bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance
Authors: Sherry Norelle L. , Horan Kristy A. , Ballard Susan A. , Gonҫalves da Silva Anders , Gorrie Claire L. , Schultz Mark B. , Stevens Kerrie , Valcanis Mary , Sait Michelle L. , Stinear Timothy P. , Howden Benjamin P. , Seemann Torsten 
Published: January 2023

AbstractRealising the promise of genomics to revolutionise identification and surveillance of antimicrobial resistance (AMR) has been a long-standing challenge in clinical and public health microbiology. Here, we report the creation and validation of abritAMR, an ISO-certified bioinformatics platform for genomics-based bacterial AMR gene detection. The abritAMR platform utilises NCBI’s AMRFinderPlus, as well as additional features that classify AMR determinants into antibiotic classes and provide customised reports. We validate abritAMR by comparing with PCR or reference genomes, representing 1500 different bacteria and 415 resistance alleles. In these analyses, abritAMR displays 99.9% accuracy, 97.9% sensitivity and 100% specificity. We also compared genomic predictions of phenotype for 864 Salmonella spp. against agar dilution results, showing 98.9% accuracy. The implementation of abritAMR in our institution has resulted in streamlined bioinformatics and reporting pathways, and has been readily updated and re-verified. The abritAMR tool and validation datasets are publicly available to assist laboratories everywhere harness the power of AMR genomics in professional practice.
The learnability of Pauli noise
Authors: Chen Senrui , Liu Yunchao , Otten Matthew , Seif Alireza , Fefferman Bill , Jiang Liang 
Published: January 2023

AbstractRecently, several quantum benchmarking algorithms have been developed to characterize noisy quantum gates on today’s quantum devices. A fundamental issue in benchmarking is that not everything about quantum noise is learnable due to the existence of gauge freedom, leaving open the question what information is learnable and what is not, which is unclear even for a single CNOT gate. Here we give a precise characterization of the learnability of Pauli noise channels attached to Clifford gates using graph theoretical tools. Our results reveal the optimality of cycle benchmarking in the sense that it can extract all learnable information about Pauli noise. We experimentally demonstrate noise characterization of IBM’s CNOT gate up to 2 unlearnable degrees of freedom, for which we obtain bounds using physical constraints. In addition, we show that an attempt to extract unlearnable information by ignoring state preparation noise yields unphysical estimates, which is used to lower bound the state preparation noise.
Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells
Authors: Galles Grace D. , Infield Daniel T. , Clark Colin J. , Hemshorn Marcus L. , Manikandan Shivani , Fazan Frederico , Rasouli Ali , Tajkhorshid Emad , Galpin Jason D. , Cooley Richard B. , Mehl Ryan A. , Ahern Christopher A. 
Published: January 2023

AbstractThe aromatic side-chains of phenylalanine, tyrosine, and tryptophan interact with their environments via both hydrophobic and electrostatic interactions. Determining the extent to which these contribute to protein function and stability is not possible with conventional mutagenesis. Serial fluorination of a given aromatic is a validated method in vitro and in silico to specifically alter electrostatic characteristics, but this approach is restricted to a select few experimental systems. Here, we report a group of pyrrolysine-based aminoacyl-tRNA synthetase/tRNA pairs (tRNA/RS pairs) that enable the site-specific encoding of a varied spectrum of fluorinated phenylalanine amino acids in E. coli and mammalian (HEK 293T) cells. By allowing the cross-kingdom expression of proteins bearing these unnatural amino acids at biochemical scale, these tools may potentially enable the study of biological mechanisms which utilize aromatic interactions in structural and cellular contexts.
Benchmarking the performance of water companies for regulatory purposes to improve its sustainability
Authors: Sala-Garrido Ramon , Mocholí-Arce Manuel , Maziotis Alexandros , Molinos-Senante Maria 
Published: January 2023

AbstractThe regulation of water companies (WCs) is essential to protect the interests of citizens, as companies are natural monopolies. Consequently, several methodological approaches are applied by water regulators to benchmark the performance of WCs, with data envelopment analysis (DEA) being one of the most widely applied. However, traditional DEA models allocate different weights to variables considered in efficiency assessments of each WC. By contrast, this study proposes and applies a common set weights (CSW) DEA model to a sample of Chilean WCs. The results showed that the DEA-CSW approach had greater discriminatory capacity compared to traditional DEA techniques. Moreover, weights allocated to input and output variables involved in efficiency assessment diverged among WCs when the traditional DEA model was employed. By contrast, the DEA-CSW approach generated reliable ranking of WCs based on their efficiency scores, thus facilitating the regulatory decision-making process.
Cost-effective mitigation of nitrogen pollution from global croplands
Authors: Gu Baojing , Zhang Xiuming , Lam Shu Kee , Yu Yingliang , van Grinsven Hans J. M. , Zhang Shaohui , Wang Xiaoxi , Bodirsky Benjamin Leon , Wang Sitong , Duan Jiakun , Ren Chenchen , Bouwman Lex , de Vries Wim , Xu Jianming , Sutton Mark A. , Chen Deli 
Published: January 2023

AbstractCropland is a main source of global nitrogen pollution1,2. Mitigating nitrogen pollution from global croplands is a grand challenge because of the nature of non-point-source pollution from millions of farms and the constraints to implementing pollution-reduction measures, such as lack of financial resources and limited nitrogen-management knowledge of farmers3. Here we synthesize 1,521 field observations worldwide and identify 11 key measures that can reduce nitrogen losses from croplands to air and water by 30–70%, while increasing crop yield and nitrogen use efficiency (NUE) by 10–30% and 10–80%, respectively. Overall, adoption of this package of measures on global croplands would allow the production of 17 ± 3 Tg (1012 g) more crop nitrogen (20% increase) with 22 ± 4 Tg less nitrogen fertilizer used (21% reduction) and 26 ± 5 Tg less nitrogen pollution (32% reduction) to the environment for the considered base year of 2015. These changes could gain a global societal benefit of 476 ± 123 billion US dollars (USD) for food supply, human health, ecosystems and climate, with net mitigation costs of only 19 ± 5 billion USD, of which 15 ± 4 billion USD fertilizer saving offsets 44% of the gross mitigation cost. To mitigate nitrogen pollution from croplands in the future, innovative policies such as a nitrogen credit system (NCS) could be implemented to select, incentivize and, where necessary, subsidize the adoption of these measures.
A DNA methylation atlas of normal human cell types
Authors: Loyfer Netanel , Magenheim Judith , Peretz Ayelet , Cann Gordon , Bredno Joerg , Klochendler Agnes , Fox-Fisher Ilana , Shabi-Porat Sapir , Hecht Merav , Pelet Tsuria , Moss Joshua , Drawshy Zeina , Amini Hamed , Moradi Patriss , Nagaraju Sudharani , Bauman Dvora , Shveiky David , Porat Shay , Dior Uri , Rivkin Gurion , Or Omer , Hirshoren Nir , Carmon Einat , Pikarsky Alon , Khalaileh Abed , Zamir Gideon , Grinbaum Ronit , Abu Gazala Machmud , Mizrahi Ido , Shussman Noam , Korach Amit , Wald Ori , Izhar Uzi , Erez Eldad , Yutkin Vladimir , Samet Yaacov , Rotnemer Golinkin Devorah , Spalding Kirsty L. , Druid Henrik , Arner Peter , Shapiro A. M. James , Grompe Markus , Aravanis Alex , Venn Oliver , Jamshidi Arash , Shemer Ruth , Dor Yuval , Glaser Benjamin , Kaplan Tommy 
Published: January 2023

AbstractDNA methylation is a fundamental epigenetic mark that governs gene expression and chromatin organization, thus providing a window into cellular identity and developmental processes1. Current datasets typically include only a fraction of methylation sites and are often based either on cell lines that underwent massive changes in culture or on tissues containing unspecified mixtures of cells2–5. Here we describe a human methylome atlas, based on deep whole-genome bisulfite sequencing, allowing fragment-level analysis across thousands of unique markers for 39 cell types sorted from 205 healthy tissue samples. Replicates of the same cell type are more than 99.5% identical, demonstrating the robustness of cell identity programmes to environmental perturbation. Unsupervised clustering of the atlas recapitulates key elements of tissue ontogeny and identifies methylation patterns retained since embryonic development. Loci uniquely unmethylated in an individual cell type often reside in transcriptional enhancers and contain DNA binding sites for tissue-specific transcriptional regulators. Uniquely hypermethylated loci are rare and are enriched for CpG islands, Polycomb targets and CTCF binding sites, suggesting a new role in shaping cell-type-specific chromatin looping. The atlas provides an essential resource for study of gene regulation and disease-associated genetic variants, and a wealth of potential tissue-specific biomarkers for use in liquid biopsies.
SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials
Authors: Eastman Peter , Behara Pavan Kumar , Dotson David L. , Galvelis Raimondas , Herr John E. , Horton Josh T. , Mao Yuezhi , Chodera John D. , Pritchard Benjamin P. , Wang Yuanqing , De Fabritiis Gianni , Markland Thomas E. 
Published: January 2023

AbstractMachine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for training potentials relevant to simulating drug-like small molecules interacting with proteins. It contains over 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and uncharged molecules, and a wide range of covalent and non-covalent interactions. It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, along with other useful quantities such as multipole moments and bond orders. We train a set of machine learning potentials on it and demonstrate that they can achieve chemical accuracy across a broad region of chemical space. It can serve as a valuable resource for the creation of transferable, ready to use potential functions for use in molecular simulations.
A Europe-wide inventory of citizen-led energy action with data from 29 countries and over 10000 initiatives
Authors: Wierling August , Schwanitz Valeria Jana , Zeiss Jan Pedro , von Beck Constantin , Paudler Heather Arghandeh , Koren Ingrid Knutsdotter , Kraudzun Tobias , Marcroft Timothy , Müller Lukas , Andreadakis Zacharias , Candelise Chiara , Dufner Simon , Getabecha Melake , Glaase Grete , Hubert Wit , Lupi Veronica , Majidi Sona , Mohammadi Shirin , Nosar Negar Safara , du Pont Yann Robiou , Roots Philippa , Rudek Tadeusz Józef , Sciullo Alessandro , Sehdev Gayatri , Ziaabadi Mehran , Zoubin Nahid 
Published: January 2023

AbstractNumerous case studies show that citizens engage in various ways in renewable and low carbon energy projects, thereby contributing to the sustainable energy transition. To date, however, a systematic and cross-country database on citizen-led initiatives and projects is lacking. By performing a major compilation and reviewing copious data sources from websites to official registries, we provide a Europe-wide inventory with over 10,000 initiatives and 16,000 production units in 29 countries, focusing on the past 20 years. Our data allow cross-country statistical analysis, supporting the elicitation of empirical insights capable of extending beyond the perspective of single case studies. Our data also align with ongoing efforts to implement two EU Directives that aim at strengthening the active role of citizens in the energy transition. While the focus of our data collection is on Europe, the data and methodology can contribute to the global analysis of citizen-led energy action.
Global-scale parameters for ecological models
Authors: Coro Gianpaolo , Bove Pasquale , Kesner-Reyes Kathleen 
Published: January 2023

AbstractThis paper presents a collection of environmental, geophysical, and other marine-related data for marine ecological models and ecological-niche models. It consists of 2132 raster data for 58 distinct parameters at regional and global scales in the ESRI-GRID ASCII format. Most data originally belonged to open data owned by the authors of this article but residing on heterogeneous repositories with different formats and resolutions. Other data were specifically created for the present publication. The collection includes 565 data with global scale range; 154 at 0.5° resolution and 411 at 0.1° resolution; 196 data with annual temporal aggregation over ~10 key years between 1950 and 2100; 369 data with monthly aggregation at 0.1° resolution from January 2017 to ~May 2021 continuously. Data were also cut out on 8 European marine regions. The collection also includes forecasts for different future scenarios such as the Representative Concentration Pathways 2.6 (63 data), 4.5 (162 data), and 8.5 (162 data), and the A2 scenario of the Intergovernmental Panel on Climate Change (180 data).
Citizen science helps in the study of fungal diversity in New Jersey
Authors: Shumskaya Maria , Filippova Nina , Lorentzen Laura , Blue Shazneka , Andrew Carrie , Lorusso Nicholas S. 
Published: January 2023

AbstractThe history of fungal diversity of the Northeastern United States is currently fragmentary and restricted to particular functional groups or limited geospatial scales. Here, we describe a unique by its size, lifespan and data originators dataset, to improve our understanding of species occurrence and distribution across the state and time. Between the years 2007 to 2019, over 30 parks and nature preserves were sampled during forays conducted by members of the New Jersey Mycological Association (USA), a nonprofit organization of fungi enthusiasts. The dataset contains over 400 000 occurrences of over 1400 species across the state, made up mostly of the phylum Basidiomycota (89%) and Ascomycota (11%), with most observations resolved at the species level (>99%). The database is georeferenced and openly accessible through the Global Biodiversity Information Facility (GBIF) repository. This dataset marks a productive endeavor to contribute to our knowledge of the biodiversity of fungi in the Northeastern United States leveraging citizen science to better resolve biodiversity of this critical and understudied kingdom.
Three-dimensional unsupervised probabilistic pose reconstruction (3D-UPPER) for freely moving animals
Authors: Ebrahimi Aghileh S. , Orlowska-Feuer Patrycja , Huang Qian , Zippo Antonio G. , Martial Franck P. , Petersen Rasmus S. , Storchi Riccardo 
Published: January 2023

AbstractA key step in understanding animal behaviour relies in the ability to quantify poses and movements. Methods to track body landmarks in 2D have made great progress over the last few years but accurate 3D reconstruction of freely moving animals still represents a challenge. To address this challenge here we develop the 3D-UPPER algorithm, which is fully automated, requires no a priori knowledge of the properties of the body and can also be applied to 2D data. We find that 3D-UPPER reduces by $$>10$$

>
10

fold the error in 3D reconstruction of mouse body during freely moving behaviour compared with the traditional triangulation of 2D data. To achieve that, 3D-UPPER performs an unsupervised estimation of a Statistical Shape Model (SSM) and uses this model to constrain the viable 3D coordinates. We show, by using simulated data, that our SSM estimator is robust even in datasets containing up to 50% of poses with outliers and/or missing data. In simulated and real data SSM estimation converges rapidly, capturing behaviourally relevant changes in body shape associated with exploratory behaviours (e.g. with rearing and changes in body orientation). Altogether 3D-UPPER represents a simple tool to minimise errors in 3D reconstruction while capturing meaningful behavioural parameters.
TNFα, IL-6, miR-103a-3p, miR-423-5p, miR-23a-3p, miR-15a-5p and miR-223-3p in the crevicular fluid of periodontopathic patients correlate with each other and at different stages of the disease
Authors: Costantini Erica , Sinjari Bruna , Di Giovanni Pamela , Aielli Lisa , Caputi Sergio , Muraro Raffaella , Murmura Giovanna , Reale Marcella 
Published: January 2023

AbstractPeriodontitis is one of the main frequent intraoral diseases. Pathogenesis triggers are the immune responses with pro-inflammatory cytokines production and non-coding RNAs expression. The purpose of the present study was to evaluate the involvement of selected miRNAs in various stages of periodontitis and their relationship with the levels of inflammatory mediators in gingival crevicular fluid (GCF). For this study, 36 subjects (21 with periodontal disease, 15 healthy controls) were selected with an age mean of 59.1 ± 3.7 years. Clinical parameters included plaque index, gingival index, sulcus bleeding index, pocket depth, and clinical attachment level. The GCF samples were taken using capillary paper. The levels of miRNAs in GCF were estimated using a Real-Time PCR and TNFα and IL-6 levels were assessed by enzyme-linked immunosorbent assay (ELISA). The results indicated that the miRNA-103a-3p, miRNA-23a-3p, miRNA-15a-5p, and miRNA-223-3p were significantly upregulated with respect to healthy controls. Significant differences were observed for miRNA-23a-3p, miRNA-103a-3p and miRNA-423-5p levels in accord with the disease stages. Inflammatory mediators evaluated in GCF correlate well with the clinical parameters and the severity of the periodontal disease. miRNAs can represent biomarkers of disease stage and can be investigated as a possible therapeutic target, as well as levels of TNFα and IL-6 may drive the disease progression by acting as prognostic markers.
Development, preparation, and evaluation of a novel non-adjuvanted polyvalent dermatophytes vaccine
Authors: Abo-Elyazeed Heidy , Soliman R. , Hassan H. , El-Seedy F. R. , Aboul-Ella Hassan 
Published: January 2023

AbstractRingworm is a worldwide distributed contagious disease infecting both man and animals that constitute an economic, zoonotic, and health problem concern all over the world. During the last decade, attention has been directed to vaccination as an ideal approach to the control of such diseases. In the present study, non-adjuvanted polyvalent vaccines were prepared from locally isolated hot and virulent dermatophyte species, namelyTrichophyton verrucosum(T. verrucosum), Trichophyton mentagrophytes(T. mentagrophytes), andMicrosporum canis(M. canis) were immunologically evaluated.The prepared vaccine evaluation was focused on the aspects of immunogenicity and protective efficacy using guinea pigs. Both in its living or inactivated forms, the vaccine-induced significant humoral and cell-mediated immune responses and achieve proper protection of guinea pigs against challenging infections with homologous and heterologous dermatophyte strains. On the other hand, investigations on dermatophyte exo-keratinases showed that it was better produced and more expressed in a mineral-based medium containing pure keratin (3 g/L) than in the same medium with human hair supplementation (2.6 g/L). The maximum dermatophyte productivity of exo-keratinases was found to be between 18 and 21 days post-incubation. Using sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE), two fractions with molecular weights of 40 kDa (fraction I) and 28 kDa (fraction II) have been identified in the culture filtrate of the three involved dermatophyte species. Both fractions demonstrated keratinolytic activity. The specific activity of the isolated keratinases (number of Keratinase units (KU)/mg protein) was stronger in fraction I, where it reached 18.75, 15.38, and 14 KU/mg protein as compared to 12.9, 8.74, and 12 KU/mg protein in fraction II ofT. verrucosum, T. mentagrophytes, and M. canis, respectively. The dermatophyte exo-keratinases proved to be immunogenic as they stimulated high keratinase-specific antibody titers and induced strong delayed skin hypersensitivity reactions in vaccinated animals. Anti-keratinase-specific IgG was detected in sera of guinea pigs immunized with the inactivated or living polyvalent dermatophyte vaccines by a homemade enzyme-linked immunosorbent assay (ELISA) using dermatophyte exo-keratinases as coating antigen. The intradermal injection of dermatophyte exo-keratinases induced specific delayed skin reactions in guinea pigs immunized with the inactivated or the living polyvalent dermatophyte vaccines. The intradermal injection of dermatophyte exo-keratinases in the control non-sensitized guinea pigs was associated with itching, swelling, and bloody scar formation, however, no skin indurations were formed. The development of those post-exo-keratinases injection reactions in the control non-sensitized apparently healthy guinea pigs group, suggests an exo-keratinases possible role in the pathogenesis of dermatophytosis.
IL-4Rα signalling in B cells and T cells play differential roles in acute and chronic atopic dermatitis
Authors: Scibiorek Martyna , Mthembu Nontobeko , Mangali Sandisiwe , Ngomti Amkele , Ikwegbue Paul , Brombacher Frank , Hadebe Sabelo 
Published: January 2023

AbstractAtopic dermatitis (AD) is a common pruritic inflammatory skin disease with complex environmental and genetic predisposing factors. Primary skin barrier dysfunction and aberrant T helper 2 (TH2) responses to common allergens, together with increased serum IgE antibodies, characterise the disease. B and T cells are essential in the disease manifestation, however, the exact mechanism of how these cells is involved is unclear. Targeting interleukin 4 receptor alpha (IL-4Rα), an IL-4/IL-13 signalling axis, with dupilumab shows efficacy in AD. We investigated the importance of IL-4Rα signalling specifically on B and T cells during acute and chronic models of AD. We used House dust mite (HDM) and Ovalbumin (OVA) in chronic models and a low-calcemic analog of vitamin D (MC903) for acute models of AD. We used mb1creIL-4Rα−/lox, iLCKcreIL-4Rα−/lox, LCKcreIL-4Rα−/lox, CD4creIL-4Rα−/lox, Foxp3creIL-4Rα−/lox and IL-4Rα−/lox littermate controls. IL-4Rα-responsive B cells were essential in serum IgE levels, but not in epidermal thickening in both chronic and acute models. IL-4Rα-responsive T cells were essential in epidermal thickening in the pan-T cell, but not CD4 or CD8 T cells suggesting the importance of γδT cells during acute AD. Our results suggest that IL-4Rα responsiveness on innate T cells regulates acute atopic dermatitis, while on B cells it regulates IgE.