bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dealing with the promise of metabarcoding in mega-event biomonitoring: EXPO2015 unedited data
Authors: Agostinetto Giulia , Bruno Antonia , Sandionigi Anna , Brusati Alberto , Manzari Caterina , Chiodi Alice , Siani Eleonora , Borruso Luigimaria , Galimberti Andrea , Pesole Graziano , Labra Massimo , Casiraghi Maurizio 
Published: January 2022

AbstractAs human activities on our planet persist, causing widespread and irreversible environmental degradation, the need to biomonitor ecosystems has never been more pressing. These circumstances have required a renewal in monitoring techniques, encouraged by necessity to develop more rapid and accurate tools which will support timely observations of ecosystem structure and function. The World Exposition (from now ‘EXPO2015’) hosted in Milan from May to October 2015 was a global event that could be categorized as a mega-event, which can be defined as an acute environmental stressor, possibly generating biodiversity alteration and disturbance.During the six months of EXPO2015, exhibitors from more than 135 countries and 22 million visitors insisted on a 1.1 million square meters area. Faced with such a massive event, we explore the potential of DNA metabarcoding using three molecular markers to improve the understanding of anthropogenic impacts in the area, both considering air and water monitoring. Furthermore, we explore the effectiveness of the taxonomy assignment phase considering different taxonomic levels of analysis and the use of data mining approaches to predict sample origin. Unless the degree of taxa identification still remains open, our results showed that DNA metabarcoding is a powerful genomic-based tool to monitor biodiversity at the microscale, allowing us to capture exact fingerprints of specific event sites and to explore in a comprehensive manner the eukaryotic community alteration. With this work, we aim to disentangle and overcome the crucial issues related to the generalization of DNA metabarcoding in order to support future applications.
Cell-based screen identifies human type I interferon-stimulated regulators ofToxoplasma gondiiInfection
Authors: Gossner Anton , Raper Anna , Hassan Musa A. 
Published: January 2022

AbstractMacrophages activated with interferons (IFNs) respond with transcriptional changes that enhance clearance of intracellular pathogens such asToxoplasma, a ubiquitous apicomplexan parasite that infects more than a billion people worldwide. Although IFNs generally inhibitToxoplasma, the parasite can also induce components of the host IFN signalling pathway to enhance survival in host cells. Compared to the type II IFN gamma (IFNγ), the role of type I IFNs in macrophage response toToxoplasmais relatively not well characterized. Here, using fluorescentToxoplasmaand a CRISPR/Cas9 knockout library that only targets interferon-stimulated genes (ISGs), we adapted a loss-of-function flow cytometry-based approach to systematically identify type I ISGs that controlToxoplasmagrowth in THP-1 cells, a human macrophage cell line. The system enabled the rapid screening of more than 1900 ISGs for type I (IFNα)-induced inhibitors and enhancers ofToxoplasmagrowth in THP-1 cells. We identified 26 genes that are associated withToxoplasmagrowth arrest out of which we confirmedMAX, SNX5, F2RL2, andSSB, as potent IFNα-induced inhibitors ofToxoplasmain THP1 cells. These findings provide a genetic and experimental roadmap to elucidate type I IFN-induced cell-autonomous responses toToxoplasma.
COVID-19 disease progression according to initial symptoms. A telemedicine cohort study
Authors: Murillo-Villanueva Karla , Velázquez-Hernández Blanca , Jácome-Mondragón José A. , Cervantes-Llamas Judit J. , Talavera Juan O. 
Published: January 2022

AbstractObjectiveCOVID-19 progression to severe or critical illness may be related to initial clinical presentation. Main objective was to identify initial symptoms related to highest risk of disease progression, in mild or moderate suspected or confirmed COVID-19 patients or in asymptomatic subjects in contact with a recently diagnosed patient.Design and methodsHistoric cohort study of Mexican patients with suspected or confirmed mild or moderate COVID-19 or asymptomatic subjects in recent contact with positive patients. They sought medical attention in “Centro Médico ABC” or claimed for remote attention, and daily telemedicine follow up until recovery or illness progression, from April 17th to October 08th 2020. Data excerpted for analysis were sex, age, body mass index, comorbidities, and signs, and symptoms presented in first day of disease manifestations and during follow up. We used logistic regression to identify initial symptoms associated with progression disease and through a conjunctive consolidation analysis a symptom index was created.Results120 of 1635 patients (7.2%) had clinical progression disease. By logistic regression we found as initial symptoms related to progression: fever OR 3 (1.89-4.77, p<0.001), cough OR 2.34 (1.56-3.52, p<0.001), myalgias or arthralgias OR 1.69 (1.09-2.63, p=0.018), and fatigue OR 1.65 (1.08-2.53, p=0.019). Conjunctive consolidation was processed with the previous symptoms, and a 3 groups score resulted C-19PAIS Index: 1) Fever with cough or fever with fatigue, with a probability of progression disease of 29% (31/106 patients), 2) Fever or cough or fatigue or cough with fatigue, 10.7% (66/615 patients) and 3) No fever, no cough, no fatigue, 2% (23/914).ConclusionsInitial symptoms predict clinical progression in COVID-19 patients.
Comparative plant transcriptome profiling of Arabidopsis and Camelina infested withMyzus persicaeaphids acquiring circulative and non-circulative viruses reveals virus- and plant-specific alterations relevant to aphid feeding behavior and transmission
Authors: Chesnais Quentin , Golyaev Victor , Velt Amandine , Rustenholz Camille , Brault Véronique , Pooggin Mikhail , Drucker Martin 
Published: January 2022

AbstractBackgroundEvidence accumulates that plant viruses alter host-plant traits in ways that modify their insect vectors’ behavior. These alterations often enhance virus transmission, which has led to the hypothesis that these effects are manipulations caused by viral adaptation. However, the genetic basis of these indirect, plant-mediated effects on vectors and their dependence on the plant host and the mode of virus transmission is hardly known.ResultsTranscriptome profiling ofArabidopsis thalianaandCamelina sativaplants infected with turnip yellows virus (TuYV) or cauliflower mosaic virus (CaMV) and infested with the common aphid vectorMyzus persicaerevealed strong virus- and host-specific differences in the gene expression patterns. CaMV infection caused more severe effects on the phenotype of both plant hosts than did TuYV infection, and the severity of symptoms correlated strongly with the proportion of differentially expressed genes, especially photosynthesis genes. Accordingly, CaMV infection modified aphid behavior and fecundity stronger than did infection with TuYV.ConclusionsOverall, infection with CaMV – relying on the non-circulative transmission mode – tends to have effects on metabolic pathways with strong potential implications for insect-vector / plant-host interactions (e.g. photosynthesis, jasmonic acid, ethylene and glucosinolate biosynthetic processes), while TuYV – using the circulative transmission mode – alters these pathways only weakly. These virus-induced deregulations of genes that are related to plant physiology and defense responses might impact aphid probing and feeding behavior on both infected host plants, with potentially distinct effects on virus transmission.
hPSC-Derived Enteric Ganglioids Model Human ENS Development and Function
Authors: Majd Homa , Samuel Ryan M , Ramirez Jonathan T , Kalantari Ali , Barber Kevin , Ghazizadeh Zaniar , Chemel Angeline K , Cesiulis Andrius , Richter Mikayla N , Das Subhamoy , Keefe Matthew G , Wang Jeffrey , Shiv Rahul K , McCann Conor J , Bhat Samyukta , Khoroshkin Matvei , Yu Johnny , Nowakowski Tomasz J , Goodarzi Hani , Thapar Nikhil , Kaltschmidt Julia A , Fattahi Faranak 
Published: January 2022

AbstractThe enteric nervous system (ENS) plays a central role in gut physiology and mediating the crosstalk between the gastrointestinal (GI) tract and other organs. The human ENS has remained elusive, highlighting the need for an in vitro modeling and mapping blueprint. Here we map out the developmental and functional features of the human ENS, by establishing robust and scalable 2D ENS cultures and 3D enteric ganglioids from human pluripotent stem cells (hPSCs). These models recapitulate the remarkable neuronal and glial diversity found in primary tissue and enable comprehensive molecular analyses that uncover functional and developmental relationships within these lineages. As a salient example of the power of this system, we performed in-depth characterization of enteric nitrergic neurons (NO neurons) which are implicated in a wide range of GI motility disorders. We conducted an unbiased screen and identified drug candidates that modulate the activity of NO neurons and demonstrated their potential in promoting motility in mouse colonic tissue ex vivo. We established a high-throughput strategy to define the developmental programs involved in NO neuron specification and discovered that PDGFR inhibition boosts the induction of NO neurons in enteric ganglioids. Transplantation of these ganglioids in the colon of NO neuron-deficient mice results in extensive tissue engraftment, providing a xenograft model for the study of human ENS in vivo and the development of cell-based therapies for neurodegenerative GI disorders. These studies provide a framework for deciphering fundamental features of the human ENS and designing effective strategies to treat enteric neuropathies.
New genomic signals underlying the emergence of human proto-genes
Authors: Grandchamp Anna , Berk Katrin , Dohmen Elias , Bornberg-Bauer Erich 
Published: January 2022

AbstractDe novo genes are novel genes which emerge from non-coding DNA. Until now, little is known about de novo genes properties, correlated to their age and mechanisms of emergence. In this study, we investigate four properties: introns, upstream regulatory motifs, 5’ UTRs and protein domains, in 23135 human proto-genes. We found that proto-genes contain introns, whose number and position correlates with the genomic position of proto-gene emergence. The origin of these introns is debated, as our result suggest that 41% proto-genes might have captured existing introns, as well as the fact that 13.7% of them do not splice the ORF. We show that proto-genes which emerged via overprinting tend to be more enriched in core promotor motifs, while intergenic and intronic ones are more enriched in enhancers, even if the motif TATA is most expressed upstream these genes. Intergenic and intronic 5’ UTRs of protogenes have a lower potential to stabilise mRNA structures than exonic proto-genes and established human genes. Finally, we confirm that proto-genes gain new putative domains with age. Overall, we find that regulatory motifs inducing transcription and translation of previously non-coding sequences may facilitate proto-gene emergence. Our paper demonstrates that introns, 5’UTRs, and domains have specific properties in proto-genes. We also show the importance of studying proto-genes in relation to their genomic position, as it strongly impacts these properties.
The tetraspanin TSPAN5 regulates AMPARs exocytosis by interacting with the AP-4 complex
Authors: Edoardo Moretto , Anna Longatti , Miozzo Federico , Bonnet Caroline , Coussen Francoise , Jaudon Fanny , Cingolani Lorenzo A. , Maria Passafaro 
Published: January 2022

AbstractIntracellular trafficking of AMPA receptors is a tightly regulated process which involves several adaptor proteins, and is crucial for the activity of excitatory synapses in both basal conditions and during synaptic plasticity. We found that, in rat hippocampal neurons, an intracellular pool of the tetraspanin TSPAN5 specifically promotes exocytosis of newly synthesised GluA2-containing AMPA receptors without affecting their internalisation. TSPAN5 mediates this function by interacting with AP-4 and Stargazin and possibly using recycling endosomes as a delivery route. This work highlights TSPAN5 as a new adaptor regulating AMPA receptor trafficking. In addition, it provides a possible mechanism for the intellectual disability symptoms that occur in AP-4 deficiency syndrome.
Reduced local mechanical stimuli in spaceflight diminishes osteocyte lacunar morphometry and spatial heterogeneity in mouse cortical bone
Authors: Coulombe Jennifer C. , Mullen Zachary A. , Weins Ashton M. , Fisher Liam E. , Lynch Maureen E. , Stodieck Louis S. , Ferguson Virginia. L 
Published: January 2022

ABSTRACTThree-dimensional (3D) imaging of osteocyte lacunae has recently substantiated the connection between lacunar shape and size, and osteocyte age, viability, and mechanotransduction. Yet it remains unclear why individual osteocytes reshape their lacunae and how networks of osteocytes change in response to local alterations in mechanical loads. We evaluated the effects of local mechanical stimuli on osteocyte lacunar morphometrics in tibial cortical bone from young female mice flown on the Space Shuttle for ∼13 days. We optimized scan parameters, using a laboratory-based submicrometer-resolution X-Ray Microscope, to achieve large ∼ 0.3 mm3 fields of view with sufficient resolution (≥ 0.3 μm) to visualize and measure thousands of lacunae per scan. Our novel approach avoids large measurement errors that are inherent in 2D and enables a facile 3D solution as compared to the lower resolution from benchtop micro-computed tomography (CT) systems or the cost and inaccessibility of synchrotron-based CT. Osteocyte lacunae were altered following microgravity exposure in a region-specific manner: more elongated (+7.0% Stretch) in predominately tensile-loaded bone as compared to those in compressively-loaded regions. In compressively-loaded bone, lacunae formed in microgravity were significantly larger (+6.9% Volume) than in the same region formed on Earth. We also evaluated lacunar heterogeneity (i.e., spatial autocorrelation of lacunar morphometric parameters) via kriging models. These statistical models demonstrated that heterogeneity varied with underlying spatial contributors, i.e. the local mechanical and biological environment. Yet in the absence of gravitational loading, osteocyte lacunae in newly formed bone were larger and were collectively more homogenous than in bone formed on Earth. Overall, this study shows that osteocyte reshape their lacunae in response to changes, or absence, in local mechanical stimuli and different biological environments. Additionally, spatial relationships among osteocytes are complex and necessitate evaluation in carefully selected regions of interest and of large cell populations.GRAPHICAL ABSTRACT
Exploring the rules of chimeric antigen receptor phenotypic output using combinatorial signaling motif libraries and machine learning
Authors: Daniels K.G. , Wang S. , Simic M.S. , Bhargava H.K. , Capponi S. , Tonai Y. , Yu W. , Bianco S. , Lim W.A. 
Published: January 2022

ABSTRACTChimeric antigen receptor (CAR) costimulatory domains steer the phenotypic output of therapeutic T cells. In most cases these domains are derived from native immune receptors, composed of signaling motif combinations selected by evolution. To explore if non-natural combinations of signaling motifs could drive novel cell fates of interest, we constructed a library of CARs containing ∼2,300 synthetic costimulatory domains, built from combinations of 13 peptide signaling motifs. The library produced CARs driving diverse fate outputs, which were sensitive to motif combinations and configurations. Neural networks trained to decode the combinatorial grammar of CAR signaling motifs allowed extraction of key design rules. For example, the non-native combination of TRAF- and PLCγ1-binding motifs was found to simultaneously enhance cytotoxicity and stemness, a clinically desirable phenotype associated with effective and durable tumor killing. The neural network accurately predicts that addition of PLCγ1-binding motifs improves this phenotype when combined with TRAF-binding motifs, but not when combined with other immune signaling motifs (e.g. PI3K-or Grb2-binding motifs). This work shows how libraries built from the minimal building blocks of signaling, combined with machine learning, can efficiently guide engineering of receptors with desired phenotypes.Graphical Abstract
Understanding host response to infectious salmon anaemia virus in an Atlantic salmon cell line using single-cell RNA sequencing
Authors: Gervais Ophélie , Gratacap Remi , Papadopoulou Athina , Houston Ross D. , Hassan Musa A. , Robledo Diego 
Published: January 2022

AbstractBackgroundInfectious Salmon Anaemia Virus (ISAV) is an Orthomixovirus that currently represents a large problem for salmonid aquaculture worldwide. Prevention and treatment methods are only partially effective. Genetic selection and genome engineering strategies have potential to develop ISAV resistant salmon stocks. However, this requires a detailed understanding of the genomic regulation of ISAV pathogenesis. Here, we used single cell RNA sequencing on a salmonid cell line to provide a high dimensional insight into the transcriptional landscape that underpin host-virus interactions during ISAV infection at the single cell level.ResultsSalmon head kidney 1 (SHK-1) cells were single-cell RNA sequenced before challenge, and at 24h, 48h, and 96h post-ISAV challenge. The results revealed marked changes in the host transcriptome at 48h and 96h post-infection, even in uninfected cells, potentially suggesting paracrine signalling. This paracrine activation of uninfected cells seemed to be unspecific, involving pathways such as mRNA sensing, ubiquitination or proteasome, and also the up-regulation of the mitochondrial ribosome genes. At 24h post infection, cells showed expression signatures consistent with viral entry, with up-regulation of genes such as PI3K, FAK or JNK. At 48h and 96h, infected cells showed a clear anti-viral response, characterised by the expression of IFNA2 or IRF2.ConclusionsThis study has increased our understanding of the cellular response of Atlantic salmon during ISAV infection, and revealed potential host-virus interactions at the cellular level. The results highlight the value of single-cell sequencing to characterise cell culture models of viral infection, and the results can be exploited in future functional studies to increase the resistance of Atlantic salmon to ISAV.
A gas migration law study of a large-scale 3D physical similarity simulation with an adaptive Kalman filter algorithm
Authors: Hao Yuyu , Li Shugang , Zhang Tianjun 
Published: January 2022

Purpose
In this study, a physical similarity simulation plays a significant role in the study of crack evolution and the gas migration mechanism. A sensor is deployed inside a comparable artificial rock formation to assure the accuracy of the experiment results. During the building of the simulated rock formation, a huge volume of acidic gas is released, causing numerous sensor measurement mistakes. Additionally, the gas concentration estimation approach is subject to uncertainty because of the complex rock formation environment. As a result, the purpose of this study is to introduce an adaptive Kalman filter approach to reduce observation noise, increase the accuracy of the gas concentration estimation model and, finally, determine the gas migration law.

Design/methodology/approach
First, based on the process of gas floatation-diffusion and seepage, the gas migration model is established according to Fick’s second law, and a simplified modeling method using diffusion flux instead of gas concentration is presented. Second, an adaptive Kalman filter algorithm is introduced to establish a gas concentration estimation model, taking into account the model uncertainty and the unknown measurement noise. Finally, according to a large-scale physical similarity simulation platform, a thorough experiment about gas migration is carried out to extract gas concentration variation data with certain ventilation techniques and to create a gas chart of the time-changing trend.

Findings
This approach is used to determine the changing process of gas distribution for a certain ventilation mode. The results match the rock fissure distribution condition derived from the microseismic monitoring data, proving the effectiveness of the approach.

Originality/value
For the first time in large-scale three-dimensional physical similarity simulations, the adaptive Kalman filter data processing method based on the inverse Wishart probability density function is used to solve the problem of an inaccurate process and measurement noise, laying the groundwork for studying the gas migration law and determining the gas migration mechanism.
Impact of the COVID-19 lockdown on the economic situation and food security of rural households in India
Authors: Suresh Veena , Fishman Ram , von Lieres Johanna Sophie , Rao Bhavani R. 
Published: January 2022

PurposeThe purpose of the study is to understand what impact the first COVID-19 lockdown in 2020 had on the income and food security of rural households in India and whether it differed across socioeconomic factors. Moreover, the study assesses the needs of rural households and determines whether they had received adequate support services during the lockdown.Design/methodology/approachThe study adopted a repeated-measures quantitative survey design with 1,319 rural women from 16 states of India and conducted a telephonic survey.FindingsThe lockdown had directly impacted rural households' employment status and income but the impact differed depending on the type of employment. For example, working in a salaried job or on one's farm led to a lower likelihood of a complete decline in income in states other than Kerala as the lockdown continued. The study also revealed a change in the pattern of food consumption, with higher consumption of subsidized staple foods. It also became evident that the aid announced by the government reached the rural population with some delay.Research limitations/implicationsA limitation of the study was that many respondents refused to participate in phase 2, which reduced the sample size when comparing the two phases because the women did not own mobile phones. Instead, they were using their husbands' phones.Originality/valueThe study's findings can help better understand the needs of rural populations during crises, such as the COVID-19 pandemic. This can help to plan better and build preventive actions for such populations once their needs are understood. In addition, this can aid disadvantaged people for a minimal level of preparedness and security during such a crisis in the future.