bluuebunny/crossref_metadata_2025_split huggingface dataset:
Super-rapid quantitation of the production of HIV-1 harboring a luminescent peptide tag
Authors: Ozono Seiya , Zhang Yanzhao , Tobiume Minoru , Kishigami Satoshi , Tokunaga Kenzo 
Published: April 2020

ABSTRACTIn virological studies using HIV-1 proviral clones, virus production is normally monitored by either an RT assay or a p24 antigen capture ELISA. However, these assays are costly and time-consuming for routine handling of a large number of HIV-1 samples. In addition, sample dilution is always required in ELISA to determine p24 protein levels because of the very narrow range of detectable concentrations in this assay. Here, we establish a novel HIV-1 production assay system to solve the aforementioned problems by using a recently developed small peptide tag called HiBiT. First, we constructed a novel full-length proviral HIV-1 DNA clone and a lentiviral packaging vector in which the HiBiT tag was added to the C terminus of the integrase. Tagging the integrase with the HiBiT sequence did not impede the production or infectivity of the resultant viruses. Electron microscopy revealed normal morphology of the virus particles. Most importantly, by comparing between ELISA and the HiBiT luciferase assay, we successfully obtained an excellent linear correlation between p24 concentrations and HiBiT-based luciferase activity. Overall, we conclude that HiBiT-tagged viruses can replace the parental HIV-1 and lentiviral vectors, which enables us to perform a super-rapid, inexpensive, convenient, simple, and highly accurate quantitative assay for HIV-1 production.
Combining sample expansion and light sheet microscopy for the volumetric imaging of virus-infected cells with optical super-resolution
Authors: Mascheroni Luca , Scherer Katharina M. , Manton James D. , Ward Edward , Dibben Oliver , Kaminski Clemens F. 
Published: April 2020

AbstractExpansion microscopy is a sample preparation technique that enables the optical imaging of biological specimens at super-resolution owing to their physical magnification, which is achieved through water-absorbing polymers. The technique uses readily available chemicals and does not require sophisticated equipment, thus offering super-resolution to laboratories that are not microscopy-specialised. Here we present a protocol combining sample expansion with light sheet microscopy to generate high-contrast, high-resolution 3D reconstructions of whole virus-infected cells. The results are superior to those achievable with comparable imaging modalities and reveal details of the infection cycle that are not discernible before expansion. An image resolution of approximately 95 nm could be achieved in samples labelled in 3 colours. We clearly resolve the concentration of viral nucleoprotein on the surface of vesicular structures within the cell and their positioning relative to cellular organelles. We provide detailed guidance and a video protocol for the optimal application of the method and demonstrate its potential to study virus-host cell interactions.
XAB2 prevents abortive recombinational repair of replication-associated DNA double-strand breaks and its loss is synthetic lethal with RAD52 inhibition
Authors: Sharma Abhishek B. , Erasimus Hélène , Pinto Lia , Caron Marie-Christine , Neumann Katrin , Nazarov Petr V. , Klink Barbara , Fritah Sabrina , Herold-Mende Christel C. , Niclou Simone P. , Calsou Patrick , Masson Jean-Yves , Britton Sébastien , Van Dyck Eric 
Published: April 2020

ABSTRACTUnrepaired O6-methylguanine lesions induced by the alkylating chemotherapy agent temozolomide lead to replication-associated single-ended DNA double-strand breaks (seDSBs) that are repaired predominantly through RAD51-mediated homologous recombination (HR). Here, we show that loss of the pre-mRNA splicing and DNA repair protein XAB2 leads to increased temozolomide sensitivity in glioblastoma cells, which reflects abortive HR due to Ku retention on resected seDSBs. XAB2-dependent Ku eviction also occurred at seDSBs generated by the topoisomerase I poison campthotecin and operated in parallel to an ATM-dependent pathway previously described. Although Ku retention elicited by loss of XAB2 did not prevent RAD51 focus formation, the resulting RAD51-ssDNA associations were unproductive, leading to increased engagement of non-homologous-end-joining in S/G2 and genetic instability. Overexpression of RAD51 or the single-stranded DNA annealing factor RAD52 rescued the XAB2 defects. RAD52 depletion led to severe temozolomide sensitivity, whereas a synthetic lethality interaction was observed between RAD52 and XAB2.
Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments
Authors: Chen Zhijie , Shaw Alan , Wilson Hugh , Woringer Maxime , Darzacq Xavier , Marqusee Susan , Wang Quan , Bustamante Carlos 
Published: April 2020

ABSTRACTTheoretical and experimental observations that catalysis enhances the diffusion of enzymes have generated exciting implications about nanoscale energy flow, molecular chemotaxis and self-powered nanomachines. However, contradictory claims on the origin, magnitude, and consequence of this phenomenon continue to arise. Experimental observations of catalysis-enhanced enzyme diffusion, to date, have relied almost exclusively on fluorescence correlation spectroscopy (FCS), a technique that provides only indirect, ensemble-averaged measurements of diffusion behavior. Here, using an Anti-Brownian ELectrokinetic (ABEL) trap and in-solution spectroscopy (FCS), a technique that provides only indirect, ensemble-averaged measurements of diffusion behavior. Here, using an Anti-Brownian ELectrokinetic (ABEL) trap and in-solution single-particle tracking (SPT), we show that catalysis does not increase the diffusion of alkaline phosphatase (ALP) at the single-molecule level, in sharp contrast to the ~20% enhancement seen in parallel FCS experiments usingp-nitrophenyl phosphate (pNPP) as substrate. Combining comprehensive FCS controls, ABEL trap, surface-based single-molecule fluorescence, and Monte-Carlo simulations, we establish thatpNPP-induced dye blinking at the ~10 ms timescale is responsible for the apparent diffusion enhancement seen in FCS. Our observations urge a crucial revisit of various experimental findings and theoretical models––including those of our own––in the field, and indicate that in-solution SPT and ABEL trap are more reliable means to investigate diffusion phenomena at the nanoscale.SIGNIFICANCE STATEMENTRecent experiments have suggested that the energy released by a chemical reaction can propel its enzyme catalyst (for example, alkaline phosphatase, ALP). However, this topic remains controversial, partially due to the indirect and ensemble nature of existing measurements. Here, we used recently developed single-molecule approaches to monitor directly the motions of individual proteins in aqueous solution and find that single ALP enzymes do not diffuse faster under catalysis. Instead, we demonstrate that interactions between the fluorescent dye and the enzyme’s substrate can produce the signature of apparent diffusion enhancement in fluorescence correlation spectroscopy (FCS), the standard ensemble assay currently used to study enzyme diffusion and indicate that single-molecule approaches provide a more robust means to investigate diffusion at the nanoscale.
The development of a novel diagnostic PCR forMadurella mycetomatisusing a comparative genome approach
Authors: Lim Wilson , Eadie Kimberly , Siddig Emmanuel , Nyuykonge Bertrand , Ahmed Sarah , Fahal Ahmed H. , Verbon Annelies , Smit Sandra , van de Sande Wendy WJ 
Published: April 2020

ABSTRACTEumycetoma is a neglected tropical disease characterized by large tumorous lesions. It is most commonly caused by the fungusMadurella mycetomatiswhich accounts for more than 70% of cases in central Africa. Currently, identification of the causative agent can only be reliably performed by a species-specific PCR. However, we recently demonstrated that ourM. mycetomatisspecific PCR can cross-react withMadurella pseudomycetomatis.We therefore used a comparative genome approach to develop a newM. mycetomatisspecific PCR for species identification. For this we compared the publishedM. mycetomatisgenome to genomes of other organisms in BLASTCLUST to identify uniqueM. mycetomatispredicted protein coding sequences. Based on 16 of these unique sequences, PCR primers were developed. The specificity of these primers was further evaluated in other eumycetoma causing agents including theMadurellasibling species. Out of the 16 tested sequences, only one was unique forM. mycetomatisand this should be used as a novel diagnostic marker forM. mycetomatis.
Predication of Pandemic COVID-19 situation in Maharashtra, India
Authors: Kumar Sunny 
Published: April 2020

AbstractPresently, the world is infected by COVID 19 virus which has created an emergency for public health. For controlling the spreading of the virus, we have to prepare for precaution and futuristic calculation for infection spreading. The coronavirus affects the population of the world including Inia. Here, we are the study the virus spreading rate on the Maharashtra state which is part of India. We are predicting the infected people by the SIR model. SIR model is one of the most effective models which can predict the spreading rate of the virus. We have validated the model with the current spreading rate with this SIR model. This study will help to stop the epidemic spreading because it is in the early stage in the Maharashtra region.
#50+ fashion Instagram influencers: cognitive age and aesthetic digital labours
Authors: McFarlane Ashleigh , Samsioe Emma 
Published: April 2020

PurposeThis paper demonstrates how #50+ fashion Instagram influencers contribute to the social construction of cognitive age through their aesthetic digital labours.Design/methodology/approachNon-participative netnography was used in the form of visual and textual analysis of over 300 Instagram posts including images, captions and comments.FindingsFindings reveal how outfit selection, background choices and bodily poses redefine expressions of look age through forms of aesthetic labour. Post-construction, hashtag and emoji usage illustrates how influencers refrain from directly posting about the fashion brands that they endorse. Instead, image and personality work visually attracts followers to politically charged posts which directly impact upon the social and cultural contexts where influencers are active. This ties into present-day wider societal discourses.Practical implications50+ fashion influencers have high spending power. Fashion brands should refrain from using #brand and collaborate in more subtle ways and concentrate on challenging the negativity of the old-age cliché.Originality/valueThe study advances theory on the social construction of age in fashion studies by combining cognitive age with aesthetic labour to identify the characteristics of the social phenomenon of the 50+ Instagram influencer. It applies principles from critical visual analysis to digital context, thereby advancing the qualitative netnographic toolkit.
Selection of Value-at-Risk models for MENA Islamic indices
Authors: Ben Ayed Wassim , Fatnassi Ibrahim , Ben Maatoug Abderrazak 
Published: April 2020

Purpose
The purpose of this study is to investigate the performance of Value-at-Risk (VaR) models for nine Middle East and North Africa Islamic indices using RiskMetrics and VaR parametric models.

Design/methodology/approach
The authors test the performance of several VaR models using Kupiec and Engle and Manganelli tests at 95 and 99 per cent levels for long and short trading positions, respectively, for the period from August 10, 2006 to December 14, 2014.

Findings
The authors’ findings show that the VaR under Student and skewed Student distribution are preferred at a 99 per cent level VaR. However, at 95 per cent level, the VaR forecasts obtained under normal distribution are more accurate than those generated using models with fat-tailed distributions. These results suggest that VaR is a good tool for measuring market risk. The authors support the use of RiskMetrics during calm periods and the asymmetric models (Generalized Autoregressive Conditional Heteroskedastic and the Asymmetric Power ARCH model) during stressed periods.

Practical implications
These results will be useful to investors and risk managers operating in Islamic markets, because their success depends on the ability to forecast stock price movements. Therefore, because a few Islamic financial institutions use internal models for their capital calculations, the regulatory committee should enhance market risk disclosure.

Originality/value
This study contributes to the knowledge in this area by improving our understanding of market risk management for Islamic assets during the stress periods. Then, it highlights important implications regarding financial risk management. Finally, this study fills a gap in the literature, as most empirical studies dealing with evaluating VaR prediction models have focused on quantifying the model risk in the conventional market.
Consistent measures of oxidative balance predict survival but not reproduction in a long‐distance migrant
Authors: Bodey Thomas W. , Cleasby Ian R. , Blount Jonathan D. , McElwaine Graham , Vigfusdottir Freydis , Bearhop Stuart 
Published: April 2020

Abstract

Physiological processes, including those that disrupt oxidative balance, have been proposed as key to understanding fundamental life‐history trade‐offs. Yet, examination of changes in oxidative balance within wild animals across time, space and major life‐history challenges remains uncommon. For example, migration presents substantial physiological challenges for individuals, and data on migratory individuals would provide crucial context for exposing the importance of relationships between oxidative balance and fitness outcomes.

Here we examined the consistency of commonly used measures of oxidative balance in longitudinally sampled free‐living individuals of a long‐lived, long‐distance migrant, the Brent goose Branta bernicla hrota over periods of months to years.

Although inter‐individual and temporal variation in measures of oxidative balance were substantial, we found high consistency in measures of lipid peroxidation and circulating non‐enzymatic antioxidants in longitudinally sampled individuals. This suggests the potential for the existence of individual oxidative phenotypes.

Given intra‐individual consistency, we then examined how these physiological measures relate to survival and reproductive success across all sampled individuals. Surprisingly, lower survival was predicted for individuals with lower levels of damage, with no measured physiological metric associated with reproductive success.

Our results demonstrate that snapshot measurements of a consistent measure of oxidative balance can inform our understanding of differences in a key demographic trait. However, the positive relationship between oxidative damage and survival emphasises the need to investigate the relationships between the oxidative system and fitness outcomes in other species undergoing similar physiologically challenging life cycles. This would highlight the extent to which variation in such traits and resource allocation trade‐offs is a result of adaptation to different life‐history strategies.
Depression and attitudes to change in referendums: The case of Brexit
Authors: BERNARDI LUCA , JOHNS ROBERT 
Published: April 2020

AbstractDepression is the most common mental illness and its profound impact on cognition and decision‐making has implications for political judgement. However, those implications are unclear in the case of referendums offering a choice between status quo and change. On one hand, one component of depression is the kind of life dissatisfaction associated with voting for change. Yet cognitive models also portray depression sufferers as biased towards the status quo: they are less inclined to research change, more pessimistic about its benefits and more likely to exaggerate its potential costs. In this paper, we use data from Understanding Society to examine the impact of those cross‐pressures on support for Brexit. Prior to the referendum, while life dissatisfaction and generally poor health predicted support for Leaving the European Union (EU), those diagnosed with depression were disproportionately likely to support Remain. Supporting our claim that the latter was a sign of status quo bias, this difference disappeared once the result was in and leaving the EU had become the widespread expectation. The study highlights the unexplored importance of mental health for political judgements, emphasises the multidimensionality of conditions like depression and illustrates the psychological role of status quo bias in referendum voting.
A powerful procedure that controls the false discovery rate with directional information
Authors: Tian Zhaoyang , Liang Kun , Li Pengfei 
Published: April 2020

AbstractIn many multiple testing applications in genetics, the signs of the test statistics provide useful directional information, such as whether genes are potentially up‐ or down‐regulated between two experimental conditions. However, most existing procedures that control the false discovery rate (FDR) are P‐value based and ignore such directional information. We introduce a novel procedure, the signed‐knockoff procedure, to utilize the directional information and control the FDR in finite samples. We demonstrate the power advantage of our procedure through simulation studies and two real applications.
Effect of temporal pulse shape on urinary stone phantom retropulsion rate and ablation efficiency using holmium:YAG and super‐pulse thulium fibre lasers
Authors: Ventimiglia Eugenio , Doizi Steeve , Kovalenko Anastasiya , Andreeva Viktoria , Traxer Olivier 
Published: April 2020

ObjectiveTo investigate the effects of laser temporal pulse shaping of the super‐pulse thulium fibre laser (SPTFL) and to compare these in controlled in vitro conditions with various holmium: yttrium aluminium garnet (Ho:YAG) pulse delivery modes.Materials and MethodsThe SPTFL (Urolase SP, IRE‐Polus, Fryazino, Russia), with an emission wavelength of 1.94 μm, and a Ho:YAG laser (P120H; Lumenis, Yokneam, Israel) with Moses technology were compared. Pulse shape, stone retropulsion and ablation efficiency were evaluated using BegoStones and compared for each laser mode: short (SP), long (LP), and Moses pulse (MP) for Ho:YAG, regular pulse (RP) and dual pulse (DP) for SPTFL.ResultsThe Ho:YAG SP mode exhibited an asymmetrical pulse shape, with a steep leading slope and a much more gradual trailing slope, without any flat section. Pulses generated by the SPTFL were significantly longer and therefore had lower peak power than those generated by the Ho:YAG laser at equivalent energy settings. Retropulsion for the holmium:YAG LP and MP modes was similar and lower than that for the SP mode, but higher than for the SPTFL (all P ≤ 0.02), with an average stone displacement approximately four times and two times lower for SPTFL as compared to the Ho:YAG laser. Comparison of ablation volumes indicated that the SPTFL induced significantly higher (twofold) ablation than the Ho:YAG laser.ConclusionsThe magnitude and initial velocity of stone retropulsion decreased with longer pulse duration and lower pulse peak power, without sacrificing ablation efficiency. These observations are manifest when comparing the Ho:YAG laser with the SPTFL. The novel SPTFL provides greater versatility and control of pulse variables than the Ho:YAG laser. Further clinical investigation of practical benefits achievable with pulse‐shaping SPTFL modes is warranted.
Basin‐scale fluvial correlation and response to the Tethyan marine transgression: An example from the Triassic of central Spain
Authors: Franzel Maximilian , Jones Stuart J. , Meadows Neil , Allen Mark B. , McCaffrey Ken , Morgan Tim 
Published: April 2020

AbstractThe relationships between large‐scale depositional processes and the stratigraphic record of alluvial systems, e.g. the origin and distribution of channel stacking patterns, changing architecture and correlation of strata, are still relatively poorly understood, in contrast to marine systems. We present a study of the Castillian Branch of the Permo‐Triassic Central Iberian Basin, north‐eastern Spain, using chemostratigraphy and a detailed sedimentological analysis to correlate the synrift Triassic fluvial sandstones for ~80 km along the south‐eastern basin margin. This study investigates the effects of Middle Triassic (Ladinian) Tethyan marine transgression on fluvial facies and architecture. Chemostratigraphy identifies a major, single axially flowing fluvial system lasting from the Early to Middle Triassic (~10 Ma). The fluvial architecture comprises basal conglomerates, followed by amalgamated sandstones and topped by floodplain‐isolated single‐ or multi‐storey amalgamated sandstone complexes with a total thickness up to ~1 km. The Tethyan marine transgression advanced into the basin with a rate of 0.04–0.02 m/year, and is recorded by a transition from the fluvial succession to a series of maximum flooding surfaces characterised by marginal marine clastic sediments and sabkha evaporites. The continued, transgression led to widespread thick carbonate deposition infilling the basin and recording the final stage of synrift to early‐post‐rift deposition. We identify the nonmarine to marine transition characterised by significant changes in the Buntsandstein succession with a transition from a predominantly tectonic‐ to a climatically driven fluvial system. The results have important implications for the temporal and spatial prediction of fluvial architecture and their transition during a marine transgression.