bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transient viral exposure drives functionally-coordinated humoral immune responses in HIV-1 post-treatment controllers
Authors: Molinos-Albert Luis M. , Lorin Valérie , Monceaux Valérie , Orr Sylvie , Essat Asma , Dufloo Jérémy , Schwartz Olivier , Rouzioux Christine , Meyer Laurence , Hocqueloux Laurent , Sáez-Cirión Asier , Mouquet Hugo ,   ANRS VISCONTI Study Group, Prazuck Thierry , Dieuleveult Barbara De , Bani-Sadr Firouzé , Hentzien Maxime , Berger Jean-Luc , Kmiec Isabelle , Pichancourt Gilles , Nasri Safa , Hittinger Gilles , Lambry Véronique , Beauey Anne-Cécile , Pialoux Gilles , Palacios Christia , Siguier Martin , Adda Anne , Foucoin Jane , Weiss Laurence , Karmochkine Marina , Meghadecha Mohamed , Ptak Magali , Salmon-Ceron Dominique , Blanche Philippe , Piétri Marie-Pierre , Molina Jean-Michel , Taulera Olivier , Lascoux-Combe Caroline , Ponscarme Diane , Bertaut Jeannine Delgado , Makhloufi Djamila , Godinot Matthieu , Artizzu Valérie , Yazdanpanah Yazdan , Matheron Sophie , Godard Cindy , Julia Zélie , Bernard Louis , Bastides Frédéric , Bourgault Olivier , Jacomet Christine , Goncalves Emilie , Meybeck Agnès , Huleux Thomas , Cornavin Pauline , Debab Yasmine , Théron David , Miailhes Patrick , Cotte Laurent , Pailhes Sophie , Ogoudjobi Stanislas , Viard Jean Paul , Dulucq Marie-Josée , Bodard Loïc , Churaqui Francoise , Guimard Thomas , Laine Laetitia 
Published: April 2022

AbstractHIV-1 post-treatment controllers are rare individuals controlling HIV-1 infection for years after antiretroviral therapy interruption. Identification of immune correlates of control in post-treatment controllers could aid in designing effective HIV-1 vaccine and remission strategies. Here, we perform comprehensive immunoprofiling of the humoral response to HIV-1 in long-term post-treatment controllers. Global multivariate analyses combining clinico-virological and humoral immune data reveal distinct profiles in post-treatment controllers experiencing transient viremic episodes off therapy compared to those stably aviremic. Virally-exposed post-treatment controllers display stronger HIV-1 humoral responses, and develop more frequently Env-specific memory B cells and cross-neutralizing antibodies. Both are linked to short viremic exposures, which are also accompanied by an increase in blood atypical memory B cells and activated subsets of circulating follicular helper T cells. Still, most humoral immune variables only correlate with Th2-like circulating follicular helper T cells. Thus, post-treatment controllers form a heterogeneous group with two distinct viral behaviours and associated immune signatures. Post-treatment controllers stably aviremic present “silent” humoral profiles, while those virally-exposed develop functionally robust HIV-specific B-cell and antibody responses, which may participate in controlling infection.
Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers
Authors: Bordeira-Carriço Renata , Teixeira Joana , Duque Marta , Galhardo Mafalda , Ribeiro Diogo , Acemel Rafael D. , Firbas Panos. N. , Tena Juan J. , Eufrásio Ana , Marques Joana , Ferreira Fábio J. , Freitas Telmo , Carneiro Fátima , Goméz-Skarmeta José Luís , Bessa José 
Published: April 2022

AbstractThe pancreas is a central organ for human diseases. Most alleles uncovered by genome-wide association studies of pancreatic dysfunction traits overlap with non-coding sequences of DNA. Many contain epigenetic marks of cis-regulatory elements active in pancreatic cells, suggesting that alterations in these sequences contribute to pancreatic diseases. Animal models greatly help to understand the role of non-coding alterations in disease. However, interspecies identification of equivalent cis-regulatory elements faces fundamental challenges, including lack of sequence conservation. Here we combine epigenetic assays with reporter assays in zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis-regulatory elements, regardless of sequence conservation. Among other potential disease-relevant enhancers, we identify a zebrafish ptf1a distal-enhancer whose deletion causes pancreatic agenesis, a phenotype previously found to be induced by mutations in a distal-enhancer of PTF1A in humans, further supporting the causality of this condition in vivo. This approach helps to uncover interspecies functionally equivalent cis-regulatory elements and their potential role in human disease.
Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24
Authors: Yang Lingguang , Zhang Laixing , Yin Peipei , Ding Hao , Xiao Yu , Zeng Jianwei , Wang Wenhe , Zhou Huan , Wang Qisheng , Zhang Yi , Chen Zeliang , Yang Maojun , Feng Yue 
Published: April 2022

AbstractCRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the crRNA-guided surveillance (Csy) complex. The HTH motif of AcrIF24 can bind the Acr promoter region and repress its transcription, suggesting its role as an Aca gene in self-regulation. AcrIF24 forms a homodimer and further induces dimerization of the Csy complex. Apart from blocking the hybridization of target DNA to the crRNA, AcrIF24 also induces the binding of non-sequence-specific dsDNA to the Csy complex, similar to AcrIF9, although this binding seems to play a minor role in AcrIF24 inhibitory capacity. Further structural and biochemical studies of the Csy-AcrIF24-dsDNA complexes and of AcrIF24 mutants reveal that the HTH motif of AcrIF24 and the PAM recognition loop of the Csy complex are structural elements essential for this non-specific dsDNA binding. Moreover, AcrIF24 and AcrIF9 display distinct characteristics in inducing non-specific DNA binding. Together, our findings highlight a multifunctional Acr and suggest potential wide distribution of Acr-induced non-specific DNA binding.
Narrowband microwave-photonic notch filters using Brillouin-based signal transduction in silicon
Authors: Gertler Shai , Otterstrom Nils T. , Gehl Michael , Starbuck Andrew L. , Dallo Christina M. , Pomerene Andrew T. , Trotter Douglas C. , Lentine Anthony L. , Rakich Peter T. 
Published: April 2022

AbstractThe growing demand for bandwidth makes photonic systems a leading candidate for future telecommunication and radar technologies. Integrated photonic systems offer ultra-wideband performance within a small footprint, which can naturally interface with fiber-optic networks for signal transmission. However, it remains challenging to realize narrowband (∼MHz) filters needed for high-performance communications systems using integrated photonics. In this paper, we demonstrate all-silicon microwave-photonic notch filters with 50× higher spectral resolution than previously realized in silicon photonics. This enhanced performance is achieved by utilizing optomechanical interactions to access long-lived phonons, greatly extending available coherence times in silicon. We use a multi-port Brillouin-based optomechanical system to demonstrate ultra-narrowband (2.7 MHz) notch filters with high rejection (57 dB) and frequency tunability over a wide spectral band (6 GHz) within a microwave-photonic link. We accomplish this with an all-silicon waveguide system, using CMOS-compatible fabrication techniques.
Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium
Authors: Bakkeren Erik , Gül Ersin , Huisman Jana S. , Steiger Yves , Rocker Andrea , Hardt Wolf-Dietrich , Diard Médéric 
Published: April 2022

AbstractIntestinal inflammation fuels the transmission of Salmonella Typhimurium (S.Tm). However, a substantial fitness cost is associated with virulence expression. Mutations inactivating transcriptional virulence regulators generate attenuated variants profiting from inflammation without enduring virulence cost. Such variants interfere with the transmission of fully virulent clones. Horizontal transfer of functional regulatory genes (HGT) into attenuated variants could nevertheless favor virulence evolution. To address this hypothesis, we cloned hilD, coding for the master regulator of virulence, into a conjugative plasmid that is highly transferrable during intestinal colonization. The resulting mobile hilD allele allows virulence to emerge from avirulent populations, and to be restored in attenuated mutants competing against virulent clones within-host. However, mutations inactivating the mobile hilD allele quickly arise. The stability of virulence mediated by HGT is strongly limited by its cost, which depends on the hilD expression level, and by the timing of transmission. We conclude that robust evolution of costly virulence expression requires additional selective forces such as narrow population bottlenecks during transmission.
Sucrose addition directionally enhances bacterial community convergence and network stability of the shrimp culture system
Authors: Guo Haipeng , Dong Pengsheng , Gao Fan , Huang Lei , Wang Sipeng , Wang Ruoyu , Yan Mengchen , Zhang Demin 
Published: April 2022

AbstractSucrose is an effective carbon source for creating more reliable and environmentally friendly conditions for shrimp growth by regulating bacteria in biofloc-based culture systems. However, the influence of sucrose addition on the interaction, co-occurrence networks, and assembly mechanisms of bacterial communities in biofloc-based culture systems remains largely unknown. Here, we comprehensively investigated the effects of sucrose addition on bacterial communities in three habitats (water, bioflocs, and gut). The bacterial community structures and compositions of these three habitats became more similar in groups with sucrose addition, compared with those in controls. More than 50% gut bacterial communities were mainly derived from water and biofloc communities in the sucrose addition groups, but only about 33% bacterial communities migrated from water and biofloc to the gut in the control culture system. Sucrose addition accordantly enriched core taxa belonging to the phylum Actinobacteria and the families Rhodobacteraceae and Flavobacteriaceae in water, biofloc, and gut habitats. These core taxa were important for maintaining bacterial network stability in the sucrose addition culture systems and some were identified as keystone taxa for improving shrimp growth. Furthermore, after sucrose addition, gut bacterial community assembly from water and biofloc was dominated by the heterogeneous select with the ratios of 55–91% and 67–83%, respectively, indicating that sucrose addition can directionally shape the bacterial assembly of the shrimp culture system. These results provide a basis for selectively regulating certain beneficial taxa to improve shrimp growth in culture systems.
Niche differentiation drives microbial community assembly and succession in full-scale activated sludge bioreactors
Authors: de Celis Miguel , Duque Javier , Marquina Domingo , Salvadó Humbert , Serrano Susana , Arregui Lucía , Santos Antonio , Belda Ignacio 
Published: April 2022

AbstractNetwork models and community phylogenetic analyses are applied to assess the composition, structure, and ecological assembly mechanisms of microbial communities. Here we combine both approaches to investigate the temporal dynamics of network properties in individual samples of two activated sludge systems at different adaptation stages. At initial assembly stages, we observed microbial communities adapting to activated sludge, with an increase in network modularity and co-exclusion proportion, and a decrease in network clustering, here interpreted as a consequence of niche specialization. The selective pressure of deterministic factors at wastewater treatment plants produces this trend and maintains the structure of highly functional and specialized communities responding to seasonal environmental changes.
MaterialsAtlas.org: a materials informatics web app platform for materials discovery and survey of state-of-the-art
Authors: Hu Jianjun , Stefanov Stanislav , Song Yuqi , Omee Sadman Sadeed , Louis Steph-Yves , Siriwardane Edirisuriya M. D. , Zhao Yong , Wei Lai 
Published: April 2022

AbstractThe availability and easy access of large-scale experimental and computational materials data have enabled the emergence of accelerated development of algorithms and models for materials property prediction, structure prediction, and generative design of materials. However, the lack of user-friendly materials informatics web servers has severely constrained the wide adoption of such tools in the daily practice of materials screening, tinkering, and design space exploration by materials scientists. Herein we first survey current materials informatics web apps and then propose and develop MaterialsAtlas.org, a web-based materials informatics toolbox for materials discovery, which includes a variety of routinely needed tools for exploratory materials discovery, including material’s composition and structure validity check (e.g. charge neutrality, electronegativity balance, dynamic stability, Pauling rules), materials property prediction (e.g. band gap, elastic moduli, hardness, and thermal conductivity), search for hypothetical materials, and utility tools. These user-friendly tools can be freely accessed at http://www.materialsatlas.org. We argue that such materials informatics apps should be widely developed by the community to speed up materials discovery processes.
Optimization of cognitive assessment in Parkinsonisms by applying artificial intelligence to a comprehensive screening test
Authors: Ortelli Paola , Ferrazzoli Davide , Versace Viviana , Cian Veronica , Zarucchi Marianna , Gusmeroli Anna , Canesi Margherita , Frazzitta Giuseppe , Volpe Daniele , Ricciardi Lucia , Nardone Raffaele , Ruffini Ingrid , Saltuari Leopold , Sebastianelli Luca , Baranzini Daniele , Maestri Roberto 
Published: April 2022

AbstractThe assessment of cognitive deficits is pivotal for diagnosis and management in patients with parkinsonisms. Low levels of correspondence are observed between evaluations assessed with screening cognitive tests in comparison with those assessed with in-depth neuropsychological batteries. A new tool, we named CoMDA (Cognition in Movement Disorders Assessment), was composed by merging Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment (MoCA), and Frontal Assessment Battery (FAB). In total, 500 patients (400 with Parkinson’s disease, 41 with vascular parkinsonism, 31 with progressive supranuclear palsy, and 28 with multiple system atrophy) underwent CoMDA (level 1–L1) and in-depth neuropsychological battery (level 2–L2). Machine learning was developed to classify the CoMDA score and obtain an accurate prediction of the cognitive profile along three different classes: normal cognition (NC), mild cognitive impairment (MCI), and impaired cognition (IC). The classification accuracy of CoMDA, assessed by ROC analysis, was compared with MMSE, MoCA, and FAB. The area under the curve (AUC) of CoMDA was significantly higher than that of MMSE, MoCA and FAB (p < 0.0001,p = 0.028 andp = 0.0007, respectively). Among 15 different algorithmic methods, the Quadratic Discriminant Analysis algorithm (CoMDA-ML) showed higher overall-metrics performance levels in predictive performance. Considering L2 as a 3-level continuous feature, CoMDA-ML produces accurate and generalizable classifications: micro-average ROC curve, AUC = 0.81; and AUC = 0.85 for NC, 0.67 for MCI, and 0.83 for IC. CoMDA and COMDA-ML are reliable and time-sparing tools, accurate in classifying cognitive profile in parkinsonisms.This study has been registered on ClinicalTrials.gov (NCT04858893).
Sound disrupts sleep-associated brain oscillations in rodents in a meaning-dependent manner
Authors: van Kronenberg Philipp , Milinski Linus , Kruschke Zoë , de Hoz Livia 
Published: April 2022

AbstractSleep is essential but places animals at risk. Filtering acoustic information according to its relevance, a process generally known as sensory gating, is crucial during sleep to ensure a balance between rest and danger detection. The mechanisms of this sensory gating and its specificity are not understood. Here, we tested the effect that sounds of different meaning have on sleep-associated ongoing oscillations. We recorded EEG and EMG from mice during REM and NREM sleep while presenting sounds with or without behavioural relevance. We found that sound presentation per se, in the form of a neutral sound, elicited a weak or no change in the power of sleep-state-dependent EEG during REM and NREM sleep. In contrast, the presentation of a sound previously conditioned in an aversive task, elicited a clear and fast decrease in the EEG power during both sleep phases, suggesting a transition to lighter sleep without awakening. The observed changes generally weakened over training days and were not present in animals that failed to learn. Interestingly, the effect could be generalized to unfamiliar neutral sounds if presented following conditioned training, an effect that depended on sleep phase and sound type. The data demonstrate that sounds are differentially gated during sleep depending on their meaning and that this process is reflected in disruption of sleep-associated brain oscillations without behavioural arousal.
Hydrocoel morphogenesis forming the pentaradial body plan in a sea cucumber, Apostichopus japonicus
Authors: Udagawa Sumio , Ikeda Takafumi , Oguchi Kohei , Kohtsuka Hisanori , Miura Toru 
Published: April 2022

AbstractEchinoderms constitute an animal phylum characterized by the pentaradial body plan. During the development from bilateral larvae to pentaradial adults, the formation of the multiple of five hydrocoel lobes, i.e., the buddings from the mesodermal coelom, is the firstly emerging pentameral character. The developmental mechanism underlying the hydrocoel-lobe formation should be revealed to understand the evolutionary process of this unique and highly derived body plan of echinoderms, although the morphogenetic mechanisms of hydrocoel lobes are largely uninvestigated. In this study, using the sea cucumberApostichopus japonicus,in which hydrocoel is easily observable, the developmental process of hydrocoel lobes was described in detail, focusing on cell proliferation and rearrangement. Cell proliferation was not specifically distributed in the growing tips of the hydrocoel lobes, and inhibition of cell proliferation did not affect lobe formation. During lobe formation, the epithelium of the hydrocoel lobes was firstly thickened and then transformed into a simple epithelium, suggesting that tissue expansion via tissue remodeling contributes to the hydrocoel-lobe formation.
PACE4-altCT isoform of proprotein convertase PACE4 as tissue and plasmatic biomarker for prostate cancer
Authors: Couture Frédéric , Wang Luojun , Dufour Frédérik , Chabot-Maheux Keena , Ekindi Ndongo Nadia , Sabbagh Robert , Day Robert 
Published: April 2022

AbstractThe proprotein convertase PACE4 has demonstrated value as a viable therapeutic target in prostate cancer (PCa). A novel isoform named PACE4-altCT, which arises in neoplastic lesions, plays an important role in tumor progression and has been validated as a pharmacological target. With the discovery of its overexpression in PCa and the alternative splicing of its pre-RNA to generate an oncogenic C-terminally modified isoform named PACE4-altCT, understanding and validating its value as a potential biomarker is of great interest either from prognostic or targeted therapy intervention. Expression of ERG in LNCaP cells was used to investigate the relationship between ERG expression occurring in PCa cells and PACE4-altCT expression by Western blot and qPCR. Using immunohistochemistry, the expression levels of PACE4 isoforms in patient tissues were investigated and correlated with ERG tumor status and Gleason score. An ELISA method was developed using affinity purified recombinant protein and used for quantitative analysis of plasma concentrations of PACE4-altCT and used for correlation. In contrast with the consensual isoform, PACE4-altCT was only strongly overexpressed in prostate cancer patients, correlated with ERG expression levels. Despite its intracellular retention PACE4-altCT could be detected in the plasma of most patients with prostate cancer, whereas it was only found at low levels in normal patients whereas total plasmatic PACE4 levels did not vary significantly between groups. Our study demonstrates that PACE4-altCT is strongly overexpressed in prostate cancer using both immunohistochemical and ELISA techniques and may have some interesting potential as a biomarker.
rs-fMRI and machine learning for ASD diagnosis: a systematic review and meta-analysis
Authors: Santana Caio Pinheiro , de Carvalho Emerson Assis , Rodrigues Igor Duarte , Bastos Guilherme Sousa , de Souza Adler Diniz , de Brito Lucelmo Lacerda 
Published: April 2022

AbstractAutism Spectrum Disorder (ASD) diagnosis is still based on behavioral criteria through a lengthy and time-consuming process. Much effort is being made to identify brain imaging biomarkers and develop tools that could facilitate its diagnosis. In particular, using Machine Learning classifiers based on resting-state fMRI (rs-fMRI) data is promising, but there is an ongoing need for further research on their accuracy and reliability. Therefore, we conducted a systematic review and meta-analysis to summarize the available evidence in the literature so far. A bivariate random-effects meta-analytic model was implemented to investigate the sensitivity and specificity across the 55 studies that offered sufficient information for quantitative analysis. Our results indicated overall summary sensitivity and specificity estimates of 73.8% and 74.8%, respectively. SVM stood out as the most used classifier, presenting summary estimates above 76%. Studies with bigger samples tended to obtain worse accuracies, except in the subgroup analysis for ANN classifiers. The use of other brain imaging or phenotypic data to complement rs-fMRI information seems promising, achieving higher sensitivities when compared to rs-fMRI data alone (84.7% versus 72.8%). Finally, our analysis showed AUC values between acceptable and excellent. Still, given the many limitations indicated in our study, further well-designed studies are warranted to extend the potential use of those classification algorithms to clinical settings.
Optimized assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation from adult Drosophila melanogaster neurons
Authors: Merrill Collin B. , Pabon Miguel A. , Montgomery Austin B. , Rodan Aylin R. , Rothenfluh Adrian 
Published: April 2022

AbstractAssay for transposase-accessible chromatin by sequencing (ATAC-seq) is rapidly becoming the assay of choice to investigate chromatin-mediated gene regulation, largely because of low input requirements, a fast workflow, and the ability to interrogate the entire genome in an untargeted manner. Many studies using ATAC-seq use mammalian or human-derived tissues, and established protocols work well in these systems. However, ATAC-seq is not yet widely used in Drosophila. Vinegar flies present several advantages over mammalian systems that make them an excellent model for ATAC-seq studies, including abundant genetic tools that allow straightforward targeting, transgene expression, and genetic manipulation that are not available in mammalian models. Because current ATAC-seq protocols are not optimized to use flies, we developed an optimized workflow that accounts for several complicating factors present in Drosophila. We examined parameters affecting nuclei isolation, including input size, freezing time, washing, and possible confounds from retinal pigments. Then, we optimized the enzymatic steps of library construction to account for the smaller Drosophila genome size. Finally, we used our optimized protocol to generate ATAC-seq libraries that meet ENCODE quality metrics. Our optimized protocol enables extensive ATAC-seq experiments in Drosophila, thereby leveraging the advantages of this powerful model system to understand chromatin-mediated gene regulation.