bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circ_0038467 regulates lipopolysaccharide-mediated cell proliferation, apoptosis, and inflammatory response by miR-195-5p/TLR4 axis through NF-κB pathway in MRC-5 cells
Authors: Zheng Yu , Wang Yuanyuan , Zhu Xiuli , Diao Yuqiao , Chen Yuqin , Chen Gang 
Published: May 2021

ABSTRACT
Infantile pneumonia (IP) is an acute lower respiratory infection and brings a heavy burden to children health. Circular RNAs (circRNAs) participate in the regulation of pneumonia process. In this research, the effects of circ_0038467 in regulating lipopolysaccharide (LPS)-induced cell injury and underlying mechanism were revealed. Results showed that circ_0038467 expression and TLR4 protein level were upregulated, while miR-195-5p expression was downregulated in LPS-induced MRC-5 cells. Circ_0038467 silencing restored LPS-mediated inhibition on cell proliferation and promotion on apoptosis and inflammatory response. Additionally, circ_0038467 acted as a sponge of miR-195-5p, which was further revealed to target TLR4. MiR-195-5p inhibitor reversed circ_0038467 silencing-mediated influences under LPS treatment. Furthermore, LPS-activated NF-κB pathway was partly blocked by circ_0038467 silencing, which was restrained by TLR4 overexpression. Circ_0038467 silencing protected MRC-5 cells from LPS-induced injury by miR-195-5p/TLR4 axis through NF-κB pathway, providing a theoretical basis for circRNA-directed IP therapy.
Memory extinction and spontaneous recovery shaping parasitoid foraging behavior
Authors: de Bruijn Jessica A C , Vet Louise E M , Smid Hans M , de Boer Jetske G 
Published: May 2021

Abstract
Animals can alter their foraging behavior through associative learning, where an encounter with an essential resource (e.g., food or a reproductive opportunity) is associated with nearby environmental cues (e.g., volatiles). This can subsequently improve the animal’s foraging efficiency. However, when these associated cues are encountered again, the anticipated resource is not always present. Such an unrewarding experience, also called a memory-extinction experience, can change an animal’s response to the associated cues. Although some studies are available on the mechanisms of this process, they rarely focus on cues and rewards that are relevant in an animal’s natural habitat. In this study, we tested the effect of different types of ecologically relevant memory-extinction experiences on the conditioned plant volatile preferences of the parasitic wasp Cotesia glomerata that uses these cues to locate its caterpillar hosts. These extinction experiences consisted of contact with only host traces (frass and silk), contact with nonhost traces, or oviposition in a nonhost near host traces, on the conditioned plant species. Our results show that the lack of oviposition, after contacting host traces, led to the temporary alteration of the conditioned plant volatile preference in C. glomerata, but this effect was plant species-specific. These results provide novel insights into how ecologically relevant memory-extinction experiences can fine-tune an animal’s foraging behavior. This fine-tuning of learned behavior can be beneficial when the lack of finding a resource accurately predicts current, but not future foraging opportunities. Such continuous reevaluation of obtained information helps animals to prevent maladaptive foraging behavior.
Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data
Authors: Zuo Chunman , Dai Hao , Chen Luonan 
Published: May 2021

Abstract

Motivation
Joint profiling of single-cell transcriptomics and epigenomics data enables us to characterize cell states and transcriptomics regulatory programs related to cellular heterogeneity. However, the highly different features on sparsity, heterogeneity and dimensionality between multi-omics data have severely hindered its integrative analysis.

Results
We proposed deep cross-omics cycle attention (DCCA) model, a computational tool for joint analysis of single-cell multi-omics data, by combining variational autoencoders (VAEs) and attention-transfer. Specifically, we show that DCCA can leverage one omics data to fine-tune the network trained for another omics data, given a dataset of parallel multi-omics data within the same cell. Studies on both simulated and real datasets from various platforms, DCCA demonstrates its superior capability: (i) dissecting cellular heterogeneity; (ii) denoising and aggregating data and (iii) constructing the link between multi-omics data, which is used to infer new transcriptional regulatory relations. In our applications, DCCA was demonstrated to have a superior power to generate missing stages or omics in a biologically meaningful manner, which provides a new way to analyze and also understand complicated biological processes.

Availability and implementation
DCCA source code is available at https://github.com/cmzuo11/DCCA, and has been deposited in archived format at https://doi.org/10.5281/zenodo.4762065.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Organization of Frontostriatal Brain Wiring in Healthy Subjects Using a Novel Diffusion Imaging Fiber Cluster Analysis
Authors: Levitt J J , Zhang F , Vangel M , Nestor P G , Rathi Y , Kubicki M , Shenton M E , O’Donnell L J 
Published: May 2021

AbstractTo assess normal organization of frontostriatal brain wiring, we analyzed diffusion magnetic resonance imaging (dMRI) scans in 100 young adult healthy subjects (HSs). We identified fiber clusters intersecting the frontal cortex and caudate, a core component of associative striatum, and quantified their degree of deviation from a strictly topographic pattern. Using whole brain dMRI tractography and an automated tract parcellation clustering method, we extracted 17 white matter fiber clusters per hemisphere connecting the frontal cortex and caudate. In a novel approach to quantify the geometric relationship among clusters, we measured intercluster endpoint distances between corresponding cluster pairs in the frontal cortex and caudate. We show first, the overall frontal cortex wiring pattern of the caudate deviates from a strictly topographic organization due to significantly greater convergence in regionally specific clusters; second, these significantly convergent clusters originate in subregions of ventrolateral, dorsolateral, and orbitofrontal prefrontal cortex (PFC); and, third, a similar organization in both hemispheres. Using a novel tractography method, we find PFC-caudate brain wiring in HSs deviates from a strictly topographic organization due to a regionally specific pattern of cluster convergence. We conjecture cortical subregions projecting to the caudate with greater convergence subserve functions that benefit from greater circuit integration.
Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study
Authors: Zhang Limin , Yang Xingyi , Cota Zuleima , Cui Hong , Ford Bruce , Chen Hsin-liang , Macklin James A , Reznicek Anton , Starr Julian 
Published: May 2021

Abstract
Producing findable, accessible, interoperable and reusable (FAIR) data cannot be accomplished solely by data curators in all disciplines. In biology, we have shown that phenotypic data curation is not only costly, but it is burdened with inter-curator variation. We intend to propose a software platform that would enable all data producers, including authors of scientific publications, to produce ontologized data at the time of publication. Working toward this goal, we need to identify ontology construction methods that are preferred by end users. Here, we employ two usability studies to evaluate effectiveness, efficiency and user satisfaction with a set of four methods that allow an end user to add terms and their relations to an ontology. Thirty-three participants took part in a controlled experiment where they evaluated the four methods (Quick Form, Wizard, WebProtégé and Wikidata) after watching demonstration videos and completing a hands-on task. Another think-aloud study was conducted with three professional botanists. The efficiency effectiveness and user confidence in the methods are clearly revealed through statistical and content analyses of participants’ comments. Quick Form, Wizard and WebProtégé offer distinct strengths that would benefit our author-driven FAIR data generation system. Features preferred by the participants will guide the design of future iterations.
Pulmonary arterial hypertension unveils itself: a cancer-like progression — a case report
Authors: Santos-Ferreira Cátia , Cardoso Daniela , Paiva Benedita , Baptista Rui 
Published: May 2021

Abstract

Background
Pulmonary arterial hypertension (PAH) is a rare disorder with a poor prognosis, characterized by progressive remodelling of the small pulmonary arteries that precede the clinical and haemodynamic manifestations of the disease. Thus, a prompt diagnosis and early intervention are crucial.

Case summary
A 39-year-old pregnant women presented with persistent severe hypoxaemia after the diagnosis of influenza B and an elective caesarean delivery at 33 weeks. Ten months after, an extensive and inconclusive investigation that included a lung biopsy, despite of a spontaneous improvement in oxygen saturation, clinical deterioration led to further testing, namely genetic screening. It revealed a fast-progressing case of hereditary PAH caused by BMRP2 mutation.

Discussion
This case highlights the challenges of a timely diagnosis of PAH and the importance of close clinical monitoring of patients at high risk of PAH. In addition, it emphasizes the fast development of severe haemodynamic changes associated with a BMPR2 mutation. The availability of a lung biopsy without signs of pulmonary vascular disease (PVD) and a right heart catheterization with mild pulmonary hypertension at the baseline assessment demonstrates that PVD can progress in a neoplastic-like manner in a matter of months.
In vivo tissue-specific chromatin profiling in Drosophila melanogaster using GFP-tagged nuclei
Authors: Jauregui-Lozano Juan , Bakhle Kimaya , Weake Vikki M 
Published: May 2021

Abstract
The chromatin landscape defines cellular identity in multicellular organisms with unique patterns of DNA accessibility and histone marks decorating the genome of each cell type. Thus, profiling the chromatin state of different cell types in an intact organism under disease or physiological conditions can provide insight into how chromatin regulates cell homeostasis in vivo. To overcome the many challenges associated with characterizing chromatin state in specific cell types, we developed an improved approach to isolate Drosophila melanogaster nuclei tagged with a GFPKASH protein. The perinuclear space-localized KASH domain anchors GFP to the outer nuclear membrane, and expression of UAS-GFPKASH can be controlled by tissue-specific Gal4 drivers. Using this protocol, we profiled chromatin accessibility using an improved version of Assay for Transposable Accessible Chromatin followed by sequencing (ATAC-seq), called Omni-ATAC. In addition, we examined the distribution of histone marks using Chromatin immunoprecipitation followed by sequencing (ChIP-seq) and Cleavage Under Targets and Tagmentation (CUT&Tag) in adult photoreceptor neurons. We show that the chromatin landscape of photoreceptors reflects the transcriptional state of these cells, demonstrating the quality and reproducibility of our approach for profiling the transcriptome and epigenome of specific cell types in Drosophila.
State Responsibility for Protracted Displacement: An International Legal Approach to Durable Solutions
Authors: Mohee Mansha 
Published: May 2021

Abstract
Since the Second World War, displacement has become increasingly protracted and return is in decline. Despite calls for greater international responsibility sharing, many displaced people are subject to a legal limbo, lacking recognition and reparation in international law. This article seeks to establish the legal contours of protracted displacement as an internationally wrongful act that can engage the responsibility of States of origin and result in redress for those displaced. The article argues that there is evidence of a customary international law right of return, which requires States to facilitate voluntary repatriation and provide restitution. Facilitation includes refraining from preventing or obstructing return, suppressing acts of retribution or discrimination, and addressing root causes of displacement. Restitution includes property restitution, compensation for material and moral damages as well as reintegration and reconciliation measures, and offering effective models for return. The article concludes that the progressive development and codification of the law on forced displacement should address temporality, the qualities of return, and the alleviation of extant crises.
Numerical methods for stochastic Volterra integral equations with weakly singular kernels
Authors: Li Min , Huang Chengming , Hu Yaozhong 
Published: May 2021

AbstractIn this paper we first establish the existence, uniqueness and Hölder continuity of the solution to stochastic Volterra integral equations (SVIEs) with weakly singular kernels, with singularities $\alpha \in (0, 1)$ for the drift term and $\beta \in (0, 1/2)$ for the stochastic term. Subsequently, we propose a $\theta $-Euler–Maruyama scheme and a Milstein scheme to solve the equations numerically and obtain strong rates of convergence for both schemes in $L^{p}$ norm for any $p\geqslant 1$. For the $\theta $-Euler–Maruyama scheme the rate is $\min \big\{1-\alpha ,\frac{1}{2}-\beta \big\}~ $ and for the Milstein scheme is $\min \{1-\alpha ,1-2\beta \}$. These results on the rates of convergence are significantly different from those it is similar schemes for the SVIEs with regular kernels. The source of the difficulty is the lack of Itô formula for the equations. To get around this difficulty we use the Taylor formula subsequently carrying out a sophisticated analysis of the equation.
Advancement of antigen-specific immunotherapy: knowledge transfer between allergy and autoimmunity
Authors: Richardson Naomi , Wraith David Cameron 
Published: May 2021

Summary
Targeted restoration of immunological tolerance to self-antigens or innocuous environmental allergens represents the ultimate aim of treatment options in autoimmune and allergic disease. Antigen-specific immunotherapy (ASI) is the only intervention that has proven disease-modifying efficacy as evidenced by induction of long-term remission in a number of allergic conditions. Mounting evidence is now indicating that specific targeting of pathogenic T cells in autoinflammatory and autoimmune settings enables effective restoration of immune homeostasis between effector and regulatory cells and alters the immunological course of disease. Here, we discuss the key lessons learned during the development of antigen-specific immunotherapies and how these can be applied to inform future interventions. Armed with this knowledge and current high-throughput technology to track immune cell phenotype and function, it may no longer be a matter of ‘if’ but ‘when’ this ultimate aim of targeted tolerance restoration is realised.
Communities and Brokers: How the Transnational Advocacy Network Simultaneously Provides Social Power and Exacerbates Global Inequalities
Authors: Cheng Huimin , Wang Ye , Ma Ping , Murdie Amanda 
Published: May 2021

Abstract
Transnational advocacy networks (TANs) are the most common example of networks in international relations. Despite their familiarity, we know little about how advocacy networks of nongovernmental organizations (NGOs) are structured. Drawing on the cross-disciplinary concepts of emergent communities and distinct brokerage roles, we argue that the network may reinforce power disparities and inequalities at the very same time that it provides social power. TANs are similar to emergent communities of practice, with some organizations acting as various types of brokers within and between communities. Preexisting resources are more likely to lead global North organizations to occupy brokerage roles that provide additional agenda-setting and resource-allocating power. We build a dataset of the 3,903 NGOs connected through 1.3 million ties occurring through meetings and conferences for NGOs put on or coordinated by the United Nations. Using community detection methods, we identify four distinct communities in the overall NGO network, with differences in distributions of brokerage roles across communities. Examining the communities, brokerage role distributions, and preexisting power disparities can help us better understand the divergent findings in previous literature and conceptualize TANs.
LYSINE KETOGLUTARATE REDUCTASE TRANS-SPLICING RELATED 1 is involved in temperature-dependent root growth in rice
Authors: Yu En , Yamaji Naoki , Mochida Keiich , Galis Ivan , Asaka Kanatani , Ma Jian Feng 
Published: May 2021

Abstract
Root length is an important root parameter directly related to the uptake of water and nutrients. However, the molecular mechanisms controlling root length are still not fully understood. Here, we isolated a short-root mutant of rice, dice2 (defective in cell elongation 2). The cell length and meristem size of the roots were decreased in dice2, but the root function in terms of mineral element uptake, root cell width, and root anatomy were hardly altered compared with wild-type (WT) rice. The root growth defect in dice2 could be partially rescued by high temperature. Map-based cloning combined with a complementation test revealed that the short-root phenotype was caused by a nonsense mutation in a gene which was annotated to encode Lysine Ketoglutarate Reductase Trans-Splicing related 1 (OsLKRT1). OsLKRT1, encoding a cytosol-localized protein, was expressed in all cells of the root tip and elongation region as well as the shoot. RNA-seq analysis showed that there was no difference between dice2 and the WT in the expression level of genes involved in root development identified so far. These results indicate that OsLKRT1 is involved in a novel pathway required for root cell elongation in rice, although its exact role remains to be further investigated.
Sugar export from Arabidopsis leaves: actors and regulatory strategies
Authors: Xu Qiyu , Liesche Johannes 
Published: May 2021

Abstract
Plant acclimation and stress responses depend on the dynamic optimization of carbon balance between source and sink organs. This optimization also applies to the leaf export rate of photosynthetically produced sugars. So far, investigations into the molecular mechanisms of how the rate is controlled have focused on sugar transporters responsible for loading sucrose into the phloem sieve element–companion cell complex of leaf veins. Here, we take a broader view of the various proteins with potential direct influence on the leaf sugar export rate in the model plant Arabidopsis thaliana, helped by the cell type-specific transcriptome data that have recently become available. Furthermore, we integrate current information on the regulation of these potential target proteins. Our analysis identifies putative control points and units of transcriptionally and post-transcriptionally co-regulated genes. Most notable is the potential regulatory unit of sucrose transporters (SUC2, SWEET11, SWEET12, and SUC4) and proton pumps (AHA3 and AVP1). Our analysis can guide future research aimed at understanding the regulatory network controlling leaf sugar export by providing starting points for characterizing regulatory strategies and identifying regulatory factors that link sugar export rate to the major signaling pathways.
Stellar intensity interferometry of Vega in photon counting mode
Authors: Zampieri Luca , Naletto Giampiero , Burtovoi Aleksandr , Fiori Michele , Barbieri Cesare 
Published: May 2021

ABSTRACT
Stellar intensity interferometry is a technique based on the measurement of the second-order spatial correlation of the light emitted from a star. The physical information provided by these measurements is the angular size and structure of the emitting source. A worldwide effort is presently underway to implement stellar intensity interferometry on telescopes separated by long baselines and on future arrays of Cherenkov telescopes. We describe an experiment of this type, realized at the Asiago Observatory (Italy), in which we performed for the first time measurements of the correlation counting photon coincidences in post-processing by means of a single photon software correlator and exploiting entirely the quantum properties of the light emitted from a star. We successfully detected the temporal correlation of Vega at zero baseline and performed a measurement of the correlation on a projected baseline of ∼2 km. The average discrete degree of coherence at zero baseline for Vega is $\lt g^{(2)} \gt \, = 1.0034 \pm 0.0008$, providing a detection with a signal-to-noise ratio S/N ≳ 4. No correlation is detected over the km baseline. The measurements are consistent with the expected degree of spatial coherence for a source with the 3.3 mas angular diameter of Vega. The experience gained with the Asiago experiment will serve for future implementations of stellar intensity interferometry on long-baseline arrays of Cherenkov telescopes.
The growth rate of cosmic structures in the local Universe with the ALFALFA survey
Authors: Avila F , Bernui A , de Carvalho E , Novaes C P 
Published: May 2021

ABSTRACT
We investigate the growth rate of structures in the local Universe. For this, we use as a cosmological tracer the HI line extra-galactic sources from the Arecibo Legacy Fast ALFA (ALFALFA) survey to obtain a measurement of the normalized growth rate parameter, fσ8, considered a powerful tool to constrain alternative models of gravity. For these analyses, we calculate the Local Group velocity due to the matter structures distribution in the ALFALFA catalogue and compare it with the Local Group velocity relative to the Cosmic Microwave Background frame to obtain the velocity scale parameter, β. Using Monte Carlo realizations and lognormal simulations, our methodology quantifies the errors introduced by shot-noise and partial sky coverage of the analysed data. The measurement of the velocity scale parameter β and the calculation of the matter fluctuation of the cosmological tracer, $\sigma _{8}^{\text{tr}}$, lead us to fσ8 = 0.46 ± 0.06 at $\bar{z} = 0.013$, in good agreement (at 1σ level) with the value expected in the ΛCDM concordance model. In addition, our analyses of the ALFALFA sample also provide a measurement of the growth rate of structures $f = 0.56 \pm 0.07$, at $\bar{z} = 0.013$.
BRIO: a web server for RNA sequence and structure motif scan
Authors: Guarracino Andrea , Pepe Gerardo , Ballesio Francesco , Adinolfi Marta , Pietrosanto Marco , Sangiovanni Elisa , Vitale Ilio , Ausiello Gabriele , Helmer-Citterich Manuela 
Published: May 2021

Abstract
The interaction between RNA and RNA-binding proteins (RBPs) has a key role in the regulation of gene expression, in RNA stability, and in many other biological processes. RBPs accomplish these functions by binding target RNA molecules through specific sequence and structure motifs. The identification of these binding motifs is therefore fundamental to improve our knowledge of the cellular processes and how they are regulated. Here, we present BRIO (BEAM RNA Interaction mOtifs), a new web server designed for the identification of sequence and structure RNA-binding motifs in one or more RNA molecules of interest. BRIO enables the user to scan over 2508 sequence motifs and 2296 secondary structure motifs identified in Homo sapiens and Mus musculus, in three different types of experiments (PAR-CLIP, eCLIP, HITS). The motifs are associated with the binding of 186 RBPs and 69 protein domains. The web server is freely available at http://brio.bio.uniroma2.it.