bluuebunny/crossref_metadata_2025_split huggingface dataset:
NMR spectroscopy analysis reveals an altered metabolic homeostasis in Arabidopsis seedlings treated with a cytokinesis inhibitor
Authors: Wilkop Thomas E. , Wang Minmin , Heringer Angelo , Zakharov Florence , Krishnan Viswanathan V. , Drakakaki Georgia 
Published: June 2020

AbstractIn plant cytokinesis,de novoformation of a cell plate evolving into the new cell wall partitions the cytoplasm of the dividing cell. Cell plate formation involves highly orchestrated vesicle accumulation, fusion, and membrane network maturation supported by the temporary integration of elastic and pliable callose. The small molecule, Endosidin 7 (ES7) arrests late cytokinesis in Arabidopsis by inhibiting callose deposition at the cell plate. Its effect is specific, as it does not broadly affect endomembrane trafficking or cytoskeletal organization. It has emerged as a very valuable tool for dissecting this essential plant process. In order to gain deeper insights regarding its mode of action and the effects of cytokinesis inhibition on overall plant growth, we investigated the effect of ES7 through a nuclear magnetic resonance spectroscopy metabolomics approach. In this case study, profiles of Arabidopsis leaf and root tissues were analyzed at different growth stages and ES7 exposure levels. The results show tissue-specific changes in the plant metabolic profile across a developmental gradient, and the effect that ES7 treatment has on the corresponding metabolome. The ES7 induced profile suggests metabolic compensations in central metabolism pathways in response to cytokinesis inhibition. Further, this study shows that long-term treatment of ES7 disrupts the homeostasis of primary metabolism in Arabidopsis seedlings, likely via alteration of hormonal regulation.
ATP induces protein folding, inhibits aggregation and antagonizes destabilization by effectively mediating water-protein-ion interactions, the heart of protein folding and aggregation
Authors: Kang Jian , Lim Liangzhong , Song Jianxing 
Published: June 2020

AbstractMany, particularly β-dominant proteins, are prone to misfolding/aggregation in the crowded cells, a hallmark of ageing and neurodegenerative diseases including ALS. ATP provides energy to drive supramolecular machineries to control protein hemostasis in modern cells. Recently ATP was decoded to hydrotropically inhibit/dissolve liquid-liquid phase separation (LLPS) and aggregation/fibrillation at millimolar concentrations. We also found that by specific binding, ATP induces and subsequently dissolves LLPS, as well as inhibits fibrillation. Nevertheless, no report shows that ATP can directly induce protein folding. Here, by selecting two aggregation-prone ALS-causing proteins with the unfolded states, we successfully visualized the effects of ATP and 11 molecules with NMR directly on their folding and aggregation. The study reveals for the first time that ATP can induce folding at molar ratios of 2-8, the highest efficiency known so far. Intriguingly, this inducing-capacity comes from triphosphate, a key intermediate in prebiotic chemistry, which, however, also triggers aggregation. Most unexpectedly, upon joining with adenosine, the ability of triphosphate to trigger aggregation is shielded. Marvelously, ATP emerged to manifest three integrated abilities: to induce folding, inhibit aggregation and increase stability, that are absent in ATPP, AMP-PCP and AMP-PNP. Our study sheds the first light on previously-unknown roles of ATP in energy-independently controlling protein folding and aggregation by effectively mediating water-protein-ion interactions. Therefore, ATP might be not just irreplaceable for solving protein folding and aggregation problems simultaneously in primitive cells for Origin of Life, but also energy-independently operating in modern cells to regulate protein homeostasis fundamentally critical for physiology and pathology.
Rapid screening and detection of inter-type viral recombinants using phylo-k-mers
Authors: Scholz Guillaume E. , Linard Benjamin , Romashchenko Nikolai , Rivals Eric , Pardi Fabio 
Published: June 2020

AbstractMotivationNovel recombinant viruses may have important medical and evolutionary significance, as they sometimes display new traits not present in the parental strains. This is particularly concerning when the new viruses combine fragments coming from phylogenetically-distinct viral types. Here, we consider the task of screening large collections of sequences for such novel recombinants. A number of methods already exist for this task. However, these methods rely on complex models and heavy computations that are not always practical for a quick scan of a large number of sequences.ResultsWe have developed SHERPAS, a new program to detect novel recombinants and provide a first estimate of their parental composition. Our approach is based on the precomputation of a large database of “phylogenetically-informedk-mers”, an idea recently introduced in the context of phylogenetic placement in metagenomics. Our experiments show that SHERPAS is hundreds to thousands of times faster than existing software, and enables the analysis of thousands of whole genomes, or long sequencing reads, within minutes or seconds, and with limited loss of accuracy.Availability and ImplementationThe source code is freely available for download athttps://github.com/phylo42/sherpasContactpardi@lirmm.fr,gllm.scholz@gmail.comSupplementary informationSupplementary Materials are available online.
HSC70, HSPA1A, and HSP90AB1 Facilitate Ebola Virus trVLPs to Induce Autophagy
Authors: Yu Dong-Shan , Yao Shu-Hao , Xi Wen-Na , Cheng Lin-Fang , Liu Fu-Min , Wu Hai-Bo , Lu Xiang-Yun , Wu Nan-Ping , Sun Shui-Lin , Yao Hang-Ping 
Published: June 2020

ABSTRACTEbola virus (EBOV) can induce autophagy to benefit the virus life cycle, but detailed mechanisms remain to be elucidated. We previously found that EBOV GP and VP40 proteins interact with HSC70 (HSPA8), HSPA1A, and HSP90AB1. Thus, we presumed that EBOV likely induced autophagy by virus protein-host HSC70 or co-chaperon interactions via chaperone-mediated autophagy (CMA). We developed EBOV-trVLPs to model the EBOV life cycle, infected 293T cells with trVLPs, evaluated CMA by GFP-LC3 and RFP-LAMP1 co-localization, transmission electron microscopy (TEM) observation, and immunoblot analysis. The results demonstrated that EBOV-trVLPs induce autophagy which could not be inhibited by 3-MA significantly; autophagosomes and autolysosomes are obviously in the cytoplasm confirming CMA in cells infected with trVLPs. Meanwhile, a knockdown of HSC70 and relevant co-chaperones could inhibit trVLPs-associated autophagy, but no effort to Akt/mTOR/PHLPP1 pathway. These data indicate that EBOV-trVLPs could induce autophagy by CMA but was not limited by the CMA pathway. HSC70, HSPA1A, and HSP90AB1 participate and regulate CMA induced by EBOV-trVLPs. This was the first study about EBOV-trVLPs-induction of CMA and provides insight into the viral protein-host protein interaction, which is probably associated with CMA.HighlightsEBOV-trVLPs induce chaperone-mediated autophagy (CMA) but are not limit by CMA.HSC70, HSPA1A, and HSP90AB1 facilitate EBOV-trVLPs to induce autophagyKnockdown of HSC70, HSPA1A, and HSP90AB1 inhibit EBOV-trVLPs-induced CMA.
Spatially and cell-type resolved quantitative proteomic atlas of healthy human skin
Authors: Dyring-Andersen Beatrice , Løvendorf Marianne Bengtson , Coscia Fabian , Santos Alberto , Møller Line Bruun Pilgaard , Colaço Ana R. , Niu Lili , Bzorek Michael , Doll Sophia , Andersen Jørgen Lock , Clark Rachael A. , Skov Lone , Teunissen Marcel B.M. , Mann Matthias 
Published: June 2020

ABSTRACTHuman skin provides both physical integrity and immunological protection from the external environment using functionally distinct layers, cell types and extracellular matrix. Despite its central role in human health and disease, the constituent proteins of skin have not been systematically characterized. Here, we combined advanced tissue dissection methods, flow cytometry and state-of-the-art proteomics to describe a spatially-resolved quantitative proteomic atlas of human skin. We quantified 10,701 proteins as a function of their spatial location and cellular origin. The resulting protein atlas and our initial data analyses demonstrate the value of proteomics for understanding cell-type diversity within the skin. We describe the quantitative distribution of structural proteins, known and novel proteins specific to cellular subsets and those with specialized immunological functions such as cytokines and chemokines. We anticipate that this proteomic atlas of human skin will become an essential community resource for basic and translational research (www.skin.science).
Spatio-temporal Characteristics of Noun and Verb Processing during Sentence Comprehension in the Brain
Authors: Jat Sharmistha , Laing Erika J C , Talukdar Partha , Mitchell Tom 
Published: June 2020

AbstractThe human brain is very effective at integrating new words one by one into the composed representation of a sentence as it is read left-to-right. This raises the important question of what happens to the neural representations of words present earlier in the sentence? For example, do the strength of word representations encountered earlier on in the sentence remain constant or do they evolve as additional words are processed? Representation of words by neural activity in the brain has been the subject of several previous studies. We perform the experiment with a naturalistic task in which the subjects read simple active and passive sentences. Naturalistic studies have tended to explore words in isolation or in a very limited context (e.g., adjective-noun phrases). Representation of previously encountered words during incremental sentence reading, and how such representation evolve as more parts of a sentence are read, is a fundamental but unexplored problem – we take a first step in this direction. In particular, we examine the spatio-temporal characteristics of neural activity encoding nouns and verbs encountered in a sentence as it is read word-by-word. We use Magnetoencephalography (MEG) to passively observe neural activity, providing 1 ms temporal resolution.Our experiments reveal that nouns and verbs read early in the sentence have a varying influence on neural activity while reading subsequent words, decreasing and increasing at particular word positions in active and passively voiced sentences, with particularly important contributions to activity in frontal and temporal cortical regions. We find the noun and verb information to be decodable from the neural activity for several seconds after sentence reading has completed. Our exploration is also the first to study the effect of question-answering task on the neural representation of the words post-sentence. We are releasing our 300 sentence MEG dataset to encourage further research in this important area.
Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein
Authors: Gerovac Milan , Mouali Youssef El , Kuper Jochen , Kisker Caroline , Barquist Lars , Vogel Jörg 
Published: June 2020

ABSTRACTRNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here establish glycerol gradient sedimentation with RNase treatment and mass spectrometry (GradR). Applied toSalmonella enterica, GradR confirms many known RBPs such as CsrA, Hfq and ProQ by their RNase-sensitive sedimentation profiles, and discovers the FopA protein as a new member of the emerging family of FinO/ProQ-like RBPs. FopA, encoded on resistance plasmid pCol1B9, primarily targets a small RNA associated with plasmid replication. The target suite of FopA dramatically differs from the related global RBP ProQ, revealing context-dependent selective RNA recognition by FinO-domain RBPs. Numerous other unexpected RNase-induced changes in gradient profiles suggest that cellular RNA helps to organize macromolecular complexes in bacteria. By enabling poly(A)-independent generic RBP discovery, GradR provides an important element in the quest to build a comprehensive catalogue of microbial RBPs.
Gas-phase endstation of electron, ion and coincidence spectroscopies for diluted samples at the FinEstBeAMS beamline of the MAX IV 1.5 GeV storage ring
Authors: Kooser Kuno , Kivimäki Antti , Turunen Paavo , Pärna Rainer , Reisberg Liis , Kirm Marco , Valden Mika , Huttula Marko , Kukk Edwin 
Published: June 2020

Since spring 2019 an experimental setup consisting of an electron spectrometer and an ion time-of-flight mass spectrometer for diluted samples has been available for users at the FinEstBeAMS beamline of the MAX IV Laboratory in Lund, Sweden. The setup enables users to study the interaction of atoms, molecules, (molecular) microclusters and nanoparticles with short-wavelength (vacuum ultraviolet and X-ray) synchrotron radiation and to follow the electron and nuclear dynamics induced by this interaction. Test measurements of N2 and thiophene (C4H4S) molecules have demonstrated that the setup can be used for many-particle coincidence spectroscopy. The measurements of the Ar 3p photoelectron spectra by linear horizontal and vertical polarization show that angle-resolved experiments can also be performed. The possibility to compare the electron spectroscopic results of diluted samples with solid targets in the case of Co2O3 and Fe2O3 at the Co and Fe L
2,3-absorption edges in the same experimental session is also demonstrated. Because the photon energy range of the FinEstBeAMS beamline extends from 4.4 eV up to 1000 eV, electron, ion and coincidence spectroscopy studies can be executed in a very broad photon energy range.
Judgments about sexual assault vary depending on whether an affirmative consent policy or a “no means no” policy is applied
Authors: Miller Monica K. 
Published: June 2020

PurposeAffirmative consent (AC) policies require potential sexual partners to clearly and positively confirm that they want to engage in sexual behavior – in contrast to standard “no means no” policies, which typically define consent through resistance. AC policies might not be effective because they do not align well with typical scripts of how consent is given in practice. This study aims to compare participants’ judgments as to what constitutes sexual assault, using either an AC policy or a standard “no means no” policy.Design/methodology/approachParticipants read 16 scenarios depicting various male-female sexual encounters and applied either an AC or a standard “no means no” policy to determine whether the encounter was consensual.FindingsWhen an AC policy was used, participants were more likely to judge the scenario as sexual assault. Aspects of the scenario (which reflect AC policy criteria), such as the type of communication (verbal or nonverbal), clarity of communication (clear or unclear) and resistance (high or low) also affected judgments of the scenario. Relationship type (stranger vs acquaintance) did not affect judgments. Students were more likely to perceive the scenarios as sexual assault than community members; they also perceived differences between scenarios based on verbal communication and clarity more than community members. Finally, there was no main effect of participant gender, however, men perceived differences between scenarios based on verbal communication type, whereas women did not.Research limitations/implicationsFindings indicate that participants are generally able to apply AC policies correctly, even though AC criteria do not generally align with common sexual scripts.Originality/valueThis is the first study known to test whether decision-makers can properly apply criteria outlined in AC policies and whether the application of these policies affect decisions-makers judgments as to whether a sexual encounter is consensual or assault.
Post‐mortem Iris Decomposition and its Dynamics in Morgue Conditions
Authors: Trokielewicz Mateusz , Czajka Adam , Maciejewicz Piotr 
Published: June 2020

AbstractWith increasing interest in employing iris biometrics as a forensic tool for identification by investigation authorities, there is a need for a thorough examination and understanding of postmortem decomposition processes that take place within the human eyeball, especially the iris. This can prove useful for fast and accurate matching of antemortem with postmortem data acquired at crime scenes or mass casualties, as well as for ensuring correct dispatching of bodies from the incident scene to a mortuary or funeral homes. Following these needs of forensic community, this paper offers an analysis of the coarse effects of eyeball decay done from a perspective of automatic iris recognition. We analyze postmortem iris images acquired for a subject with a very long postmortem observation time horizon (34 days), in both visible light and near‐infrared light (860 nm), as the latter wavelength is used in commercial iris recognition systems. Conclusions and suggestions are provided that may aid forensic examiners in successfully utilizing iris patterns in postmortem identification of deceased subjects. Initial guidelines regarding the imaging process, types of illumination, and resolution are also given, together with expectations with respect to the iris features decomposition rates. Visible iris features possible for human, expert‐based matching persists even up to 407 h postmortem, and near‐infrared illumination is suggested for better mitigation of corneal opacity while imaging cadaver eyes (Post‐mortem iris decomposition and its dynamics in morgue conditions. ArXiv pre‐print, 2019).
Attenuation of ataxia telangiectasia mutated signalling mitigates age‐associated intervertebral disc degeneration
Authors: Han Yingchao , Zhou Chao‐Ming , Shen Hongxing , Tan Jun , Dong Qing , Zhang Lei , McGowan Sara J. , Zhao Jing , Sowa Gwendolyn A. , Kang James D. , Niedernhofer Laura J. , Robbins Paul D. , Vo Nam N. 
Published: June 2020

AbstractPreviously, we reported that persistent DNA damage accelerates ageing of the spine, but the mechanisms behind this process are not well understood. Ataxia telangiectasia mutated (ATM) is a protein kinase involved in the DNA damage response, which controls cell fate, including cell death. To test the role of ATM in the human intervertebral disc, we exposed human nucleus pulposus (hNP) cells directly to the DNA damaging agent cisplatin. Cisplatin‐treated hNP cells exhibited rapid phosphorylation of ATM and subsequent increased NF‐κB activation, aggrecanolysis, decreased total proteoglycan production and increased expression of markers of senescence, including p21, γH2AX and SA‐ß‐gal. Treating cisplatin‐exposed hNP cells with an ATM‐specific inhibitor negated these effects. In addition, genetic reduction of ATM reduced disc cellular senescence and matrix proteoglycan loss in the progeroid Ercc1−/∆ mouse model of accelerated ageing. These findings suggest that activation of ATM signalling under persistent genotoxic stress promotes disc cellular senescence and matrix homeostatic perturbation. Thus, the ATM signalling pathway represents a therapeutic target to delay the progression of age‐associated spine pathologies.
A Pilot Trial of Topical Capsaicin Cream for Treatment of Cannabinoid Hyperemesis Syndrome
Authors: Dean Diana J. , Sabagha Noor , Rose Kaitlin , Weiss Alexander , France John , Asmar Timothy , Rammal Jo‐Ann , Beyer Margaret , Bussa Rebecca , Ross Jacob , Chaudhry Kaleem , Smoot Thomas , Wilson Kathleen , Miller Joseph 
Published: June 2020

AbstractObjectivesPatients with cannabinoid hyperemesis syndrome (CHS) present frequently to the emergency department. Previous case studies suggest dramatic symptomatic improvement with topical capsaicin treatment. This exploratory study examined the potential effectiveness of topical capsaicin in patients with nausea and vomiting due to a suspected CHS exacerbation.MethodsThis was a double‐blind, randomized placebo‐controlled pilot trial. Adults who presented with vomiting suspected to be from CHS were eligible for enrollment. We excluded pregnant women and those with resolution of symptoms. Following randomization, topical 0.1% capsaicin or placebo cream was applied to the anterior abdomen in a uniform manner. The primary outcome was the severity of nausea on a visual analog scale (VAS) of 0 to 10 cm assessed at 30 minutes. Secondary outcomes were adverse events, occurrence of posttreatment vomiting, nausea by VAS at 60 minutes, and hospital admission.ResultsThis pilot trial enrolled 30 patients, 17 in the capsaicin arm and 13 in the placebo arm. One patient in the capsaicin arm did not tolerate treatment due to skin irritation. Mean ± SD nausea severity at 30 minutes was 4.1 ± 2.3 cm in the capsaicin arm and 6.1 ± 3.3 cm in the placebo arm (difference = −2.0 cm, 95% confidence interval [CI] = 0.2 to −4.2 cm). At 60 minutes, mean ± SD nausea severity was 3.2 ± 3.2 cm versus 6.4 ± 2.8 cm (difference = −3.2 cm, 95% CI = −0.9 to −5.4 cm). The percent reduction in nausea at 60 minutes from baseline was 46.0% in the capsaicin arm and 24.9% in the placebo arm (difference = 21.1%, 95% CI = −5.6% to 47.9%). A higher proportion of capsaicin group patients (29.4% vs. 0%) had complete resolution of nausea (relative risk = 3.4, 95% CI = 1.6 to 7.1).ConclusionIn this pilot trial, the application of topical capsaicin cream was associated with a significant reduction in nausea at 60 minutes but not at 30 minutes and provided more complete relief of nausea.
Baby boomers’ attitudes to maintaining sexual and intimate relationships in long‐term care
Authors: Rahn Alison , Jones Tiffany , Bennett Cary , Lykins Amy 
Published: June 2020

AbstractObjectivesAustralian aged care policy is wholly focused on individual “consumers” and consequently neglects the needs of dyadic partners. This paper highlights partnered baby boomers’ attitudes to maintaining sexual and intimate relationships in residential care.MethodsIn 2016, cross‐sectional data were collected using an online survey of partnered baby boomers recruited using social media. Qualitative data were analysed using word frequency, keywords‐in‐context and thematic analysis. Descriptive statistics were generated from quantitative data.ResultsThere were 168 participants (85% female), aged 51‐71 years. Many reported that remaining together and continuing physical and sexual contact were important in aged care contexts—necessitating private couple's suites, shared beds, access to condoms, lubricants and sexual health professionals.ConclusionsConsiderable cultural change will be required to raise residential aged care to the standard expected by some partnered baby boomers. Shifting to a more couple‐centred approach may benefit partnered residents’ health and well‐being.