nanosized SNP layer onto the surface of polyvinyl alcohol film through the thermal evaporation process. By inserting the SA into an EDFL cavity, stable mode-locked operation is achieved at 1561.5 nm with the maximum pulse energy up to 52.3 nJ. The laser operates at a pulse repetition frequency of 1.0 MHz with a pulse width of 202 ns. These results suggest that SNPs could be developed as an effective SA for mode-locking pulse generation.
Mechanical Properties of Formamidinium Halide Perovskites FABX3 (FA=CH(NH2)2; B=Pb, Sn; X=Br, I) by First-Principles Calculations*
Authors: Guo Lei , Tang Gang , Hong Jiawang
Published: May 2019

The mechanical properties of formamidinium halide perovskites FABX3 (FA=CH(NH2)2; B=Pb, Sn; X=Br, I) are systematically investigated using first-principles calculations. Our results reveal that FABX3 perovskites possess excellent mechanical flexibility, ductility and strong anisotropy. We shows that the planar organic cation FA+ has an important effect on the mechanical properties of FABX3 perovskites. In addition, our results indicate that (i) the moduli (bulk modulus B, Young’s modulus E, and shear modulus G) of FABBr3 are larger than those of FABI3 for the same B atom, and (ii) the moduli of FAPbX3 are larger than those of FASnX3 for the same halide atom. The reason for the two trends is demonstrated by carefully analyzing the bond strength between B and X atoms based on the projected crystal orbital Hamilton population method.
Anisotropic Transport on Monolayer and Multilayer Phosphorene in the Presence of an Electric Field*
Authors: Fu Gufeng , Cheng Fang
Published: May 2019

We demonstrate theoretically the anisotropic quantum transport of electrons through an electric field on monolayer and multilayer phosphorene. Using the long-wavelength Hamiltonian with continuum approximation, we find that the transmission probability for transport through an electric field is an oscillating function of incident angle, electric field intensity, as well as the incident energy of electrons. By tuning the electric field intensity and incident angle, the channels can be transited from opaque to transparent. The conductance through the quantum waveguides depends sensitively on the transport direction because of the anisotropic effective mass, and the anisotropy of the conductance can be tuned by the electric field intensity and the number of layers. These behaviors provide us an efficient way to control the transport of phosphorene-based microstructures.
Growth of TlBa2Ca2Cu3O9 Epitaxial Thin Films by Two-Step Method in Argon*
Authors: Xing Jian , Wang Li-Tian , Gao Xiao-Xin , Liang Xue-Lian , He Kai-Yong , Xu Ting , Zhao Sheng-Hui , Zhang Jin-Li , He Ming , Zhao Xin-Jie , Yan Shao-Lin , Wang Pei , Ji Lu
Published: May 2019

TlBa2Ca2Cu3O9 (Tl-1223) films have promising applications due to their high critical temperature and strong magnetic flux pinning. Nevertheless, the preparation of pure phase Tl-1223 film is still a challenge. We successfully fabricate Tl-1223 thin films on LaAlO3 (001) substrates using dc magnetic sputtering and a post annealing two-step method in argon atmosphere. The crystallization temperature of Tl-1223 films in argon is reduced by 100°C compared to that in oxygen. This greatly reduces the volatilization of Tl and improves the surface morphology of films. The lower annealing temperature can effectively improve the repeatability of the Tl-1223 film preparation. In addition, pure Tl-1223 phase can be obtained in a broad temperature zone, from 790°C to 830°C. In our study, the films show homogenous and dense surface morphology using the presented method. The best critical temperature of Tl-1223 films is characterized to be 110 K, and the critical current J
c (77 K, 0 T) is up to 2.13 × 106 A/cm2.
Local standard of rest based on Gaia DR2 catalog
Authors: Ding Ping-Jie , Zhu Zi , Liu Jia-Cheng
Published: May 2019

The local standard of rest (LSR) provides a reference framework for studies of Galactic kinematics. Determination of the LSR corresponds to the measurement of solar peculiar motion, which is under debate due to the fact that different methods and samples have been used. Adopting the astrometric data and line-of-sight velocities of main sequence stars from Gaia DR2, we present a detailed analytical study of stellar kinematics in the solar neighborhood. Based on an improved version of the Strömberg relation, we obtain a robust estimation of the solar peculiar motion, which is given by (U
⊙, V
⊙, W
⊙) = (8.63±0.64, 4.76±0.49, 7.26±0.36) kms−1. The corresponding radial scalelength is yielded as Rd
∼ 2.5 kpc. The radial and vertical components of solar peculiar motion are basically consistent with the classical values, while the tangential component is a few km s−1 smaller than most estimates in literature.
CCD astrometric observations of 2017 VR12, Camillo and Midas
Authors: Zhang Zhen-Jun , Zhang Yi-Gong , Chen Xiang-Ming , Wang Jian-Cheng , Su Jie
Published: May 2019

We have observed three near-Earth objects (NEOs), 2017 VR12, Camillo and Midas, during 2018. The observations were made with the 1-m telescope, operated by Yunnan Observatories, over two nights. Their precise astrometric positions are derived from 989 CCD observations. The theoretical positions of asteroids are retrieved from the Jet Propulsion Laboratory (JPL) Horizons System and Institut de Mécanique Céleste et de Calcul des Éphémérides (IMCCE). The positions of three asteroids are measured with respect to stars in the Gaia DR2 star catalog. For 2017 VR12, the means (O−C) of right ascension and declination are −0.090′′ and −0.623′′ respectively based on the published JPL ephemeris, but the correspondingmeans (O − C) are 3.122′′ and −0.636′′ based on the published IMCCE ephemeris. The great difference in declination could be explained by several factors. (1) The degraded CCD images caused by the fast apparent motion of the objects lead to a reduction in positioning accuracy. (2) The poor timing system may introduce systematic errors, especially in the high speed direction. (3) The asteroid may be perturbed by Earth when it approaches the Earth too closely. These astrometric results demonstrate that the centroid centering method can reduce the dispersion of non-Gaussian images as compared with the PSF modeling method. For Camillo and Midas, the astrometric results are consistent based on the two ephemerides. Implementing a high-precision timing system, and analyzing some astronomical effects and geometric distortions in CCD images should be carefully considered in future works.
Do alternative irrigation strategies for rice cultivation decrease water footprints at the cost of long-term soil health?
Authors: Livsey John , Kätterer Thomas , Vico Giulia , Lyon Steve W , Lindborg Regina , Scaini Anna , Da Chau Thi , Manzoni Stefano
Published: May 2019

The availability of water is a growing concern for flooded rice production. As such, several water-saving irrigation practices have been developed to reduce water requirements. Alternate wetting and drying and mid-season drainage have been shown to potentially reduce water requirements while maintaining rice yields when compared to continuous flooding. With the removal of permanently anaerobic conditions during the growing season, water-saving irrigation can also reduce CO2 equivalent (CO2eq) emissions, helping reduce the impact of greenhouse gas (GHG) emissions. However, the long-term impact of water-saving irrigation on soil organic carbon (SOC)—used here as an indicator of soil health and fertility—has not been explored. We therefore conducted a meta-analysis to assess the effects of common water-saving irrigation practices (alternate wetting and drying and mid-season drainage) on (i) SOC, and (ii) GHG emissions. Despite an extensive literature search, only 12 studies were found containing data to constrain the soil C balance in both continuous flooding and water-saving irrigation plots, highlighting the still limited understanding of long-term impacts of water-saving irrigation on soil health and GHG emissions. Water-saving irrigation was found to reduce emissions of CH4 by 52.3% and increased those of CO2 by 44.8%. CO2eq emissions were thereby reduced by 18.6% but the soil-to-atmosphere carbon (C) flux increased by 25% when compared to continuous flooding. Water-saving irrigation was also found to have a negative effect on both SOC—reducing concentrations by 5.2%—and soil organic nitrogen—potentially depleting stocks by more than 100 kg N/ha per year. While negative effects of water-saving irrigation on rice yield may not be visible in short-term experiments, care should be taken when assessing the long-term sustainability of these irrigation practices because they can decrease soil fertility. Strategies need to be developed for assessing the more long-term effects of these irrigation practices by considering trade-offs between water savings and other ecosystem services.
GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs
Authors: Shrikumar Avanti , Prakash Eva , Kundaje Anshul
Published: May 2019

Support Vector Machines with gapped k-mer kernels (gkm-SVMs) have been used to learn predictive models of regulatory DNA sequence. However, interpreting predictive sequence patterns learned by gkm-SVMs can be challenging. Existing interpretation methods such as deltaSVM, in-silico mutagenesis (ISM) or SHAP either do not scale well or make limiting assumptions about the model that can produce misleading results when the gkm kernel is combined with nonlinear kernels. Here, we propose GkmExplain: a computationally efficient feature attribution method for interpreting predictive sequence patterns from gkm-SVM models that has theoretical connections to the method of Integrated Gradients. Using simulated regulatory DNA sequences, we show that GkmExplain identifies predictive patterns with high accuracy while avoiding pitfalls of deltaSVM and ISM and being orders of magnitude more computationally efficient than SHAP. By applying GkmExplain and a recently developed motif discovery method called TF-MoDISco to gkm-SVM models trained on in vivo transcription factor (TF) binding data, we recover consolidated, non-redundant TF motifs. Mutation impact scores derived using GkmExplain consistently outperform deltaSVM and ISM at identifying regulatory genetic variants from gkm-SVM models of chromatin accessibility in lymphoblastoid cell-lines.

Availability and implementation

Code and example notebooks to reproduce results are at https://github.com/kundajelab/gkmexplain.

Supplementary information

Supplementary data are available at Bioinformatics online.
Drug repositioning based on bounded nuclear norm regularization
Authors: Yang Mengyun , Luo Huimin , Li Yaohang , Wang Jianxin
Published: May 2019

Motivation

Computational drug repositioning is a cost-effective strategy to identify novel indications for existing drugs. Drug repositioning is often modeled as a recommendation system problem. Taking advantage of the known drug–disease associations, the objective of the recommendation system is to identify new treatments by filling out the unknown entries in the drug–disease association matrix, which is known as matrix completion. Underpinned by the fact that common molecular pathways contribute to many different diseases, the recommendation system assumes that the underlying latent factors determining drug–disease associations are highly correlated. In other words, the drug–disease matrix to be completed is low-rank. Accordingly, matrix completion algorithms efficiently constructing low-rank drug–disease matrix approximations consistent with known associations can be of immense help in discovering the novel drug–disease associations.

Results

In this article, we propose to use a bounded nuclear norm regularization (BNNR) method to complete the drug–disease matrix under the low-rank assumption. Instead of strictly fitting the known elements, BNNR is designed to tolerate the noisy drug–drug and disease–disease similarities by incorporating a regularization term to balance the approximation error and the rank properties. Moreover, additional constraints are incorporated into BNNR to ensure that all predicted matrix entry values are within the specific interval. BNNR is carried out on an adjacency matrix of a heterogeneous drug–disease network, which integrates the drug–drug, drug–disease and disease–disease networks. It not only makes full use of available drugs, diseases and their association information, but also is capable of dealing with cold start naturally. Our computational results show that BNNR yields higher drug–disease association prediction accuracy than the current state-of-the-art methods. The most significant gain is in prediction precision measured as the fraction of the positive predictions that are truly positive, which is particularly useful in drug design practice. Cases studies also confirm the accuracy and reliability of BNNR.

Availability and implementation

The code of BNNR is freely available at https://github.com/BioinformaticsCSU/BNNR.

Supplementary information

Supplementary data are available at Bioinformatics online.
Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data
Authors: Handl Lisa , Jalali Adrin , Scherer Michael , Eggeling Ralf , Pfeifer Nico
Published: May 2019

Motivation

Predictive models are a powerful tool for solving complex problems in computational biology. They are typically designed to predict or classify data coming from the same unknown distribution as the training data. In many real-world settings, however, uncontrolled biological or technical factors can lead to a distribution mismatch between datasets acquired at different times, causing model performance to deteriorate on new data. A common additional obstacle in computational biology is scarce data with many more features than samples. To address these problems, we propose a method for unsupervised domain adaptation that is based on a weighted elastic net. The key idea of our approach is to compare dependencies between inputs in training and test data and to increase the cost of differently behaving features in the elastic net regularization term. In doing so, we encourage the model to assign a higher importance to features that are robust and behave similarly across domains.

Results

We evaluate our method both on simulated data with varying degrees of distribution mismatch and on real data, considering the problem of age prediction based on DNA methylation data across multiple tissues. Compared with a non-adaptive standard model, our approach substantially reduces errors on samples with a mismatched distribution. On real data, we achieve far lower errors on cerebellum samples, a tissue which is not part of the training data and poorly predicted by standard models. Our results demonstrate that unsupervised domain adaptation is possible for applications in computational biology, even with many more features than samples.

Availability and implementation

Source code is available at https://github.com/PfeiferLabTue/wenda.

Supplementary information

Supplementary data are available at Bioinformatics online.
Cram-JS: reference-based decompression in node and the browser
Authors: Buels Robert , Dider Shihab , Diesh Colin , Robinson James , Holmes Ian
Published: May 2019

Motivation

The CRAM format addresses rising DNA storage costs for short-read sequencing by aligning reads to a reference genome and encoding the resulting alignment with Huffman, subexponential, Elias gamma, rANS, gzip and other codes. The CRAM codec is complex, and until now, there has been no JavaScript implementation.

Results

We have developed a JavaScript library, Cram-JS, that natively reads and decompresses the CRAM format on-the-fly. The library is used in the JBrowse and IGV-JS genome browsers and can readily be used by other JavaScript applications, in the web browser or in Node.

Availability and implementation

Cram-JS is written to the ES-6 standard and is available from the GitHub repository at https://github.com/GMOD/cram-js.
Long-term Outcomes of Paediatric Patients Admitted With Acute Severe Colitis— A Multicentre Study From the Paediatric IBD Porto Group of ESPGHAN
Authors: Krauthammer Alex , Tzivinikos Christos , Assa Amit , Miele Erasmo , Strisciuglio Caterina , Urlep Darja , Serban Elena Daniela , Singh Avantika , Winter Harland S , Russell Richard K , Hojsak Iva , Malham Mikkel , Navas-López Víctor Manuel , Croft Nicholas M , Lee Huey Miin , Ledder Oren , Shamasneh Ibrahim , Hussey Seamus , Huynh Hien Q , Wine Eytan , Shah Neil , Sladek Margaret , de Meij Tim G , Romano Claudio , Dipasquale Valeria , Lionetti Paolo , Afzal Nadeem A , Aloi Marina , Lee Kwangyang , Martín-de-Carpi Javier , Yerushalmy-Feler Anat , Subramanian Sreedhar , Weiss Batia , Shouval Dror S
Published: May 2019

Background and Aim

Acute severe colitis [ASC] is associated with significant morbidity in paediatric patients with ulcerative colitis [UC]. Most outcome studies in ASC since tumour necrosis factor alpha [TNFα] antagonists became available have focused on the first year after admission. The aim of this study was to characterise the longer-term outcomes of paediatric patients admitted with ASC.

Methods

This retrospective study was conducted in 25 centres across Europe and North America. Data on patients with UC aged <18 years, admitted with ASC (defined as paediatric ulcerative colitis activity index [PUCAI] score ≥65) between 2009 and 2011, were collected at discharge and 1, 3 and 5 years after admission. The primary outcome was colectomy-free rates at each time point.

Results

Of the 141 patients admitted with ASC, 137 [97.1%] were treated with intravenous corticosteroids. Thirty-one [22.6%] patients were escalated to second-line therapy, mainly to infliximab. Sixteen patients [11.3%] underwent colectomy before discharge. Long-term follow-up showed colectomy-free rates were 71.3%, 66.4% and 63.6% at 1, 3 and 5 years after initial ASC admission, respectively, and were similar across different age groups. Sub-analysis of colectomy rates in patients with new-onset disease [42.5% of the cohort] yielded similar results. In a multivariate analysis, use of oral steroids in the 3 months before admission, erythrocyte sedimentation rate >70 mm/h, and albumin <2.5 g/dL, were significantly associated with 5-year colectomy risk.

Conclusions

High colectomy rates were demonstrated in paediatric UC patients admitted with ASC. Additional studies are required to determine whether intensification of anti-TNFα treatment, close therapeutic drug monitoring, and use of new drugs alter this outcome.
Production under input endogeneity and farm-specific risk aversion: evidence from contract farming and Bayesian method
Authors: Mishra Ashok K , Rezitis Anthony N , Tsionas Mike G
Published: May 2019

Contract farming (CF) has been offered as a solution to missing markets in developing economies. However, little is known as to how the presence of CF affects production risk, technical efficiency and risk attitudes of the smallholder. This study investigates production risk, technical efficiency, output price uncertainty and risk attitudes of contract and independent farmers. Using a Bayesian estimation method and farm-level data from Nepal, we find that contract farmers are more risk-averse than the independent farmers. Contract farmers can increase output by reducing the scale more than independent farmers. We find that labour and capital are risk-reducing, while land and other inputs are risk increasing for both contract and independent farmers. Finally, independent growers consistently over-predict output prices.
Does culture affect soil erosion? Empirical evidence from Europe
Authors: Wuepper David
Published: May 2019

I investigate whether cultural differences explain why some European regions are more effective in mitigating soil erosion than others. Specifically, I consider environmental preferences and beliefs as well as time preferences. For causal identification, I use a control function approach. The estimates suggest that a 1 standard deviation increase in pro-environmental culture increases erosion mitigation by 2–9 percentage points. This has important implications for research and policy making, which I discuss.
Fibers on the Fly: Multiscale Mechanisms of Fiber Formation in the Capture Slime of Velvet Worms
Authors: Baer Alexander , Schmidt Stephan , Mayer Georg , Harrington Matthew J
Published: May 2019

Many organisms have evolved a capacity to form biopolymeric fibers outside their bodies for functions such as defense, prey capture, attachment, and protection. In particular, the adhesive capture slime of onychophorans (velvet worms) is remarkable for its ability to rapidly form stiff fibers through mechanical drawing. Notably, fibers that are formed ex vivo from extracted slime can be dissolved in water and new fibers can be drawn from the solution, indicating that fiber formation is encoded in the biomolecules that comprise the slime. This review highlights recent findings on the biochemical and physicochemical principles guiding this circular process in the Australian onychophoran Euperipatoides rowelli. A multiscale cross-disciplinary approach utilizing techniques from biology, biochemistry, physical chemistry, and materials science has revealed that the slime is a concentrated emulsion of nanodroplets comprised primarily of proteins, stabilized via electrostatic interactions, possibly in a coacervate phase. Upon mechanical agitation, droplets coalesce, leading to spontaneous self-assembly and fibrillation of proteins—a completely reversible process. Recent investigations highlight the importance of subtle transitions in protein structure and charge balance. These findings have clear relevance for better understanding this adaptive prey capture behavior and providing inspiration toward sustainable polymer processing.
Occupational asthma; the limited role of air-fed respiratory protective equipment
Authors: Ilgaz Aslihan , Moore Vicky C , Robertson Alastair S , Walters Gareth I , Burge P Sherwood
Published: May 2019

Background

Evidence-based reviews have found that evidence for the efficacy of respiratory protective equipment (RPE) in the management of occupational asthma (OA) is lacking.

Aims

To quantify the effectiveness of air-fed RPE in workers with sensitizer-induced OA exposed to metal-working fluid aerosols in a car engine and transmission manufacturing facility.

Methods

All workers from an outbreak of metal-working fluid-induced OA who had continuing peak expiratory flow (PEF) evidence of sensitizer-induced OA after steam cleaning and replacement of all metal-working fluid were included. Workers kept 2-hourly PEF measurements at home and work, before and after a strictly enforced programme of RPE with air-fed respirators with charcoal filters. The area-between-curve (ABC) score from the Oasys plotter was used to assess the effectiveness of the RPE.

Results

Twenty workers met the inclusion criteria. Records were kept for a mean of 24.6 day shifts and rest days before and 24.7 after the institution of RPE. The ABC score improved from 26.6 (SD 16.2) to 17.7 (SD 25.4) l/min/h (P > 0.05) post-RPE; however, work-related decline was <15 l/min/h in only 12 of 20 workers, despite increased asthma treatment in 5 workers.

Conclusions

Serial PEF measurements assessed with the ABC score from the Oasys system allowed quantification of the effect of RPE in sensitized workers. The RPE reduced falls in PEF associated with work exposure, but this was rarely complete. This study suggests that RPE use cannot be relied on to replace source control in workers with OA, and that monitoring post-RPE introduction is needed.
Providing ‘the bigger picture’: benefits and feasibility of integrating remote monitoring from smartphones into the electronic health record
Authors: Austin Lynn , Sharp Charlotte A , van der Veer Sabine N , Machin Matthew , Humphreys John , Mellor Peter , McCarthy Jill , Ainsworth John , Sanders Caroline , Dixon William G
Published: May 2019

Objectives

To establish the acceptability and feasibility of collecting daily patient-generated health data (PGHD) using smartphones and integrating PGHD into the electronic health record, using the example of RA.

Methods

The Remote Monitoring of RA smartphone app was co-designed with patients, clinicians and researchers using qualitative semi-structured interviews and focus groups, including selection of question sets for symptoms and disease impact. PGHD were integrated into the electronic health record of one hospital and available in graphical form during consultations. Acceptability and feasibility were assessed with 20 RA patients and two clinicians over 3 months. A qualitative evaluation included semi-structured interviews with patients and clinicians before and after using the app, and audio-recordings of consultations to explore impact on the consultation. PGHD completeness was summarized descriptively, and qualitative data were analysed thematically.

Results

Patients submitted data on a median of 91% days over 3 months. Qualitative analysis generated three themes: RA as an invisible disease; providing the bigger picture of RA; and enabling person-centred consultations. The themes demonstrated that the system helped render patients’ RA more visible by providing the ‘bigger picture’, identifying real-time changes in disease activity and capturing symptoms that would otherwise have been missed. Graphical summaries during consultations enabled a more person-centred approach whereby patients felt better able to participate in consultations and treatment plans.

Conclusion

Remote Monitoring of RA has uniquely integrated daily PGHD from smartphones into the electronic health record. It has delivered proof-of-concept that such integrated remote monitoring systems are feasible and can transform consultations for clinician and patient benefit.
Voice After Exit: Explaining Diaspora Mobilization for the Arab Spring
Authors: Moss Dana M
Published: May 2019

Research demonstrates that diaspora movements play a powerful role in contentious politics and social change in their homelands under a range of conditions. However, few have systematically explained the conditions that facilitate diaspora movements’ “voice” after “exit” across cases or over time. The article addresses this shortcoming by explaining how and to what extent diaspora movements became auxiliary forces for anti-regime rebellions during the Arab Spring. Using data that include 239 original interviews on Libyan, Syrian, and Yemeni mobilization from the US and Great Britain, the analysis finds that only some diaspora groups played a sustained, full-spectrum role in their home-country’s rebellion by broadcasting their allies’ claims, remitting resources homeward, representing the rebellion to external audiences, brokering between parties, and volunteering on the front lines. The article then demonstrates how differences in (1) the rebellion’s needs, (2) geopolitical support, (3) activist resources, and (4) access to the front lines produced variation in auxiliary activism by national group, host-country, and over time. In so doing, the article contributes to theories of transnationalism, social movements, diaspora politics, and cross-border contentious politics more generally.
Aquaculture role in global food security with nutritional value: a review
Authors: Pradeepkiran Jangampalli Adi
Published: May 2019

Food security is the main path to develop the socioeconomic status in any country in the world to defeat malnutrition. The present scenario in an under developed countries are still facing this problem. Hence the human nutrition deficiencies focus on the importance of animal protein in their regular diet. To overcome this problem, fisheries contribute a significant amount of animal protein to the diets of people worldwide. The aquatic animals are the highly nutritious and cheapest protein sources, which serves as a valuable supplement in diets by providing essential vitamins, proteins, micronutrients, and minerals, for the poor people. Aquaculture is playing a vital role in the developing countries in national economic development, and global food supply. Food and agricultural organization (FAO) declared that this aquaculture has the continuous potentiality to create a developmental goals for the country economy and better human welfare.
Tubewell use protects against rotavirus infection during the monsoons in an urban setting
Authors: Martinez Pamela P. , Mahmud Ayesha , Yunus Mohammad , Faruque A.S.G , Ahmed Tahmeed , Pascual Mercedes , Buckee Caroline O.
Published: May 2019

Rotavirus, a diarrheal pathogen spread via fecal-oral transmission, is typically characterized by a winter incidence peak in most countries. Unlike for cholera and other water-borne infections, the role of environmental and socioeconomic factors on the spatial variation of rotavirus seasonality remains unclear. Here, we analyze their association with rotavirus seasonality, specifically the odds of monsoon cases, across 46 locations from 2001 to 2012 in Dhaka. Drinking water from tubewells, compared to other sources, has a clear protective effect against cases during the monsoon, when flooding and water contamination are more likely. This finding supports a significant environmental component of transmission.
Is asthma associated with exposure to smoke from a coal mine fire?
Authors: Taylor S , Borg B , Gao C , Brown D , Hoy R , Makar A , McCrabb T , Ikin J , Thompson BR , Abramson MJ
Published: May 2019

In 2014, a fire at the Hazelwood open cut coal mine (Victoria, Australia) burned for about 6 weeks. Residents of the adjacent town of Morwell were exposed to high levels of fine particulate matter (PM2.5) during this period. Three and a half years after the event, this study aimed to investigate the long-term impact of short-term exposure to coal mine fire smoke on asthma.

A cross-sectional analysis was undertaken on a group of exposed participants with asthma from Morwell (n=165) and a group of unexposed participants with asthma from the control town of Sale (n=64). Town exposure status was determined by modelled PM2.5data for the mine fire period. Respiratory symptoms were assessed with a validated respiratory health questionnaire and symptom severity score. Asthma control was assessed with an asthma control questionnaire. Lung function testing included spirometry, bronchodilator response, and fraction of exhaled nitric oxide.

There was no evidence that exposed Morwell participants had more severe asthma symptoms, worse lung function, or more eosinophilic airway inflammation compared to unexposed Sale participants. However there was some evidence that Morwell participants had more uncontrolled than well-controlled asthma, compared to the participants from Sale (adjusted relative risk ratio 2.71 95%CI: 1.02, 7.21, p=0.046).

Three and a half years after exposure, coal mine fire smoke does not appear to be associated with more severe asthma symptoms or worse lung function, but may be associated with poorer asthma control.

Summary take home message

In people with asthma, short-term coal mine fire smoke exposure does not appear to have long-term impact on severity of asthma symptoms, lung function or eosinophilic airway inflammation, but may affect asthma control.
Bioorthogonal protein-DNA conjugation methods for force spectroscopy
Authors: Synakewicz Marie , Bauer Daniela , Rief Matthias , Itzhaki Laura S.
Published: May 2019

Accurate and stable site-specific attachment of DNA molecules to proteins is a requirement for many single-molecule force spectroscopy techniques. The most commonly used method still relies on maleimide chemistry involving cysteine residues in the protein of interest. Studies have consequently often focused on model proteins that either have no cysteines or with a small number of cysteines that can be deleted so that cysteines can then be introduced at specific sites. However, many proteins, especially in eukaryotes, contain too many cysteine residues to be amenable to this strategy, and therefore there is tremendous need for new and broadly applicable approaches to site-specific conjugation. Here we present bioorthogonal approaches for making DNA-protein conjugates required in force spectroscopy experiments. Unnatural amino acids are introduced site-specifically and conjugated to DNA oligos bearing the respective modifications to undergo either strain-promoted azide-alkyne cycloaddition (SPAAC) or inverse-electron-demand Diels-Alder (IE-DA) reactions. We furthermore show that SPAAC is compatible with a previously published peptide-based attachment approach. By expanding the available toolkit to tag-free methods based on bioorthogonal reactions, we hope to enable researchers to interrogate the mechanics of a much broader range of proteins than is currently possible.
Intra-individual changes in the frequency of mosaic loss of chromosome Y over time estimated with a new method
Authors: Danielsson Marcus , Halvardson Jonatan , Davies Hanna , Moghadam Behrooz Torabi , Mattisson Jonas , Rychlicka-Buniowska Edyta , Jaszczyński Janusz , Heintz Julia , Lannfelt Lars , Giedraitis Vilmantas , Ingelsson Martin , Dumanski Jan P. , Forsberg Lars A.
Published: May 2019

Background

Mosaic loss of chromosome Y (LOY) is the most common somatic mutation and is associated with all-cause mortality, non-haematological cancers and Alzheimer’s disease among other outcomes. The predominant method used for estimating LOY is the intensity data generated by SNP-arrays, which is difficult to interpret due to its logarithmic scale. Here we describe a new way to convert the LOY mosaicism into a non-logarithmic scale, which instead represents the percentage of affected cells.

Methods

We compared three independent LOY readouts from matched samples, generated by SNP-array, whole genome sequencing and droplet digital PCR. The SNP-array standardization was derived from this comparison and was applied in analyses of serially collected samples from a large cohort of aging men. The sampling was performed up to five times, spanning up to 22 years.

Results

We observed a higher correlation between the LOY measurements from SNP-array and the two other readouts when using the standardized, instead of the logarithmic, SNP-array data. We also observed a pronounced intra-individual variation of changes in the frequency of LOY within individual males over time.

Conclusions

Describing LOY measurements generated from SNP-arrays in percentage of cells without the Y chromosome makes comparisons to WGS and ddPCR measurements more precise and easier to interpret. This standardization could be applied to the vast amount of SNP-array data already generated in the scientific community, allowing further discoveries of LOY associated disease and outcomes. Additionally, the frequency of LOY in this study changed profoundly within men over time, likely as a result of aberrant clonal expansions.
High risk glioblastoma cells revealed by machine learning and single cell signaling profiles
Authors: Leelatian Nalin , Sinnaeve Justine , Mistry Akshitkumar M. , Barone Sierra M. , Diggins Kirsten E. , Greenplate Allison R. , Weaver Kyle D. , Thompson Reid C. , Chambless Lola B. , Mobley Bret C. , Ihrie Rebecca A. , Irish Jonathan M.
Published: May 2019

Recent developments in machine learning implemented dimensionality reduction and clustering tools to classify the cellular composition of patient-derived tissue in multi-dimensional, single cell studies. Current approaches, however, require prior knowledge of either categorical clinical outcomes or cell type identities. These algorithms are not well suited for application in tumor biology, where clinical outcomes can be continuous and censored and cell identities may be novel and plastic. Risk Assessment Population IDentification (RAPID) is an unsupervised, machine learning algorithm that identifies single cell phenotypes and assesses clinical risk stratification as a continuous variable. Single cell mass cytometry evaluated 34 different phospho-proteins, transcription factors, and cell identity proteins in tumor tissue resected from patients bearingIDHwild-type glioblastomas. RAPID identified and characterized multiple biologically distinct tumor cell subsets that independently and continuously stratified patient outcome. RAPID is broadly applicable for single cell studies where atypical cancer and immune cells may drive disease biology and treatment responses.
Chloroplast nucleoids are highly dynamic in ploidy, number, and structure during angiosperm leaf development
Authors: Greiner Stephan , Golczyk Hieronim , Malinova Irina , Pellizzer Tommaso , Bock Ralph , Börner Thomas , Herrmann Reinhold G.
Published: May 2019

Chloroplast nucleoids are large, compact nucleoprotein structures containing multiple copies of the plastid genome. Studies on structural and quantitative changes of plastid DNA (ptDNA) during leaf development are scarce and have produced controversial data. We have systematically investigated nucleoid dynamics and ptDNA quantities in mesophyll ofArabidopsis, tobacco, sugar beet, and maize from the early post-meristematic stage until necrosis. DNA of individual nucleoids was quantified by DAPI-based supersensitive epifluorescence microscopy. Nucleoids occurred in scattered, stacked or ring-shaped arrangements and in recurring patterns during leaf development remarkably similar between the species studied. Nucleoids per organelle varied from few in meristematic plastids to >30 in mature chloroplasts (corresponding to about 20-750 nucleoids per cell). Nucleoid ploidies ranged from haploid to >20-fold even within individual organelles, with average values between 2.6- and 6.7-fold and little changes during leaf development. DNA quantities per organelle increased gradually from about a dozen plastome copies in tiny plastids of apex cells to 70-130 copies in chloroplasts of about 7 μm diameter in mature mesophyll tissue, and from about 80 plastome copies in meristematic cells to 2,600-3,300 copies in mature diploid mesophyll cells without conspicuous decline during leaf development. Pulsed-field electrophoresis, restriction of high-molecular weight DNA from chloroplasts and gerontoplasts, and CsCl equilibrium centrifugation of single- and double-stranded ptDNA revealed no noticeable fragmentation of the organelle DNA during leaf development, implying that plastid genomes in mesophyll tissues are remarkably stable until senescence.

Significance Statement

Plastid DNA is organized in nucleoids that are highly dynamic in organization, structure and amount during leaf development. The present investigation fully resolves now this dynamic and is a precise cytogenetic characterization of nucleoids DNA spanning the entire life cycle of the leaf.
Nanoscale spatial dependence of avidity in an IgG1 antibody
Authors: Jendroszek Agnieszka , Kjaergaard Magnus
Published: May 2019

Antibodies are secreted proteins that are crucial to recognition of pathogens by the immune system and are also efficient pharmaceuticals. The affinity and specificity of target recognition can increase remarkably through avidity effects, when the antibody can bind a multivalent antigen through more than one epitope simultaneously. A key goal of antibody engineering is thus to optimize avidity, but little is known about the nanoscale spatial dependence of avidity in antibodies. Here, we develop a set of anti-parallel coiled-coils spanning from 8-21 nm and validate their structure using biophysical techniques. We use the coiled-coils to control the spacing between two epitopes, and measure how antigen spacing affects the stability of the bivalent antibody:antigen complex. We find a maximal avidity enhancement at a spacing of 14 nm, but only see a ∼2-fold variation of avidity in the range from 8-21 nm. In contrast to recent studies, we find the avidity to be relatively insensitive to epitope spacing near the avidity maximum as long as it is within the spatial tolerance of the antibody. The coiled-coil systems developed here may prove a useful protein nanocaliper for profiling the spatial tolerance and avidity profile of bispecific antibodies.
The phosphatase inhibitor Sds23 regulates cell division symmetry in fission yeast
Authors: Schutt Katherine L. , Moseley James B.
Published: May 2019

Animal and fungal cells divide through the assembly, anchoring, and constriction of a contractile actomyosin ring (CAR) during cytokinesis. The timing and position of the CAR must be tightly controlled to prevent defects in cell division, but many of the underlying signaling events remain unknown. The conserved heterotrimeric protein phosphatase PP2A controls the timing of events in mitosis, and upstream pathways including Greatwall-Ensa regulate PP2A activity. A role for PP2A in CAR regulation has been less clear, although loss of PP2A in yeast causes defects in cytokinesis. Here, we report that Sds23, an inhibitor of PP2A family protein phosphatases, promotes the symmetric division of fission yeast cells through spatial control of cytokinesis. We found thatsds23Δ cells divide asymmetrically due to misplaced CAR assembly, followed by sliding of the CAR away from its assembly site. These mutant cells exhibit delayed recruitment of putative CAR anchoring proteins including the glucan synthase Bgs1. Our observations likely reflect a broader role for regulation of PP2A in cell polarity and cytokinesis becausesds23Δ phenotypes were exacerbated when combined with mutations in the fission yeast Ensa homolog, Igo1. These results identify the PP2A regulatory network as a critical component in the signaling pathways coordinating cytokinesis.