bluuebunny/crossref_metadata_2025 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

Realising 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

Recently, 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

The 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

The 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

Cropland 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

DNA 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

Machine 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

Numerous 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

This 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

The 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

A 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

Periodontitis 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

Ringworm 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

Atopic 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.
Myzomyia and Pyretophorus series of Anopheles mosquitoes acting as probable vectors of the goat malaria parasite Plasmodium caprae in Thailand
Authors: Nguyen Anh Hoang Lan , Pattaradilokrat Sittiporn , Kaewlamun Winai , Kaneko Osamu , Asada Masahito , Kaewthamasorn Morakot
Published: January 2023

Unlike malaria parasites in humans, non-human primates, rodents, and birds, ungulate malaria parasites and their vectors have received little attention. As a result, understanding of the hosts, vectors, and biology of ungulate malaria parasites has remained limited. In this study, we aimed to identify the vectors of the goat malaria parasite Plasmodium caprae. A total of 1019 anopheline and 133 non-anopheline mosquitoes were collected from goat farms in Thailand, where P. caprae-infected goats were discovered. Anopheline mosquitoes were identified using molecular biological methods that target the cytochrome c oxidase subunit 1 (cox1), the cytochrome c oxidase subunit 2 (cox2) genes, and the internal transcribed spacer 2 (ITS2) region. Pool and individual mosquitoes were tested for P. caprae using the head-thorax parts that contain the salivary glands, with primers targeting three genetic markers including cytochrome b, cytochrome c oxidase subunit 1, and 18S small subunit ribosomal RNA genes. Additionally, goat blood samples were collected concurrently with mosquito surveys and screened to determine the status of malaria infection. This study revealed nine mosquito species belonging to six groups on goat farms, including Hyrcanus, Barbirostris, Subpictus, Funestus, Tessellatus, and Annularis. The DNA of P. caprae was detected in Anopheles subpictus and Anopheles aconitus. This is the first time An. subpictus and An. aconitus have been implicated as probable vectors of P. caprae.
Addressing diffusion behavior and impact in an epoxy–amine cure system using molecular dynamics simulations
Authors: Kwon Sung Hyun , Kang Haisu , Kim Byeong-Joo , Lee Hyung Ik , Lee Jung Min , Kim Jungchul , Lee Seung Geol
Published: January 2023

To deepen understanding of diffusion-controlled crosslinking, molecular dynamics (MD) simulations are carried out by taking the diffusion image of 3,3′-diamino diphenyl sulfone (3,3′-DDS) and polyethersulfone (PES) with epoxy resin varying temperatures from 393.15 to 473.15 K over crosslinking conversion of 0–85%. The diffusion of PES and 3,3′-DDS into the bulk increased with increasing the temperature as a result of enhanced mobility of the molecules when the difference between the glass-transition temperature (Tg) and the curing temperature. Beyond the onset points of the converged crosslinking conversion ratio of 3,3′-DDS and PES, their diffusion properties are obviously restricted with crosslinking conversion ratio. At low crosslinking conversion ratios (> 10%), the diffusion coefficients of triglycidyl p-aminophenol (TGAP) were 1.1 times higher than those of diglycidyl ether of bisphenol F (DGEBF) because of the lower molecular weight of TGAP. On the other hand, the diffusion coefficients of TGAP decreased when the crosslinking ratio was up to ~ 60% because, compared with DGEBF, it had more functional groups available to react with the curing agent. At higher crosslinking ratios, the diffusion coefficients of both resins converged to zero as a result of their highly crosslinked structures.
Protective effects of hesperidin in cyclophosphamide-induced parotid toxicity in rats
Authors: Mostafa Ola A. Abdelwahab , Ibrahim Fatma , Borai Eman
Published: January 2023

Cyclophosphamide (CYP) is an alkylating agent that is used on a wide range as a treatment of malignancies and autoimmune diseases. Previous studies have shown the promising role of hesperidin (HSP) as an antioxidant agent against various models of toxic agents. The protective effect of the HSP against CYP-induced parotid damage was evaluated in this study. Forty rats (180–200 g) were divided into four equal groups: Group I (received normal saline), Group II (HSP-treated at a dose of 100 mg/kg/day for 7 consecutive days), Group III (CYP-treated at a dose of 200 mg/kg single intraperitoneal injection on the 7th day of the experiment), Group IV (CYP + HSP); HSP-treated at a dose of 100 mg/kg/day for 7 consecutive days and CYP (200 mg/kg) single intraperitoneal injection on the 7th day of the experiment. Afterwards, the oxidative stress and inflammatory markers, the histopathological and immunohistochemical alterations of the parotid tissues in the studied groups were evaluated. CYP intoxication induced a significant parotid tissue injury represented by the elevation in the values of malondialdehyde (MDA), tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) and decrease in the catalase activity and glutathione peroxidase (GPx). Histologically, extensive histopathological alterations e.g., widely spaced serous acini with irregular shapes and congested blood vessels as well as downregulated ki-67 and alpha-smooth muscle actin (α-SMA) immunoexpression were induced by CYP. HSP administration markedly improved the biochemical and the histopathological studies. We can conclude that HSP elicited protective effects against the CYP-induced parotid toxicity.
Prevalence and associated factors of physical inactivity among adult diabetes mellitus patients in Felege Hiwot Referral Hospital, Bahir Dar, Northwest Ethiopia
Authors: Enyew Addis , Nigussie Kalkidan , Mihrete Tewodros , Jemal Musa , kedir Shemsu , Alemu Emana , Mohammed Bekri
Published: January 2023

Physical inactivity has been viewed as an emerging public health problem in developing countries including Ethiopia. Diabetes mellitus (DM) is a group metabolic disorder characterized by chronic hyperglycemia resulting from defects in insulin secretion, function, or both. Its prevalence increases with changing lifestyles including physical inactivity across the globe. However, there is limited research, and not yet received attention in Ethiopia. This study aimed to assess the prevalence and associated factors of physical inactivity among adult diabetic patients in Felege Hiwot Referral Hospital, Bahir Dar, Northwest Ethiopia. An institutional-based cross-sectional study design was conducted among 308 participants from February to June 2018 at Felege Hiwot Referral Hospital. A face-to-face interview was conducted using a structured questionnaire by trained data collectors. Participants were selected through a systematic random sampling technique. Physical inactivity was assessed by the international physical activity questionnaire (IPAQ). Collected data were entered in Epi info version 7 and transferred to SPSS version 20 for analysis. A summary of descriptive statistics and multiple binary logistic regression analyses were computed to identify associated factors of physical inactivity among adult diabetic patients. P < 0.05 with 95% CI was considered statistically significant. The overall prevalence of physical inactivity among diabetic patients was 30.5% ( 95% CI: 22.8–33.5%). Gender (AOR = 1.5, 95% CI: 1.1, 3.62), Old age (AOR = 18.17, 95% CI: 22.7, 61.9) Residence (AOR = 4.24, 95% CI: 1,12,16.028), Low self-efficacy (AOR = 20.59, 95% CI: 10.598, 41.608), Poor attitude (AOR = 2.75, 95%CI: 1.44,5.28), and Lack of social support (AOR = 4.22, 95% CI: 1.28,4.07) were found significantly predictor factors of physical inactivity. The prevalence of physical inactivity in this study was high. Being female, old age, dwelling in an urban, having low efficacy, poor attitude, and lack of social support was greater risk factors for being physically inactive. Diabetic education should focus on engagement in physical activity by overcoming barriers to performing physical activity. Government and health professionals should emphasize that evidence-based physical activity important to change their attitudes and require reaching a consensus on social support by their families.
Reliability of the active knee joint position sense test and influence of limb dominance and sex
Authors: Busch Aglaja , Bangerter Christian , Mayer Frank , Baur Heiner
Published: January 2023

The output of a sensorimotor performance can be measured with the joint position sense (JPS) test. However, investigations of leg dominance, sex and quality measures on this test are limited. Therefore, these potential influencing factors as well as reliability and consistency measures were evaluated for angular reproduction performance and neuromuscular activity during the active knee JPS test in healthy participants. Twenty healthy participants (10 males; 10 females; age 29 ± 8 years; height 165 ± 39 cm; body mass 69 ± 13 kg) performed a seated knee JPS test with a target angle of 50°. Measurements were conducted in two sessions separated by two weeks and consisted of two blocks of continuous angular reproduction (three minutes each block). The difference between reproduced and target angle was identified as angular error measured by an electrogoniometer. During reproduction, the neuromuscular activity of the quadriceps muscle was assessed by surface electromyography. Neuromuscular activity was normalized to submaximal voluntary contraction (subMVC) and displayed per muscle and movement phase. Differences between leg dominance and sex were calculated using Friedman-test (α = 0.05). Reliability measures including intraclass correlation coefficient (ICC), Bland–Altman analysis (bias ± limits of agreement (LoA)) and minimal detectable change (MDC) were analysed. No significant differences between leg dominance and sex were found in angular error and neuromuscular activity. Angular error demonstrated inter-session ICC scores of 0.424 with a bias of 2.4° (± 2.4° LoA) as well as MDC of 6.8° and moderate intra-session ICC (0.723) with a bias of 1.4° (± 1.65° LoA) as well as MDC of 4.7°. Neuromuscular activity for all muscles and movement phases illustrated inter-session ICC ranging from 0.432 to 0.809 with biases between − 2.5 and 13.6% subMVC and MDC from 13.4 to 63.9% subMVC. Intra-session ICC ranged from 0.705 to 0.987 with biases of − 7.7 to 2.4% subMVC and MDC of 2.7 to 46.5% subMVC. Leg dominance and sex seem not to influence angular reproduction performance and neuromuscular activity. Poor to excellent relative reliability paired with an acceptable consistency confirm findings of previous studies. Comparisons to pathological populations should be conducted with caution.
Emotional face recognition when a colored mask is worn: a cross-sectional study
Authors: Gil Sandrine , Le Bigot Ludovic
Published: January 2023

Studies of the impact of face masks on emotional facial expression recognition are sparse in children. Moreover, to our knowledge no study has so far considered mask color (in adults and in children), even though this esthetic property is thought to have an impact on information processing. In order to explore these issues, the present study looked at whether first- and fifth-graders and young adults were influenced by the absence or presence (and color: pink, green, red, black, or white) of a face mask when asked to judge emotional facial expressions of fear, anger, sadness, or neutrality. Analysis of results suggested that the presence of a mask did affect the recognition of sad or fearful faces but did not influence significantly the perception of angry and neutral faces. Mask color slightly modulated the recognition of facial emotional expressions, without a systematic pattern that would allow a clear conclusion to be drawn. Moreover, none of these findings varied according to age group. The contribution of different facial areas to efficient emotion recognition is discussed with reference to methodological and theoretical considerations, and in the light of recent studies.
Absorption of pressurized methane in normal and supercooled p-xylene revealed via high-resolution neutron imaging
Authors: Vopička Ondřej , Durďáková Tereza-Markéta , Číhal Petr , Boillat Pierre , Trtik Pavel
Published: January 2023

Supercooling of liquids leads to peculiarities which are scarcely studied under high-pressure conditions. Here, we report the surface tension, solubility, diffusivity, and partial molar volume for normal and supercooled liquid solutions of methane withp-xylene. Liquid bodies of perdeuteratedp-xylene (p-C8D10), and, for comparison,o-xylene (o-C8D10), were exposed to pressurized methane (CH4, up to 101 bar) at temperatures ranging 7.0–30.0 °C and observed at high spatial resolution (pixel size 20.3 μm) using a non-tactile neutron imaging method. Supercooling led to the increase of diffusivity and partial molar volume of methane. Solubility and surface tension were insensitive to supercooling, the latter substantially depended on methane pressure. Overall, neutron imaging enabled to reveal and quantify multiple phenomena occurring in supercooled liquidp-xylene solutions of methane under pressures relevant to the freeze-out in the production of liquefied natural gas.
Dual-energy computed tomography as a lower radiation dose alternative to perfusion computed tomography in tumor viability assessment
Authors: Zegadło Arkadiusz , Różyk Aleksandra , Żabicka Magdalena , Więsik–Szewczyk Ewa , Maliborski Artur
Published: January 2023

To present the utility of dual-energy computed tomography (DECT) in the assessment of angiogenesis of focal lesions as an example of a solitary pulmonary nodule (SPN). This prospective study comprised 28 patients with SPN who underwent DECT and perfusion computed tomography (CTP), according to a proprietary protocol. Two radiologists independently analyzed four perfusion parameters, namely blood flow (BF), blood volume (BV), the time to maximum of the tissue residue function (Tmax), permeability surface area product (PS) from CTP, in addition to the iodine concentration (IC) and normalized iodine concentration (NIC) of the SPN from DECT. We used the Pearson R correlation and interclass correlation coefficients (ICCs). Statistical significance was assumed at p < 0.05. The mean tumor size was 23.5 ± 6.5 mm. We observed good correlations between IC and BF (r = 0.78, p < 0.000) and NIC and BF (r = 0.71, p < 0.000) as well as between IC and BV (r = 0.73, p < 0.000) and NIC and BV (r = 0.73, p < 0.000) and poor correlation between IC and PS (r = 0.38, p = 0.044).There was no correlation between NIC and PS (r = 0.35, p = 0.064), IC content and Tmax (r = − 0.28, p = 0.147) and NIC and Tmax (r = − 0.21, p = 0.266). Inter-reader agreement on quantitative parameters at CTP (ICCPS = 0.97, ICCTmax = 0.96, ICCBV = 0.98, and ICCBF = 0.99) and DECT (ICCIC = 0.98) were excellent. The radiation dose was significantly lower in DECT than that in CTP (4.84 mSv vs. 9.07 mSv, respectively). DECT is useful for the functional assessment of oncological lesions with less exposure to radiation compared to perfusion computed tomography.
Efficacy and safety of sitagliptin treatment in older adults with moderately controlled type 2 diabetes: the STREAM study
Authors: Nagao Mototsugu , Sasaki Jun , Sugihara Hitoshi , Tanimura-Inagaki Kyoko , Harada Taro , Sakuma Ichiro , Oikawa Shinichi ,   STREAM Study Investigators, Asano T. , Aoyama S. , Fukushima T. , Yan J. , Hasegawa O. , Hosokawa K. , Ishimaru Y. , Kaito H. , Kanbara R. , Kanno K. , Kimura K. , Moritani S. , Okuda T. , Okuma M. , Okumura T. , Omuro H. , Sawayama Y. , Shuto H. , Tanaka J. , Tada T. , Tateoka K. , Terada T. , Tsuzuki H. , Yamada M.
Published: January 2023

Sitagliptin has been suggested as a treatment option for older adults with type 2 diabetes (T2D). However, no randomized controlled trial has been performed to evaluate the efficacy and safety of sitagliptin treatment in older Japanese patients with T2D. The STREAM study was a multicenter, open-label, randomized controlled trial. T2D outpatients aged 65–80 years with moderately controlled glycemic levels (HbA1c 7.4–10.4%) under lifestyle interventions without or with oral anti-diabetic drugs excluding DPP4 inhibitors or GLP-1 receptor agonists were recruited (n = 176). The participants were randomized into sitagliptin group (n = 88) who received sitagliptin as an initial or an additive anti-diabetic drug and control group (n = 88) who did not. The treatment goal was HbA1c level < 7.4%. Efficacy and safety during 12-month treatment period were investigated. The mean (± SD) ages were 70.6 ± 3.9 and 71.9 ± 4.4 years old in sitagliptin and control groups, respectively. According to a mixed-effects model analysis, average changes from baseline over the treatment period in fasting plasma glucose (FPG), HbA1c, and glycated albumin (GA) were − 27.2 mg/dL, − 0.61%, and − 2.39%, respectively, in sitagliptin group, and 0.50 mg/dL, − 0.29%, and − 0.93%, respectively, in control group. The reductions in FPG, HbA1c, and GA were significantly greater in sitagliptin group (P < 0.0001, P < 0.01, and P < 0.0001, respectively). There were no differences in the incidence of adverse effects, except for cystatin C elevation and platelet count reduction in sitagliptin group. Sitagliptin treatment effectively improved the glycemic profile without any serious adverse effects in older T2D patients.

Trial registration number: UMIN000010376.
Tubule-U-Net: a novel dataset and deep learning-based tubule segmentation framework in whole slide images of breast cancer
Authors: Tekin Eren , Yazıcı Çisem , Kusetogullari Huseyin , Tokat Fatma , Yavariabdi Amir , Iheme Leonardo Obinna , Çayır Sercan , Bozaba Engin , Solmaz Gizem , Darbaz Berkan , Özsoy Gülşah , Ayaltı Samet , Kayhan Cavit Kerem , İnce Ümit , Uzel Burak
Published: January 2023

The tubule index is a vital prognostic measure in breast cancer tumor grading and is visually evaluated by pathologists. In this paper, a computer-aided patch-based deep learning tubule segmentation framework, named Tubule-U-Net, is developed and proposed to segment tubules in Whole Slide Images (WSI) of breast cancer. Moreover, this paper presents a new tubule segmentation dataset consisting of 30820 polygonal annotated tubules in 8225 patches. The Tubule-U-Net framework first uses a patch enhancement technique such as reflection or mirror padding and then employs an asymmetric encoder-decoder semantic segmentation model. The encoder is developed in the model by various deep learning architectures such as EfficientNetB3, ResNet34, and DenseNet161, whereas the decoder is similar to U-Net. Thus, three different models are obtained, which are EfficientNetB3-U-Net, ResNet34-U-Net, and DenseNet161-U-Net. The proposed framework with three different models, U-Net, U-Net++, and Trans-U-Net segmentation methods are trained on the created dataset and tested on five different WSIs. The experimental results demonstrate that the proposed framework with the EfficientNetB3 model trained on patches obtained using the reflection padding and tested on patches with overlapping provides the best segmentation results on the test data and achieves 95.33%, 93.74%, and 90.02%, dice, recall, and specificity scores, respectively.
Insight into pathway of monosaccharide production from integrated enzymatic hydrolysis of rice straw waste as feed stock for anaerobic digestion
Authors: Khantibongse Piyathida , Ratanatamskul Chavalit
Published: January 2023

This research examined the possible pathway of monosaccharide production from the rice straw waste using three integrated enzymatic hydrolysis approaches: boiled hot water pre-treatment with enzyme, alkaline pre-treatment with enzyme, and acid pre-treatment with enzyme, that can be further used as the feedstock for anaerobic digestion. Two cellulase enzymes: SIGMA-ALDRICH laboratory grade cellulase from Aspergillus niger and atres Zymix plus as a commercial cellulase enzyme were applied. It was found that the boiled hot water pre-treatment with the commercial cellulase gave the highest total monosaccharides yields. Glucose was the most significant part (78–86%) of the monosaccharides. For the pre-treatment with dilute acid, glucose was also the main component of monosaccharides; however, for the alkali pre-treatment, xylose was the main monosaccharide. It made up 48–85% of the total monosaccharide compared to glucose that made up 5–49% of total monosaccharide. Boiled rice straw with commercial cellulase enzyme provided the highest glucose yield compared to other experiments. Moreover, the obtained results from GC–MS/MS analysis show that up to 62 species of phenolic compound could be found in enzymatic hydrolysis of the rice straw waste. Aromatic and aliphatic hydrocarbon substances were also detected in the FEEM analysis. From the overall results, the integrated enzymatic hydrolysis with boil hot water pre-treatment was the most efficient method for monosaccharide production from the rice straw waste.
CNTNAP4 signaling regulates osteosarcoma disease progression
Authors: Qin Qizhi , Ramesh Sowmya , Gomez-Salazar Mario , Zhong Lingke , Cherief Masnsen , Pratapneni Aniket , Morris Carol D. , McCarthy Edward F. , Zhang Xinli , James Aaron W.
Published: January 2023

Improved treatment strategies for sarcoma rely on clarification of the molecular mediators of disease progression. Recently, we reported that the secreted glycoprotein NELL-1 modulates osteosarcoma (OS) disease progression in part via altering the sarcomatous extracellular matrix (ECM) and cell-ECM interactions. Of known NELL-1 interactor proteins, Contactin-associated protein-like 4 (Cntnap4) encodes a member of the neurexin superfamily of transmembrane molecules best known for its presynaptic functions in the central nervous system. Here, CRISPR/Cas9 gene deletion of CNTNAP4 reduced OS tumor growth, sarcoma-associated angiogenesis, and pulmonary metastases. CNTNAP4 knockout (KO) in OS tumor cells largely phenocopied the effects of NELL-1 KO, including reductions in sarcoma cell attachment, migration, and invasion. Further, CNTNAP4 KO cells were found to be unresponsive to the effects of NELL-1 treatment. Transcriptomic analysis combined with protein phospho-array demonstrated notable reductions in the MAPK/ERK signaling cascade with CNTNAP4 deletion, and the ERK1/2 agonist isoproterenol restored cell functions among CNTNAP4 KO tumor cells. Finally, human primary cells and tissues in combination with sequencing datasets confirmed the significance of CNTNAP4 signaling in human sarcomas. In summary, our findings demonstrate the biological importance of NELL-1/CNTNAP4 signaling axis in disease progression of human sarcomas and suggest that targeting the NELL-1/CNTNAP4 signaling pathway represents a strategy with potential therapeutic benefit in sarcoma patients.
Transmembrane protein 135 regulates lipid homeostasis through its role in peroxisomal DHA metabolism
Authors: Landowski Michael , Bhute Vijesh J. , Grindel Samuel , Haugstad Zachary , Gyening Yeboah K. , Tytanic Madison , Brush Richard S. , Moyer Lucas J. , Nelson David W. , Davis Christopher R. , Yen Chi-Liang Eric , Ikeda Sakae , Agbaga Martin-Paul , Ikeda Akihiro
Published: January 2023

Transmembrane protein 135 (TMEM135) is thought to participate in the cellular response to increased intracellular lipids yet no defined molecular function for TMEM135 in lipid metabolism has been identified. In this study, we performed a lipid analysis of tissues from Tmem135 mutant mice and found striking reductions of docosahexaenoic acid (DHA) across all Tmem135 mutant tissues, indicating a role of TMEM135 in the production of DHA. Since all enzymes required for DHA synthesis remain intact in Tmem135 mutant mice, we hypothesized that TMEM135 is involved in the export of DHA from peroxisomes. The Tmem135 mutation likely leads to the retention of DHA in peroxisomes, causing DHA to be degraded within peroxisomes by their beta-oxidation machinery. This may lead to generation or alteration of ligands required for the activation of peroxisome proliferator-activated receptor a (PPARa) signaling, which in turn could result in increased peroxisomal number and beta-oxidation enzymes observed in Tmem135 mutant mice. We confirmed this effect of PPARa signaling by detecting decreased peroxisomes and their proteins upon genetic ablation of Ppara in Tmem135 mutant mice. Using Tmem135 mutant mice, we also validated the protective effect of increased peroxisomes and peroxisomal beta-oxidation on the metabolic disease phenotypes of leptin mutant mice which has been observed in previous studies. Thus, we conclude that TMEM135 has a role in lipid homeostasis through its function in peroxisomes.
Effects ofNemacystus decipienspolysaccharide on mice with antibiotic associated diarrhea and colon inflammation
Authors: Pan Haoyu , Chen Xia , Wang PeiPei , Peng Junfeng , Li Judong , Ding Kan
Published: January 2023

Antibiotic associated diarrhea (AAD) is a common side effect of antibiotic therapy in which gut microbiota plays an important role in the disease.
MIP integrated surface plasmon resonance in vitro detection of sodium benzoate
Authors: Maurya Pratiksha , Verma Roli
Published: January 2023

We report a Kretschmann-based SPR sensor for the detection of sodium benzoate using the molecularly imprinted polymer (MIP) method over silver-coated SF-11 glass.
Investigation of metal modulation of oxytocin structure receptor-mediated signaling
Authors: O’Sullivan Justin J. , Uyeda Kylie S. , Stevenson Michael J. , Heffern Marie C.
Published: January 2023

Oxytocin and a library of analogs show metal-dependent modulation of MAPK activation in oxytocin-receptor-expressing HEK293 cells.