bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance
Authors: Simonetti Michele , Zhang Ning , Harbers Luuk , Milia Maria Grazia , Brossa Silvia , Huong Nguyen Thi Thu , Cerutti Francesco , Berrino Enrico , Sapino Anna , Bienko Magda , Sottile Antonino , Ghisetti Valeria , Crosetto Nicola 
Published: June 2021

AbstractWhile mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow—COVseq—which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.
Climate change favours large seasonal loss of Arctic ozone
Authors: von der Gathen Peter , Kivi Rigel , Wohltmann Ingo , Salawitch Ross J. , Rex Markus 
Published: June 2021

AbstractChemical loss of Arctic ozone due to anthropogenic halogens is driven by temperature, with more loss occurring during cold winters favourable for formation of polar stratospheric clouds (PSCs). We show that a positive, statistically significant rise in the local maxima of PSC formation potential (PFPLM) for cold winters is apparent in meteorological data collected over the past half century. Output from numerous General Circulation Models (GCMs) also exhibits positive trends in PFPLMover 1950 to 2100, with highest values occurring at end of century, for simulations driven by a large rise in the radiative forcing of climate from greenhouse gases (GHGs). We combine projections of stratospheric halogen loading and humidity with GCM-based forecasts of temperature to suggest that conditions favourable for large, seasonal loss of Arctic column O3could persist or even worsen until the end of this century, if future abundances of GHGs continue to steeply rise.
Rapid proliferation due to better metabolic adaptation results in full virulence of a filament-deficient Candida albicans strain
Authors: Dunker Christine , Polke Melanie , Schulze-Richter Bianca , Schubert Katja , Rudolphi Sven , Gressler A. Elisabeth , Pawlik Tony , Prada Salcedo Juan P. , Niemiec M. Joanna , Slesiona-Künzel Silvia , Swidergall Marc , Martin Ronny , Dandekar Thomas , Jacobsen Ilse D. 
Published: June 2021

AbstractThe ability of the fungal pathogen Candida albicans to undergo a yeast-to-hypha transition is believed to be a key virulence factor, as filaments mediate tissue damage. Here, we show that virulence is not necessarily reduced in filament-deficient strains, and the results depend on the infection model used. We generate a filament-deficient strain by deletion or repression of EED1 (known to be required for maintenance of hyphal growth). Consistent with previous studies, the strain is attenuated in damaging epithelial cells and macrophages in vitro and in a mouse model of intraperitoneal infection. However, in a mouse model of systemic infection, the strain is as virulent as the wild type when mice are challenged with intermediate infectious doses, and even more virulent when using low infectious doses. Retained virulence is associated with rapid yeast proliferation, likely the result of metabolic adaptation and improved fitness, leading to high organ fungal loads. Analyses of cytokine responses in vitro and in vivo, as well as systemic infections in immunosuppressed mice, suggest that differences in immunopathology contribute to some extent to retained virulence of the filament-deficient mutant. Our findings challenge the long-standing hypothesis that hyphae are essential for pathogenesis of systemic candidiasis by C. albicans.
Quantitative comparison of geological data and model simulations constrains early Cambrian geography and climate
Authors: Wong Hearing Thomas W. , Pohl Alexandre , Williams Mark , Donnadieu Yannick , Harvey Thomas H. P. , Scotese Christopher R. , Sepulchre Pierre , Franc Alain , Vandenbroucke Thijs R. A. 
Published: June 2021

AbstractMarine ecosystems with a diverse range of animal groups became established during the early Cambrian (~541 to ~509 Ma). However, Earth’s environmental parameters and palaeogeography in this interval of major macro-evolutionary change remain poorly constrained. Here, we test contrasting hypotheses of continental configuration and climate that have profound implications for interpreting Cambrian environmental proxies. We integrate general circulation models and geological observations to test three variants of the ‘Antarctocentric’ paradigm, with a southern polar continent, and an ‘equatorial’ configuration that lacks polar continents. This quantitative framework can be applied to other deep-time intervals when environmental proxy data are scarce. Our results show that the Antarctocentric palaeogeographic paradigm can reconcile geological data and simulated Cambrian climate. Our analyses indicate a greenhouse climate during the Cambrian animal radiation, with mean annual sea-surface temperatures between ~9 °C to ~19 °C and ~30 °C to ~38 °C for polar and tropical palaeolatitudes, respectively.
Reconstruction of plant–pollinator networks from observational data
Authors: Young Jean-Gabriel , Valdovinos Fernanda S. , Newman M. E. J. 
Published: June 2021

AbstractEmpirical measurements of ecological networks such as food webs and mutualistic networks are often rich in structure but also noisy and error-prone, particularly for rare species for which observations are sparse. Focusing on the case of plant–pollinator networks, we here describe a Bayesian statistical technique that allows us to make accurate estimates of network structure and ecological metrics from such noisy observational data. Our method yields not only estimates of these quantities, but also estimates of their statistical errors, paving the way for principled statistical analyses of ecological variables and outcomes. We demonstrate the use of the method with an application to previously published data on plant–pollinator networks in the Seychelles archipelago and Kosciusko National Park, calculating estimates of network structure, network nestedness, and other characteristics.
Human cytomegalovirus-induced host protein citrullination is crucial for viral replication
Authors: Griffante Gloria , Gugliesi Francesca , Pasquero Selina , Dell’Oste Valentina , Biolatti Matteo , Salinger Ari J. , Mondal Santanu , Thompson Paul R. , Weerapana Eranthie , Lebbink Robert J. , Soppe Jasper A. , Stamminger Thomas , Girault Virginie , Pichlmair Andreas , Oroszlán Gábor , Coen Donald M. , De Andrea Marco , Landolfo Santo 
Published: June 2021

AbstractCitrullination is the conversion of arginine-to-citrulline by protein arginine deiminases (PADs), whose dysregulation is implicated in the pathogenesis of various types of cancers and autoimmune diseases. Consistent with the ability of human cytomegalovirus (HCMV) to induce post-translational modifications of cellular proteins to gain a survival advantage, we show that HCMV infection of primary human fibroblasts triggers PAD-mediated citrullination of several host proteins, and that this activity promotes viral fitness. Citrullinome analysis reveals significant changes in deimination levels of both cellular and viral proteins, with interferon (IFN)-inducible protein IFIT1 being among the most heavily deiminated one. As genetic depletion of IFIT1 strongly enhances HCMV growth, and in vitro IFIT1 citrullination impairs its ability to bind to 5’-ppp-RNA, we propose that viral-induced IFIT1 citrullination is a mechanism of HCMV evasion from host antiviral resistance. Overall, our findings point to a crucial role of citrullination in subverting cellular responses to viral infection.
Single-component near-infrared optogenetic systems for gene transcription regulation
Authors: Kaberniuk Andrii A. , Baloban Mikhail , Monakhov Mikhail V. , Shcherbakova Daria M. , Verkhusha Vladislav V. 
Published: June 2021

AbstractNear-infrared (NIR) optogenetic systems for transcription regulation are in high demand because NIR light exhibits low phototoxicity, low scattering, and allows combining with probes of visible range. However, available NIR optogenetic systems consist of several protein components of large size and multidomain structure. Here, we engineer single-component NIR systems consisting of evolved photosensory core module of Idiomarina sp. bacterial phytochrome, named iLight, which are smaller and packable in adeno-associated virus. We characterize iLight in vitro and in gene transcription repression in bacterial and gene transcription activation in mammalian cells. Bacterial iLight system shows 115-fold repression of protein production. Comparing to multi-component NIR systems, mammalian iLight system exhibits higher activation of 65-fold in cells and faster 6-fold activation in deep tissues of mice. Neurons transduced with viral-encoded iLight system exhibit 50-fold induction of fluorescent reporter. NIR light-induced neuronal expression of green-light-activatable CheRiff channelrhodopsin causes 20-fold increase of photocurrent and demonstrates efficient spectral multiplexing.
Single-cell transcriptomic analysis reveals disparate effector differentiation pathways in human Treg compartment
Authors: Luo Yuechen , Xu Changlu , Wang Bing , Niu Qing , Su Xiuhua , Bai Yingnan , Zhu Shuxian , Zhao Chunxiao , Sun Yunyan , Wang Jiali , Liu Maolan , Sun Xiaolei , Song Ge , Cui Haidong , Chen Xiaoli , Huang Huifang , Wang Haikun , Han Mingzhe , Jiang Erlie , Shi Lihong , Feng Xiaoming 
Published: June 2021

AbstractHuman FOXP3+ regulatory T (Treg) cells are central to immune tolerance. However, their heterogeneity and differentiation remain incompletely understood. Here we use single-cell RNA and T cell receptor sequencing to resolve Treg cells from healthy individuals and patients with or without acute graft-versus-host disease (aGVHD) who undergo stem cell transplantation. These analyses, combined with functional assays, separate Treg cells into naïve, activated, and effector stages, and resolve the HLA-DRhi, LIMS1hi, highly suppressive FOXP3hi, and highly proliferative MKI67hi effector subsets. Trajectory analysis assembles Treg subsets into two differentiation paths (I/II) with distinctive phenotypic and functional programs, ending with the FOXP3hi and MKI67hi subsets, respectively. Transcription factors FOXP3 and SUB1 contribute to some Path I and Path II phenotypes, respectively. These FOXP3hi and MKI67hi subsets and two differentiation pathways are conserved in transplanted patients, despite having functional and migratory impairments under aGVHD. These findings expand the understanding of Treg cell heterogeneity and differentiation and provide a single-cell atlas for the dissection of Treg complexity in health and disease.
Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave
Authors: Zavala Elena I. , Jacobs Zenobia , Vernot Benjamin , Shunkov Michael V. , Kozlikin Maxim B. , Derevianko Anatoly P. , Essel Elena , de Fillipo Cesare , Nagel Sarah , Richter Julia , Romagné Frédéric , Schmidt Anna , Li Bo , O’Gorman Kieran , Slon Viviane , Kelso Janet , Pääbo Svante , Roberts Richard G. , Meyer Matthias 
Published: June 2021

AbstractDenisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1–4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8–11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly—possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.
Protective efficacy of Ad26.COV2.S against SARS-CoV-2 B.1.351 in macaques
Authors: Yu Jingyou , Tostanoski Lisa H. , Mercado Noe B. , McMahan Katherine , Liu Jinyan , Jacob-Dolan Catherine , Chandrashekar Abishek , Atyeo Caroline , Martinez David R. , Anioke Tochi , Bondzie Esther A. , Chang Aiquan , Gardner Sarah , Giffin Victoria M. , Hope David L. , Nampanya Felix , Nkolola Joseph , Patel Shivani , Sanborn Owen , Sellers Daniel , Wan Huahua , Hayes Tammy , Bauer Katherine , Pessaint Laurent , Valentin Daniel , Flinchbaugh Zack , Brown Renita , Cook Anthony , Bueno-Wilkerson Deandre , Teow Elyse , Andersen Hanne , Lewis Mark G. , Martinot Amanda J. , Baric Ralph S. , Alter Galit , Wegmann Frank , Zahn Roland , Schuitemaker Hanneke , Barouch Dan H. 
Published: June 2021

AbstractThe emergence of SARS-CoV-2 variants that partially evade neutralizing antibodies poses a threat to the efficacy of current COVID-19 vaccines1,2. The Ad26.COV2.S vaccine expresses a stabilized spike protein from the WA1/2020 strain of SARS-CoV-2, and has recently demonstrated protective efficacy against symptomatic COVID-19 in humans in several geographical regions—including in South Africa, where 95% of sequenced viruses in cases of COVID-19 were the B.1.351 variant3. Here we show that Ad26.COV2.S elicits humoral and cellular immune responses that cross-react with the B.1.351 variant and protects against B.1.351 challenge in rhesus macaques. Ad26.COV2.S induced lower binding and neutralizing antibodies against B.1.351 as compared to WA1/2020, but elicited comparable CD8 and CD4 T cell responses against the WA1/2020, B.1.351, B.1.1.7, P.1 and CAL.20C variants. B.1.351 infection of control rhesus macaques resulted in higher levels of virus replication in bronchoalveolar lavage and nasal swabs than did WA1/2020 infection. Ad26.COV2.S provided robust protection against both WA1/2020 and B.1.351, although we observed higher levels of virus in vaccinated macaques after B.1.351 challenge. These data demonstrate that Ad26.COV2.S provided robust protection against B.1.351 challenge in rhesus macaques. Our findings have important implications for vaccine control of SARS-CoV-2 variants of concern.
The COUGHVID crowdsourcing dataset, a corpus for the study of large-scale cough analysis algorithms
Authors: Orlandic Lara , Teijeiro Tomas , Atienza David 
Published: June 2021

AbstractCough audio signal classification has been successfully used to diagnose a variety of respiratory conditions, and there has been significant interest in leveraging Machine Learning (ML) to provide widespread COVID-19 screening. The COUGHVID dataset provides over 25,000 crowdsourced cough recordings representing a wide range of participant ages, genders, geographic locations, and COVID-19 statuses. First, we contribute our open-sourced cough detection algorithm to the research community to assist in data robustness assessment. Second, four experienced physicians labeled more than 2,800 recordings to diagnose medical abnormalities present in the coughs, thereby contributing one of the largest expert-labeled cough datasets in existence that can be used for a plethora of cough audio classification tasks. Finally, we ensured that coughs labeled as symptomatic and COVID-19 originate from countries with high infection rates. As a result, the COUGHVID dataset contributes a wealth of cough recordings for training ML models to address the world’s most urgent health crises.
Genome assembly using quantum and quantum-inspired annealing
Authors: Boev A. S. , Rakitko A. S. , Usmanov S. R. , Kobzeva A. N. , Popov I. V. , Ilinsky V. V. , Kiktenko E. O. , Fedorov A. K. 
Published: June 2021

AbstractRecent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for de novo genome assembly, which is used for the analysis of genomic rearrangements, chromosome phasing, and reconstructing genomes without a reference, require solving tasks of high computational complexity. Here we demonstrate a method for solving genome assembly tasks with the use of quantum and quantum-inspired optimization techniques. Within this method, we present experimental results on genome assembly using quantum annealers both for simulated data and the $$\phi $$
ϕ
X 174 bacteriophage. Our results pave a way for an increase in the efficiency of solving bioinformatics problems with the use of quantum computing and, in particular, quantum annealing. We expect that the new generation of quantum annealing devices would outperform existing techniques for de novo genome assembly. To the best of our knowledge, this is the first experimental study of de novo genome assembly problems both for real and synthetic data on quantum annealing devices and quantum-inspired techniques.
Enhancement and analysis of Anthracene degradation by Tween 80 in LMS-HOBt
Authors: Yang Zuoyi , Mao Xingchen , Cui Jiahao , Wang Yujie , Zhang Yaping 
Published: June 2021

AbstractThis study examines the specific effect of Tween 80 on the conversion of anthracene (ANT) in laccase medium system regarding surfactant chemical changes and mechanism. The conversion rate and degradation products of ANT were investigated in different concentrations of Tween 80 solution. Between Tween 80 concentration 0–40 critical micelle concentrations (CMC), the kinetic parameter-k (h−1) and corresponding half-life T1/2 decreased with increasing concentration. When Tween 80 was above 20 CMC the laccase-medium system converted > 95% of ANT to anthraquinone within 12 h. During the entire enzymatic reaction, the laccase activity in the system increased with increasing Tween 80 concentration. Combined with GC/MS analysis of the product, it was speculated that hydrogens belonging to the ether-oxygen bond and carbon–carbon double bond α-CH of Tween 80, were removed by the laccase-media system, promoting its degradation. Additionally, enhanced activity caused by oxygen free radicals (ROS) such as RO• and ROO•, continuously oxidized Tween 80, which in turn produced free radicals while converting ANT. This study provides new theoretical support toward the application of surfactants in the elimination of polycyclic aromatic hydrocarbons.
A novel computer-aided diagnostic system for accurate detection and grading of liver tumors
Authors: Alksas Ahmed , Shehata Mohamed , Saleh Gehad A. , Shaffie Ahmed , Soliman Ahmed , Ghazal Mohammed , Khelifi Adel , Khalifeh Hadil Abu , Razek Ahmed Abdel , Giridharan Guruprasad A. , El-Baz Ayman 
Published: June 2021

AbstractLiver cancer is a major cause of morbidity and mortality in the world. The primary goals of this manuscript are the identification of novel imaging markers (morphological, functional, and anatomical/textural), and development of a computer-aided diagnostic (CAD) system to accurately detect and grade liver tumors non-invasively. A total of 95 patients with liver tumors (M = 65, F = 30, age range = 34–82 years) were enrolled in the study after consents were obtained. 38 patients had benign tumors (LR1 = 19 and LR2 = 19), 19 patients had intermediate tumors (LR3), and 38 patients had hepatocellular carcinoma (HCC) malignant tumors (LR4 = 19 and LR5 = 19). A multi-phase contrast-enhanced magnetic resonance imaging (CE-MRI) was collected to extract the imaging markers. A comprehensive CAD system was developed, which includes the following main steps: i) estimation of morphological markers using a new parametric spherical harmonic model, ii) estimation of textural markers using a novel rotation invariant gray-level co-occurrence matrix (GLCM) and gray-level run-length matrix (GLRLM) models, and iii) calculation of the functional markers by estimating the wash-in/wash-out slopes, which enable quantification of the enhancement characteristics across different CE-MR phases. These markers were subsequently processed using a two-stages random forest-based classifier to classify the liver tumor as benign, intermediate, or malignant and determine the corresponding grade (LR1, LR2, LR3, LR4, or LR5). The overall CAD system using all the identified imaging markers achieved a sensitivity of 91.8%±0.9%, specificity of 91.2%±1.9%, and F$$_{1}$$

1

score of 0.91±0.01, using the leave-one-subject-out (LOSO) cross-validation approach. Importantly, the CAD system achieved overall accuracies of $$88\%\pm 5\%$$

88
%
±
5
%

, 85%±2%, 78%±3%, 83%±4%, and 79%±3% in grading liver tumors into LR1, LR2, LR3, LR4, and LR5, respectively. In addition to LOSO, the developed CAD system was tested using randomly stratified 10-fold and 5-fold cross-validation approaches. Alternative classification algorithms, including support vector machine, naive Bayes classifier, k-nearest neighbors, and linear discriminant analysis all produced inferior results compared to the proposed two stage random forest classification model. These experiments demonstrate the feasibility of the proposed CAD system as a novel tool to objectively assess liver tumors based on the new comprehensive imaging markers. The identified imaging markers and CAD system can be used as a non-invasive diagnostic tool for early and accurate detection and grading of liver cancer.