bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenges in the implementation of food safety and quality assurance systems in small-scale fisheries
Authors: GarridoGamarro Esther , Svanevik Cecilie Smith , Lundebye Anne-Katrine , Sanden Monica , D’Agostino Enrica , Kjellevold Marian , Pincus Lauren , Pucher Johannes 
Published: January 2023

AbstractNinety percent of the world’s fishers are directly involved in small-scale fisheries (SSFs), and many food safety and quality issues along the food value chains may be both irreversible and cumulative. Ensuring safe, high-quality aquatic products are key to sustaining life, promoting good health, and avoiding adverse health effects.ObjectiveThis paper aimed to highlight factors preventing the implementation of safety and quality assurance systems in SSFs by analysing the results from surveys on the implementation of Article 11 of the Food and Agriculture Organization of the United Nations (FAO) Code of Conduct for Responsible Fisheries (2017, 2019, and 2022).Materials and methodsThe analysis considered responses to 15 closed-ended questions on food safety and quality obtained from 143 FAO Members and the European Union, and 87 open-ended replies addressing challenges in SSFs.ResultsThe major factors preventing the implementation of the Code’s food safety and quality provisions were lack of sanitation and monitoring programmes, lack of infrastructure (particularly refrigeration facilities) lack of technical capacities and limited management of food safety risks along the value chains. Safety and quality assurance efforts were focused on international markets, resulting in less attention being paid to domestic markets where a high degree of informality was reported.ConclusionsImproved implementation of safety and quality assurance systems will lead to safer food with higher nutritional quality, extended shelf-life and reduced post-harvest loss. Increased awareness of food safety issues in SSFs is a prerequisite for achieving several of the UN Sustainable Development Goals.
Involvement of the Streptococcus mutans PgfE and GalE 4-epimerases in protein glycosylation, carbon metabolism, and cell division
Authors: Andresen Silke , de Mojana di Cologna Nicholas , Archer-Hartmann Stephanie , Rogers Ashley M , Samaddar Sandip , Ganguly Tridib , Black Ian M , Glushka John , Ng Kenneth K S , Azadi Parastoo , Lemos José A , Abranches Jacqueline , Szymanski Christine M 
Published: January 2023

Abstract
Streptococcus mutans is a key pathogen associated with dental caries and is often implicated in infective endocarditis. This organism forms robust biofilms on tooth surfaces and can use collagen-binding proteins (CBPs) to efficiently colonize collagenous substrates, including dentin and heart valves. One of the best characterized CBPs of S. mutans is Cnm, which contributes to adhesion and invasion of oral epithelial and heart endothelial cells. These virulence properties were subsequently linked to post-translational modification (PTM) of the Cnm threonine-rich repeat region by the Pgf glycosylation machinery, which consists of 4 enzymes: PgfS, PgfM1, PgfE, and PgfM2. Inactivation of the S. mutans pgf genes leads to decreased collagen binding, reduced invasion of human coronary artery endothelial cells, and attenuated virulence in the Galleria mellonella invertebrate model. The present study aimed to better understand Cnm glycosylation and characterize the predicted 4-epimerase, PgfE. Using a truncated Cnm variant containing only 2 threonine-rich repeats, mass spectrometric analysis revealed extensive glycosylation with HexNAc2. Compositional analysis, complemented with lectin blotting, identified the HexNAc2 moieties as GlcNAc and GalNAc. Comparison of PgfE with the other S. mutans 4-epimerase GalE through structural modeling, nuclear magnetic resonance, and capillary electrophoresis demonstrated that GalE is a UDP-Glc-4-epimerase, while PgfE is a GlcNAc-4-epimerase. While PgfE exclusively participates in protein O-glycosylation, we found that GalE affects galactose metabolism and cell division. This study further emphasizes the importance of O-linked protein glycosylation and carbohydrate metabolism in S. mutans and identifies the PTM modifications of the key CBP, Cnm.
Association between exposure to combustion-related air pollution and multiple sclerosis risk
Authors: Hedström Anna Karin , Segersson David , Hillert Jan , Stridh Pernilla , Kockum Ingrid , Olsson Tomas , Bellander Tom , Alfredsson Lars 
Published: January 2023

Abstract

Background
Smoking and occupational pulmonary irritants contribute to multiple sclerosis (MS) development. We aimed to study the association between ambient air pollution and MS risk and potential interaction with the human leukocyte antigen (HLA)-DRB1*15:01 allele.

Methods
Exposure to combustion-related air pollution was estimated as outdoor levels of nitrogen oxides (NOx) at the participants’ residence locations, by spatially resolved dispersion modelling for the years 1990–18. Using two population-based case-control studies (6635 cases, 8880 controls), NOx levels were associated with MS risk by calculating odds ratios (OR) with 95% confidence intervals (CI) using logistic regression models. Interaction between high NOx levels and the HLA-DRB1*15:01 allele regarding MS risk was calculated by the attributable proportion due to interaction (AP). In addition, a register study was performed comprising all MS cases in Sweden who had received their diagnosis between 1993 and 2018 (n = 22 173), with 10 controls per case randomly selected from the National Population register.

Results
Residential air pollution was associated with MS risk. NOx levels (3-year average) exceeding the 90th percentile (24.6 µg/m3) were associated with an OR of 1.37 (95% CI 1.10–1.76) compared with levels below the 25th percentile (5.9 µg/m3), with a trend of increasing risk of MS with increasing levels of NOx (P &lt;0.0001). A synergistic effect was observed between high NOx levels (exceeding the lower quartile among controls) and the HLA-DRB1*15:01 allele regarding MS risk (AP 0.26, 95% CI 0.13–0.29).

Conclusions
Our findings indicate that moderate levels of combustion-related ambient air pollution may play a role in MS development.
Corrigendum: A geometric model for the module category of a gentle algebra
Authors: Baur Karin , Coelho Simões Raquel 
Published: January 2023

Abstract
In this note we correct an oversight in [A geometric model for the module category of a gentle algebra, Int. Math. Res. Not. IMRN 2021, no. 15, 11357–11392] regarding morphisms between indecomposable modules of a gentle algebra. The oversight only occurs when bands are involved, which can be easily corrected by considering infinite periodic strings associated to bands and the universal cover of the surface associated to the gentle algebra.
The effect of CO2 concentration on yeast fermentation: rates, metabolic products, and yeast stress indicators
Authors: Guadalupe-Daqui Mario , Goodrich-Schneider Renee M , Sarnoski Paul J , Carriglio John C , Sims Charles A , Pearson Brian J , MacIntosh Andrew J 
Published: January 2023

Abstract

This research aimed to assess how the partial removal of carbon dioxide affects fermentations to provide a better understanding of how the manipulation of carbon dioxide concentration can be used to optimize industrial fermentations. To achieve this, fermentation kinetics, fermentation metabolic products, and yeast stress indicators were analyzed throughout ongoing brewing fermentations conducted under partial vacuum with atmospheric pressure controls. The partial vacuum reduced the solubility of carbon dioxide in the media and decreased the time necessary to reach carbon dioxide saturation. The effect was an increased rate of fermentation, and significantly more viable cells produced under vacuum pressure compared to controls. Ethanol, glycerol, and volatile organic compound concentrations were all significantly increased under partial vacuum, while indicators of yeast stress (trehalose) were reduced. Additionally, as the number of yeast cells was higher under partial vacuum, less sugar was consumed per volume of yeast cell. This study measured fermentation kinetics, metabolic products, and yeast health to holistically assess the effect of partial vacuum during a batch fermentation and found significant differences in each that can be individually exploited by researchers and industry.

Summary
An exploration of batch yeast fermentation in a low-pressure environment, with a focus on the health and productivity of the yeast cells.
Aboveground carbon sequestration rate in alpine forests on the eastern Tibetan Plateau: impacts of future forest management options
Authors: Lin Yang , Xiao Jiang-Tao , Kou Yong-Ping , Zu Jia-Xing , Yu Xin-Ran , Li Yuan-Yuan 
Published: January 2023

AbstractAlpine forests in the eastern Tibetan Plateau are important ecological barriers in the upper reaches of the Yangtze River. However, due to continuous high-intensity harvesting, a large number of plantings, and the complete harvesting ban measures in recent decades, the forest tree species and age cohorts have become relatively homogenous, and the biodiversity and ecological functions have been reduced. To design effective forest management options to optimize forest structure and increase carbon sequestration capacity, Mao County in Sichuan Province was selected as the study site and six forest management options (harvesting, planting) of different intensities were tested using the LANDIS-II model to simulate and compare the differences in forest aboveground carbon sequestration rate (ACSR) between these options and the current management option over the next 100 years. Our results showed that (i) the different harvesting and planting intensities significantly changed the ACSR compared with the current management options; (ii) different communities responded differently to the management options, with the ACSR differing significantly in cold temperate conifers and temperate conifers but not in broad-leaved trees (P &lt; 0.05); and (iii) a comprehensive consideration of forest management options at the species, community and landscape levels was necessary. Our results suggest that implementing a longer harvesting and planting interval (20 years) at the study site can maximize forest ACSR. This study provides an important reference for evaluating the ability of forest management options to restore forest ecological functions and increase carbon sequestration capacity and for selecting effective forest management programs in the eastern Tibetan Plateau.
Analysis of the chloroplast crotonylome of wheat seedling leaves reveals the roles of crotonylated proteins involved in salt-stress responses
Authors: Zhu Dong , Liu Junxian , Duan Wenjing , Sun Haocheng , Zhang Liping , Yan Yueming 
Published: January 2023

AbstractLysine crotonylation (Kcr) is a novel post-translational modification and its function in plant salt-stress responses remains unclear. In this study, we performed the first comprehensive chloroplast crotonylome analysis of wheat seedling leaves to examine the potential functions of Kcr proteins in salt-stress responses. In a total of 471 chloroplast proteins, 1290 Kcr sites were identified as significantly regulated by salt stress, and the Kcr proteins were mainly involved in photosynthesis, protein folding, and ATP synthesis. The identified Kcr sites that responded to salt stress were concentrated within KcrK and KcrF motifs, with the conserved KcrF motif being identified in the Kcr proteins of wheat chloroplasts for the first time. Notably, 10 Kcr sites were identified in fructose-1,6-bisphosphate aldolase (TaFBA6), a key chloroplast metabolic enzyme involved in the Calvin–Benson cycle. Site-directed mutagenesis of TaFBA6 showed that the Kcr at K367 is critical in maintaining its enzymatic activity and in conferring salt tolerance in yeast. Further molecular dynamic simulations and analyses of surface electrostatic potential indicated that the Kcr at K367 could improve the structural stability of TaFBA6 by decreasing the distribution of positive charges on the protein surface to resist alkaline environments, thereby promoting both the activity of TaFBA6 and salt tolerance.
Comparative phosphoproteomic analysis reveals that phosphorylation of sucrose synthase GhSUS2 by Ca2+-dependent protein kinases GhCPK84/93 affects cotton fiber development
Authors: Wang Yao , Li Yu , Cheng Fan , Zhang Shi-Peng , Zheng Yong , Li Yang , Li Xue-Bao 
Published: January 2023

AbstractCotton fiber elongation is a critical growth phase that affects final fiber length. Morphological analysis indicated an asynchronous fiber elongation pattern between two cotton varieties, J7-1 and J14-1. Through phosphoproteomic analysis, a total of 89 differentially-phosphorylated proteins (DPPs) were identified in elongating fibers between J7-1 and J14-1. Gene ontology (GO) analysis showed that these DPPs were mainly enriched in sucrose synthase activity, transferase activity, and UDP-glycosyltransferase activity. In J14-1, the phosphorylation level of GhSUS2, a key sucrose synthase in the sucrose metabolism pathway, was significantly higher than that in J7-1. We further revealed that GhSUS2 positively regulates fiber elongation, and GhSUS2-silenced transgenic cotton displayed the phenotype of ‘short fibers’ compared with the controls. During fiber development, the residue Ser11 in the GhSUS2 protein is phosphorylated by the Ca2+-dependent protein kinases GhCPK84 and GhCPK93. Phosphorylated GhSUS2 is localized in the cytoplasm, whereas unphosphorylated GhSUS2 is localized in the plasma membrane. Moreover, abscisic acid (ABA) could promote the transcription and translation of GhCPK84 and GhCPK93, thereby enhancing the phosphorylation of GhSUS2 to impede fiber elongation. Thus, our data demonstrates that GhSUS2 plays a positive role in fiber development, but its phosphorylation by GhCPK84 and GhCPK93 hinders fiber elongation of cotton.
A New Method for Evaluating the Accuracy of the Orientation Measured by Different Kikuchi Pole Combinations in Kikuchi Patterns
Authors: Peng Fan , Zhang Yongsheng , Li Wei , Miao Hong , Zeng Yi 
Published: January 2023

Abstract
In this study, high-precision coordinates of Kikuchi poles were obtained for orientation calculation by locating the lattice plane traces of Kikuchi patterns of stainless steel. Orientation can be measured by selecting three noncoincident Kikuchi poles in a Kikuchi pattern, and different combinations of Kikuchi poles provide different orientation solutions. The “deviation” defined in this study and the orientation calculation error of each combination are generally positively correlated. Therefore, the deviation can be used to evaluate the accuracy of the orientation calculation for each combination without the theoretical orientation, and can also be used as a criterion for selecting Kikuchi pole combinations for orientation calculations. The results show that the average misorientation angles for all combinations are 1.983° (orientation a), 2.768° (orientation b), and 2.175° (orientation c) before the screening of the Kikuchi pole combinations by deviation. For each pattern, the first five combinations with the smallest deviation are selected, and the average misorientation angles of these combinations are 0.791° (orientation a), 0.789° (orientation b), and 0.910° (orientation c). The orientation calculation errors are reduced by 60, 71, and 58%, respectively. The accuracy of the orientation calculation is greatly improved, thus avoiding the appearance of orientation solutions with large errors.
Micro- and Nanoscale Surface Analysis of Late Iron Age Glass from Broborg, a Vitrified Swedish Hillfort
Authors: Matthews Bethany E , Neeway James J , Farias Lorena Nava , Marcial José , Arey Bruce W , Soltis Jennifer , Kovarik Libor , Zhu Zihua , Schweiger Michael J , Canfield Nathan , Varga Tamas , Bowden Mark E , Weaver Jamie L , McCloy John S , Sjöblom Rolf , Hjärthner-Holdar Eva , Englund Mia , Ogenhall Erik , Vicenzi Edward P , Corkhill Claire L , Thorpe Clare , Hand Russell J , Peeler David K , Pearce Carolyn I , Kruger Albert A 
Published: January 2023

AbstractArchaeological glasses with prolonged exposure to biogeochemical processes in the environment can be used to understand glass alteration, which is important for the safe disposal of vitrified nuclear waste. Samples of mafic and felsic glasses with different chemistries, formed from melting amphibolitic and granitoid rocks, were obtained from Broborg, a Swedish Iron Age hillfort. Glasses were excavated from the top of the hillfort wall and from the wall interior. A detailed microscopic, spectroscopic, and diffraction study of surficial textures and chemistries were conducted on these glasses. Felsic glass chemistry was uniform, with a smooth surface showing limited chemical alteration (&lt;150 nm), irrespective of the position in the wall. Mafic glass was heterogeneous, with pyroxene, spinel, feldspar, and quartz crystals in the glassy matrix. Mafic glass surfaces in contact with topsoil were rougher than those within the wall and had carbon-rich material consistent with microbial colonization. Limited evidence for chemical or physical alteration of mafic glass was found; the thin melt film that coated all exposed surfaces remained intact, despite exposure to hydraulically unsaturated conditions, topsoil, and associated microbiome for over 1,500 years. This supports the assumption that aluminosilicate nuclear waste glasses will have a high chemical durability in near-surface disposal facilities.
Impact of instrument and data characteristics in the interferometric reconstruction of the 21 cm power spectrum
Authors: Gorce Adélie , Ganjam Samskruthi , Liu Adrian , Murray Steven G , Abdurashidova Zara , Adams Tyrone , Aguirre James E , Alexander Paul , Ali Zaki S , Baartman Rushelle , Balfour Yanga , Beardsley Adam P , Bernardi Gianni , Billings Tashalee S , Bowman Judd D , Bradley Richard F , Bull Philip , Burba Jacob , Carey Steven , Carilli Chris L , Cheng Carina , DeBoer David R , Acedo Eloy de Lera , Dexter Matt , Dillon Joshua S , Eksteen Nico , Ely John , Ewall-Wice Aaron , Fagnoni Nicolas , Fritz Randall , Furlanetto Steven R , Gale-Sides Kingsley , Glendenning Brian , Gorthi Deepthi , Greig Bradley , Grobbelaar Jasper , Halday Ziyaad , Hazelton Bryna J , Hewitt Jacqueline N , Hickish Jack , Jacobs Daniel C , Julius Austin , Kariseb MacCalvin , Kern Nicholas S , Kerrigan Joshua , Kittiwisit Piyanat , Kohn Saul A , Kolopanis Matthew , Lanman Adam , Plante Paul La , Loots Anita , MacMahon David Harold Edward , Malan Lourence , Malgas Cresshim , Malgas Keith , Marero Bradley , Martinot Zachary E , Mesinger Andrei , Molewa Mathakane , Morales Miguel F , Mosiane Tshegofalang , Neben Abraham R , Nikolic Bojan , Nuwegeld Hans , Parsons Aaron R , Patra Nipanjana , Pieterse Samantha , Pober Jonathan C , Razavi-Ghods Nima , Robnett James , Rosie Kathryn , Sims Peter , Swarts Hilton , Thyagarajan Nithyanandan , van Wyngaarden Pieter , Williams Peter K G , Zheng Haoxuan 
Published: January 2023

ABSTRACT
Combining the visibilities measured by an interferometer to form a cosmological power spectrum is a complicated process. In a delay-based analysis, the mapping between instrumental and cosmological space is not a one-to-one relation. Instead, neighbouring modes contribute to the power measured at one point, with their respective contributions encoded in the window functions. To better understand the power measured by an interferometer, we assess the impact of instrument characteristics and analysis choices on these window functions. Focusing on the Hydrogen Epoch of Reionization Array (HERA) as a case study, we find that long-baseline observations correspond to enhanced low-k tails of the window functions, which facilitate foreground leakage, whilst an informed choice of bandwidth and frequency taper can reduce said tails. With simple test cases and realistic simulations, we show that, apart from tracing mode mixing, the window functions help accurately reconstruct the power spectrum estimator of simulated visibilities. The window functions depend strongly on the beam chromaticity and less on its spatial structure – a Gaussian approximation, ignoring side lobes, is sufficient. Finally, we investigate the potential of asymmetric window functions, down-weighting the contribution of low-k power to avoid foreground leakage. The window functions presented here correspond to the latest HERA upper limits for the full Phase I data. They allow an accurate reconstruction of the power spectrum measured by the instrument and will be used in future analyses to confront theoretical models and data directly in cylindrical space.
ATR inhibition overcomes platinum tolerance associated with ERCC1- and p53-deficiency by inducing replication catastrophe
Authors: Heyza Joshua R , Ekinci Elmira , Lindquist Jacob , Lei Wen , Yunker Christopher , Vinothkumar Vilvanathan , Rowbotham Rachelle , Polin Lisa , Snider Natalie G , Van Buren Eric , Watza Donovan , Back Jessica B , Chen Wei , Mamdani Hirva , Schwartz Ann G , Turchi John J , Bepler Gerold , Patrick Steve M 
Published: January 2023

Abstract
ERCC1/XPF is a heterodimeric DNA endonuclease critical for repair of certain chemotherapeutic agents. We recently identified that ERCC1- and p53-deficient lung cancer cells are tolerant to platinum-based chemotherapy. ATR inhibition synergistically re-stored platinum sensitivity to platinum tolerant ERCC1-deficient cells. Mechanistically we show this effect is reliant upon several functions of ATR including replication fork protection and altered cell cycle checkpoints. Utilizing an inhibitor of replication protein A (RPA), we further demonstrate that replication fork protection and RPA availability are critical for platinum-based drug tolerance. Dual treatment led to increased formation of DNA double strand breaks and was associated with chromosome pulverization. Combination treatment was also associated with increased micronuclei formation which were capable of being bound by the innate immunomodulatory factor, cGAS, suggesting that combination platinum and ATR inhibition may also enhance response to immunotherapy in ERCC1-deficient tumors. In vivo studies demonstrate a significant effect on tumor growth delay with combination therapy compared with single agent treatment. Results of this study have led to the identification of a feasible therapeutic strategy combining ATR inhibition with platinum and potentially immune checkpoint blockade inhibitors to overcome platinum tolerance in ERCC1-deficient, p53-mutant lung cancers.
Targeted zinc-finger repressors to the oncogenic HBZ gene inhibit adult T-cell leukemia (ATL) proliferation
Authors: Scott Tristan A , Soemardy Citradewi , Ray Roslyn M , Morris Kevin V 
Published: January 2023

Abstract
Human T-lymphotropic virus type I (HTLV-I) infects CD4+ T-cells resulting in a latent, life-long infection in patients. Crosstalk between oncogenic viral factors results in the transformation of the host cell into an aggressive cancer, adult T-cell leukemia/lymphoma (ATL). ATL has a poor prognosis with no currently available effective treatments, urging the development of novel therapeutic strategies. Recent evidence exploring those mechanisms contributing to ATL highlights the viral anti-sense gene HTLV-I bZIP factor (HBZ) as a tumor driver and a potential therapeutic target. In this work, a series of zinc-finger protein (ZFP) repressors were designed to target within the HTLV-I promoter that drives HBZ expression at highly conserved sites covering a wide range of HTLV-I genotypes. ZFPs were identified that potently suppressed HBZ expression and resulted in a significant reduction in the proliferation and viability of a patient-derived ATL cell line with the induction of cell cycle arrest and apoptosis. These data encourage the development of this novel ZFP strategy as a targeted modality to inhibit the molecular driver of ATL, a possible next-generation therapeutic for aggressive HTLV-I associated malignancies.