bluuebunny/crossref_metadata_2025_split huggingface dataset:
Velocity-based optoretinography for clinical applications
Authors: Vienola Kari V. , Valente Denise , Zawadzki Robert J. , Jonnal Ravi S. 
Published: May 2022

AbstractOptoretinography (ORG) is an emerging tool for testing neural function in the retina. Unlike existing methods, it is noninvasive, objective, and provides information about retinal structure and function at once. As such, it has great potential to transform ophthalmic care and clinical trials of novel therapeutics designed to restore or preserve visual function. Recent efforts have demonstrated the feasibility of the ORG using state-of-the-art optical coherence tomography systems. These methods measure the stimulus-evoked movement of subcellular features in the retina, using the phase of the reflected light to monitor their position. Here we present an alternative approach that monitors the velocity of these features instead. This conceptual shift has significant implications for the nascent field of optoretinography. By avoiding the need to track specific cells over time, it obviates costly and laborious aspects of the position-based approaches, such as adaptive optics, digital aberration correction, real-time tracking, and three-dimensional segmentation and registration. We used this novel velocity-based approach to measure the photoreceptor ORG responses in three healthy subjects. The resulting responses were reproducible and exhibited dependence on dose and retinal eccentricity. The position of the relevant structures was reconstructed through numerical integration of velocity.
Allelic variation in theArabidopsisTNL CHS3/CSA1 immune receptor pair reveals two functional regulatory modes
Authors: Yang Yu , Kim Nak Hyun , Cevik Volkan , Jacob Pierre , Wan Li , Furzer Oliver J. , Dangl Jeffery L. 
Published: May 2022

AbstractSome plant NLR immune receptors are encoded in head-to-head pairs that function together. Alleles of the NLR pair CHS3/CSA1 form three clades. The clade 1 sensor CHS3 contains an integrated domain (ID) with homology to regulatory domains, which is lacking in clades 2 and 3. We defined two regulatory modes for CHS3/CSA1 pairs. One is likely mediated by effector binding to the clade 1 ID of CHS3 and the other relies on CHS3/CSA1 pairs from all clades detecting effector modification of an associated pattern recognition receptor. We suggest that an ancestral Arabidopsis CHS3/CSA1 pair gained a second recognition specificity and regulatory mechanism through ID acquisition, while retaining its original specificity as a ‘Guard’ against perturbation of pattern recognition receptor targeting by a pathogen effector. This likely comes with a cost, since both ID and non-ID alleles of the pair persist in diverse Arabidopsis populations through balancing selection.SummaryWe dissect a novel case where two regulatory modes emerged across three clades of the co-evolved CHS3/CSA1 plant immune receptor pairs, which features recruitment of an integrated domain (ID) into the clade 1 CHS3 alleles. Pre- and post-ID integration alleles maintain functionality; balancing selection maintains both in the Arabidopsis pan-genome.
Evaluation of operational characteristics and performance of HIV rapid diagnostic tests (RDTs): Systematic review and meta-analysis of the literature from 2012 to 2020
Authors: Kingwara Leonard , Bowen Nancy , Panpradist Nuttada , Lokamar Peter , Morangi Vera , Madada Rukia Sarah , Nyakeriga Emmanuel , Awuor Christabel , Onentia Jonah , Masyuko Sarah , Wafula Rose , Kiiru John Ndemi 
Published: May 2022

AbstractBackgroundMost countries have rolled out HIV Rapid diagnostic tests (RDTs) due to their significant advantages over laboratory-based serological testing. These advantages are lower cost, ease of use, interpretation speed, and relatively high acceptability; the HIV diagnostic landscape has evolved fast, and newer technologies have been developed and deployed. Given the many options available, selecting an HIV rapid diagnostic test for a particular clinical program, self-test, or research setting can be daunting without the precise knowledge of their performance characteristics. This systematic review and meta-analysis aimed to compare the field diagnostic performance of available HIV rapid test kits, cost-effectiveness, ease of use, and acceptability.MethodsPubMed and Web of Science were searched for publications on rapid HIV tests using blood specimens. We then performed a meta-analysis and systematic analysis to quantitatively and qualitatively evaluate the diagnostic performance of rapid HIV tests compared with the western blot (WB), enzyme-linked immunosorbent assay (ELISA), or an HIV diagnostic algorithm in terms of pooled sensitivity, specificity, area under the summary receiver operating characteristic (SROC) curve, and diagnostic odds ratio (DOR).ResultsThe meta-analysis for the diagnostic test included 26 studies for diagnostic accuracy, while the qualitative analysis included 15 studies. On average, the RDT sensitivities were 99%; [95% CI=0.99-100%], while specificity was optimal at 100%; [95% CI=99%-100%]. The diagnostic odds ratio estimates that a single test performed better than a dual test: dual test DOR=44612.33 and single test DOR=14323.1. The impact of unobserved heterogeneity using the quantity I2 for sensitivity was 99.47%, while that for specificity was 99.96, indicating significant heterogeneity and justifying stratified analysis of the selected studies. The diagnostic test from Unigold had the best-pooled sensitivity, specificity, and diagnostic odds ratio at 99%, 99.35%, and 2896.667, respectively. Qualitative data indicate shorter time to results is preferred by both the clients and health care providers.ConclusionThe average of the RDT sensitivities for diagnostic accuracy were 99% (95% CI=0.99-100%), while specificity was optimal at 100%; 95% CI=99-100. The diagnostic odds ratio was DOR=44612 (95% CI=14323-138954), thus indicating better RDT test performance. The performance of single test kits in HIV diagnosis was better than those for dual tests.
Botrytis cinerea identifies host plants via the recognition of antifungal capsidiol to induce expression of a specific detoxification gene
Authors: Kuroyanagi Teruhiko , Bulasag Abriel , Fukushima Keita , Suzuki Takamasa , Tanaka Aiko , Camagna Maurizio , Sato Ikuo , Chiba Sotaro , Ojika Makoto , Takemoto Daigo 
Published: May 2022

AbstractThe gray mold pathogen Botrytis cinerea has a broad host range, causing disease in over 400 plant species, but it is not known how this pathogen evolved this polyxenous nature. B. cinerea can metabolize a wide range of phytoalexins, including the stilbenoid, resveratrol, and the sesquiterpenoids capsidiol in tobacco, and rishitin in potato and tomato. In this study, we analyzed the metabolism of sesquiterpenoid phytoalexins by B. cinerea. Capsidiol was dehydrogenated to capsenone which was then further oxidized, while rishitin was directly oxidized to epoxy-or hydroxy-rishitins indicating that B. cinerea has separate mechanisms to detoxify structurally similar sesquiterpenoid phytoalexins. RNAseq analysis revealed that a distinct set of genes were induced in B. cinerea when treated with capsidiol or rishitin, suggesting that B. cinerea can distinguish structurally similar phytoalexins to activate appropriate detoxification mechanisms. The gene most highly upregulated by capsidiol treatment encoded a dehydrogenase, designated Bccpdh. Heterologous expression of Bccpdh in a capsidiol-sensitive plant symbiotic fungus, Epichloë festucae, resulted in an acquired tolerance of capsidiol and the ability to metabolize capsidiol to capsenone, while B. cinerea Δbccpdh mutants became relatively sensitive to capsidiol. The Δbccpdh mutant showed reduced virulence on the capsidiol producing Nicotiana and Capsicum species but remained fully pathogenic on potato and tomato. Homologs of Bccpdh are not found in taxonomically distant Ascomycota fungi but not in related Leotiomycete species, suggesting that B. cinerea acquired the ancestral Bccpdh by horizontal gene transfer, thereby extending the pathogenic host range of this polyxenous pathogen to capsidiol-producing plant species.Significance StatementB. cinerea can metabolize a wide range of phytoalexins, however, the extent to which phytoalexin detoxification contributes to pathogenicity is largely unknown. In this study, we have shown that B. cinerea recognizes structurally resembling sesquiterpenoid phytoalexins, rishitin and capsidiol, to activate appropriate detoxification mechanisms. We identify Bccpdh, encoding a dehydrogenase for capsidiol detoxification, which is upregulated in B. cinerea exclusively during the infection of capsidiol producing plant species, and is required to exert full virulence. Analysis of the Bccpdh locus implicates that the gene was acquired via horizontal gene transfer. This work highlights that the polyxenous plant pathogen B. cinerea can distinguish its host plants by its anti-microbial compounds, to activate appropriate mechanisms for enhanced virulence.
RNA binding proteins Smaug and Cup induce CCR4-NOT-dependent deadenylation of the nanos mRNA in a reconstituted system
Authors: Pekovic Filip , Rammelt Christiane , Kubíková Jana , Metz Jutta , Jeske Mandy , Wahle Elmar 
Published: May 2022

ABSTRACTPosttranscriptional regulation of the maternal nanos mRNA is essential for the development of the anterior – posterior axis of the Drosophila embryo. The nanos RNA is regulated by the protein Smaug. Binding to Smaug recognition elements (SREs) in the nanos 3’-UTR, Smaug nucleates the assembly of a larger repressor complex including the eIF4E-T paralog Cup and five additional proteins. The Smaug-dependent complex represses translation of nanos and induces its deadenylation by the CCR4-NOT deadenylase. Here we report an in vitro reconstitution of the Drosophila CCR4-NOT complex and Smaug-dependent deadenylation. We find that Smaug by itself is sufficient to cause deadenylation by the Drosophila or human CCR4-NOT complexes in an SRE-dependent manner. CCR4-NOT subunits NOT10 and NOT11 are dispensable, but the NOT module, consisting of NOT2, NOT3 and the C-terminal part of NOT1, is required. Smaug interacts with the C-terminal domain of NOT3. Both catalytic subunits of CCR4-NOT contribute to Smaug-dependent deadenylation. Whereas the CCR4-NOT complex itself acts distributively, Smaug induces a processive behavior. The cytoplasmic poly(A) binding protein (PABPC) has but a minor effect on Smaug-dependent deadenylation. Among the additional constituents of the Smaug-dependent repressor complex, Cup also facilitates CCR4-NOT-dependent deadenylation, both independently and in cooperation with Smaug.
An in vivo and in silico evaluation of the magical hepatoprotective potentialities of Gynura procumbens: a promising agent for combating hepatotoxicity
Authors: Tithi Tanzia Islam , Tahsin Md. Rafat , Zaman Tasnuva Sharmin , Anjum Juhaer , Bahar Nasiba Binte , Sen Priyanka , Tasnim Sabiha , Sultana Arifa , Koly Fahima Jannat , Jahan Ishrat , Aktar Fahima , Chowdhury Jakir Ahmed , Kabir Shaila , Chowdhury Abu Asad , Amran Md. Shah 
Published: May 2022

AbstractIntroductionLiver being the most important metabolic organ of the body performs a wide variety of vital functions. Hepatic cell injury occurs by the activation of reactive oxygen species (ROS) by CCl4, xenobiotics and other toxic substances generated through cytochrome P450 dependent step resulting from covalent bond formation with lipoproteins and nucleic acids. Observing the alarming state of hepatotoxic patients worldwide, different medicinal plants and their properties can be explored to combat against such free radical degermation of liver. This paper evaluates the antioxidant property ofGynura procumbensin both in silico and in an in vivo assay, and its hepatoprotective activity in CCl4induced hepatotoxicity.Materials and MethodsGynura procumbensleaves were collected and extracted using 50% ethanol. Required chemicals (CCl4), standard drug (Silymarin) and blood serum analyzing kits were stocked. The in vivo tests were performed in 140 healthy Wister albino male rats under well controlled parameters dividing into 14 groups, strictly maintaining IEAC protocols. In silico molecular docking and ADMET studies were performed and the results were analyzed statistically.Results and discussionThe body weight increased significantly in CCl4induced,G. procumbensadministered hepatotoxic rats. The increase in SGPT, SGOT, ALP, creatinine, LFH, triglycerides, LDL, SOD, MDA, total cholesterol, DNA fragmentation ranges, γGT levels of CCl4treated group was decreased by both standard drug Silymarin andG. procumbensleaf extract. On the other hand,G. procumbensincreased HDL levels and displayed contrasting results in CAT level tests. Some results contradicted with the negative controlled group displaying varying efficacy between leaf extract and Silymarin. In the molecular docking analysis,G. procumbensphytoconstituents performed poorly against TGF-β1 compared to the control drug Galunisertib while 26 phytoconstituents scored better than the control, bezafibrate against PPAR-α. Flavonoids and phenolic compounds performed better than other constituents in providing hepatoprotective activity.
MEAHNE: MiRNA-disease association prediction based on semantic information in heterogeneous networks
Authors: Huang Chen , Cen Keliang , Zhang Yang , Liu Bo , Wang Yadong , Li Junyi 
Published: May 2022

AbstractPrior studies have suggested close associations between miRNAs and diseases. Correct prediction of potential miRNA-disease pairs by computational methods is able to greatly accelerate the experimental process in biomedical research. However, many methods cannot effectively learn the complex information in the multi-source data, and limits the performance of the prediction model. A heterogeneous network prediction model MEAHNE is proposed to make full use of the complex information in multi-source data. We first constructed a heterogeneous network using miRNA-disease associations, miRNA-gene associations, disease-gene associations, and gene-gene associations. Because the rich semantic information in the heterogeneous network contains a lot of relational information of the network. To mine the relational information in heterogeneous network, we use neural networks to extract semantic information in metapath instances. We encode the obtained semantic information into weights using the attention mechanism, and use the weights to aggregate nodes in the network. At the same time, we also aggregate the semantic information in the metapath instances into the nodes associated with the instances, which can make the node embedding have excellent ability to represent the network. MEAHNE optimizes parameters through end-to-end training. MEAHNE is compared with other state-of-the-art heterogeneous graph neural network methods. The values of area under precision-recall curve and receiver operating characteristic curve show the superiority of MEAHNE. Additionally, MEAHNE predicted 50 miRNAs for lung cancer and esophageal cancer each and verified 49 miRNAs associated with lung cancer and 44 miRNAs associated with esophageal cancer by consulting relevant databases. MEAHNE has good performance and interpretability by experimental verification.
A phospho-switch provided by LRR receptor-like kinase, ALK1/QSK1/KIN7, prioritizes ABCG36/PEN3/PDR8 transport toward defense
Authors: Aryal Bibek , Xia Jian , Hu Zehan , Tsering Tashi , Liu Jie , Huynh John , Fukao Yoichiro , Glöckner Nina , Huang Hsin-Yao , Sáncho-Andrés Gloria , Pakula Konrad , Gorzolka Karin , Zwiewka Marta , Nodzynski Tomasz , Harter Klaus , Sánchez-Rodríguez Clara , Jasiński Michał , Rosahl Sabine , Geisler Markus 
Published: May 2022

AbstractBased on its proposed substrate preferences, the ABC transporter, ABCG36/PDR8/PEN3, from the model plant Arabidopsis stands at the cross-road between growth and defence. Recently, ABCG36 was shown to export a few indolic compounds, including the auxin precursor, indole-3-butyric acid (IBA), and to be implicated in the export of the major phytoalexin of Arabidopsis, camalexin, although clear-cut proof of camalexin transport activity is still lacking.Here we provide strong evidence that ABCG36 catalyses the direct, ATP-dependent export of camalexin over the plasma membrane, however, most likely in functional interplay with non-camalexin transporting ABCG isoforms. We identify the leucin-rich repeat receptor-like kinase, Auxin-induced LRR Kinase1 (ALK1/KIN7/QSK1), as a functional kinase to physically interact with and phosphorylate ABCG36. ABCG36 phosphorylation by ALK1 represses unilaterally IBA but not camalexin export leading to a prioritization of ABCG transport toward defense. As a consequence, phospho-dead mutants of ABCG36, likealk1andabcg36alleles, are hypersensitive toward infection with the root pathogen,F. oxysporum, caused by elevated fungal progression.Our findings indicate a novel, direct regulatory circuit between a receptor kinase and an ABC transporter determining transporter substrate specificity. It appears that growth and defense balance decisions in plants are performed on the transporter level by means of a reversible phospho-switch.
In situ identification of secondary structures in unpurifiedBombyx morisilk fibrils using polarized two-dimensional infrared spectroscopy
Authors: Giubertoni Giulia , Caporaletti Federico , Roeters Steven , Chatterley Adam S. , Weidner Tobias , Laity Peter , Holland Chris , Woutersen Sander 
Published: May 2022

AbstractThe mechanical properties of biomaterials are dictated by the interactions and conformations of their building blocks, typically proteins. Although the macroscopic behaviour of biomaterials is widely studied, our understanding of the underlying molecular properties is generally limited. Among the non-invasive and label-free methods to investigate molecular structures, infrared spectroscopy is one of the most commonly used tools, because the absorption bands of the amide groups strongly depend on protein secondary structure. However, spectral congestion usually complicates the analysis of the amide spectrum. Here, we apply polarized two-dimensional (2D) infrared spectroscopy (IR) to directly identify the protein secondary structures in native silk filks cast fromBombyx morisilk feedstock. Without any additional analysis, such as peak fitting, we find that the initial effect of hydration is an increase of the random-coil content at the expense of theα-helix content, while theβ-sheet content is unchanged, and only increases at a later stage. This paper demonstrates that 2D-IR can be a valuable tool for characterizing biomaterials.
Methodological comparison of different approaches to cultivate postnatal organotypic hippocampal cultures
Authors: Czapla Vivien , Reiterer Pia , Funke Klaus 
Published: May 2022

ABSTRACTTo study molecular and cellular processes of the brainin vitro, the cultivation of postnatal organotypic hippocampal slices should be established. The methodological approach had to be optimized several times because the result of the cultivation was not optimal. Initially, cultivation was performed by roller tube culture, which is the first developed cultivation method for these cultures. As the cultures detached or even dissolved, further cultivation was carried out using inserts, which represent a modification of the roller tube cultures. In the further course it came also to the use of different preparation methods and to the exchange of the medium and the incubator, in order to obtain a result of the organ cultivation corresponding to the expectations. The results show that cultivation on semi-permeable membranes has an advantage over roller tube cultures. On the one hand, there is no detachment and dissolution of hippocampal slices due to the mechanical influence and on the other hand, the tissue shows an improvement in general condition compared to roller tube cultures. Furthermore, it was found that an acceleration of the preparation time has positive effects on the neurons. In addition, it could be shown by the recorded time series that a cultivation over a longer period of time stabilizes the tissue. If the hippocampi remain connected to the entorhinal cortex, wallerian degeneration does not occur, resulting in longer survival of the cells in the postnatal cultures and thus strengthening the tissue.
The length of the thalamo-cortical white matter fibers brings insight into sex differences in sleep spindle frequency
Authors: Gaudreault Pierre-Olivier , Lina Jean-Marc , Descoteaux Maxime , Gosselin Nadia , Doyon Julien , Deslauriers-Gauthier Samuel , Carrier Julie 
Published: May 2022

AbstractSleep spindles (SS) are crucial to brain functions like memory and learning. SS characteristics result from the propagation of nerve impulses along white matter (WM) projections underlying an intricate loop between the thalamus and the cortex. SS amplitude and density have been associated with WM diffusion microarchitecture but physiological mechanisms underlying individual and sex-related variations in SS frequency are unknown. Here, we tested a model of traveling signals along the thalamo-cortico-thalamic projections to explain individual differences in spindle frequency. We predicted the presence of a relationship between the length of the thalamo-cortical WM bundles and a specific characteristic of this functional network, SS frequency.Thirty young participants underwent a polysomnographic recording and a 3T MRI including a diffusion sequence. The length of WM fiber bundles between the thalamus and the frontal cortex was derived from probabilistic tractography computed through constrained spherical deconvolution.Longer WM fiber bundles between the thalamus and specific regions of the frontal cortex (rostral middle frontal gyrus and anterior and middle part of the superior frontal gyrus) were associated with slower SS frequency. Moreover, the length of these WM fiber bundles statistically mediated the sex-related differences in SS frequency.By providing a neuroanatomical marker of individual and sex-related differences in SS frequency, this study is the first to highlight the association between the anatomy of a specific brain network and a specific functional characteristic of this network, the frequency of oscillations produced during sleep.
Eudicot primary cell wall glucomannan is related in synthesis, structure and function to xyloglucani
Authors: Yu Li , Yoshimi Yoshihisa , Cresswell Rosalie , Wightman Raymond , Lyczakowski Jan J. , Wilson Louis F.L. , Ishida Konan , Stott Katherine , Yu Xiaolan , Charalambous Stephan , Wurman-Rodrich Joel , Dupree Ray , Terrett Oliver M. , Brown Steven P. , Temple Henry , Krogh Kristian B.R.M. , Dupree Paul 
Published: May 2022

AbstractThe functional differences between plant cell wall hemicelluloses such as glucomannan, xylan and xyloglucan (XyG) remain unclear. These polysaccharides influence assembly and properties of the wall, perhaps by interacting with cellulose to affect the deposition and bundling of the fibrils. As the most abundant hemicellulose, XyG is considered important in eudicot primary cell walls (PCWs), but plants devoid of XyG show relatively mild phenotypes. We report here that a patterned β-galactoglucomannan (β-GGM) is widespread in PCW of eudicots and shows remarkable similarities to XyG. The sugar linkages forming the backbone and side chains of β-GGM are analogous to those that make up XyG, and moreover, these linkages are formed by glycosyltransferases from the same CAZy families. Solid-state NMR indicated that β-GGM shows low mobility in the cell wall, consistent with interaction with cellulose. Although Arabidopsis β-GGM synthesis mutants show no obvious growth defects, genetic crosses between β-GGM and XyG mutants produce exacerbated phenotypes compared to XyG mutants. These findings demonstrate a related role of these two similar but distinct classes of hemicelluloses in PCWs. This work will provide new avenues to study the roles of both β-GGM and XyG in PCWs.One sentence summaryPatterned β-GGM resembles xyloglucan in structure, biosynthesis and function.